Starting phenix.real_space_refine on Sun Feb 18 00:30:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/02_2024/7u4t_26334_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/02_2024/7u4t_26334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/02_2024/7u4t_26334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/02_2024/7u4t_26334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/02_2024/7u4t_26334_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u4t_26334/02_2024/7u4t_26334_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 380 5.16 5 C 45606 2.51 5 N 12205 2.21 5 O 13405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 94": "OE1" <-> "OE2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 182": "OE1" <-> "OE2" Residue "H TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "K ASP 97": "OD1" <-> "OD2" Residue "K PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 280": "OD1" <-> "OD2" Residue "U ASP 304": "OD1" <-> "OD2" Residue "V ASP 332": "OD1" <-> "OD2" Residue "0 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 98": "OE1" <-> "OE2" Residue "0 PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 166": "OD1" <-> "OD2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "1 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 139": "OE1" <-> "OE2" Residue "2 ASP 83": "OD1" <-> "OD2" Residue "2 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 82": "OD1" <-> "OD2" Residue "4 GLU 9": "OE1" <-> "OE2" Residue "4 TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 82": "OD1" <-> "OD2" Residue "4 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 139": "OE1" <-> "OE2" Residue "4 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 139": "OE1" <-> "OE2" Residue "6 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 82": "OD1" <-> "OD2" Residue "9 ASP 83": "OD1" <-> "OD2" Residue "Q PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 279": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "Z TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 170": "OE1" <-> "OE2" Residue "X GLU 173": "OE1" <-> "OE2" Residue "X TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "N GLU 72": "OE1" <-> "OE2" Residue "N GLU 95": "OE1" <-> "OE2" Residue "W PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 502": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 71598 Number of models: 1 Model: "" Number of chains: 40 Chain: "R" Number of atoms: 5876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5876 Classifications: {'peptide': 753} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 32, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 178 Chain: "O" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 1817 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 355} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1202 Unresolved non-hydrogen angles: 1536 Unresolved non-hydrogen dihedrals: 1003 Unresolved non-hydrogen chiralities: 108 Planarities with less than four sites: {'GLN:plan1': 16, 'ARG:plan': 14, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 6, 'HIS:plan': 6, 'PHE:plan': 14, 'GLU:plan': 25, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 651 Chain: "J" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1774 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 219} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "I" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 215} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 86 Chain: "L" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 748 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 1, 'TRANS': 111} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 123 Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1611 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 11, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 735 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 1, 'TRANS': 112} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 132 Chain: "S" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 631 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "T" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "U" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1662 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "V" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 411 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "0" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1498 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain: "1" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "2" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "3" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "4" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "5" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "6" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "7" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "8" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1065 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "Q" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2844 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "C" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 30, 'TRANS': 569} Chain: "A" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "B" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "E" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "Z" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2110 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 257} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2111 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1717 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "P" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 2121 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 385} Link IDs: {'PTRANS': 9, 'TRANS': 417} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1457 Unresolved non-hydrogen angles: 1855 Unresolved non-hydrogen dihedrals: 1231 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 33, 'HIS:plan': 11, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 8, 'ASP:plan': 18, 'PHE:plan': 17, 'GLU:plan': 38, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 859 Chain: "W" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3023 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 19, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 355 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 11, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "F" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3666 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 27.42, per 1000 atoms: 0.38 Number of scatterers: 71598 At special positions: 0 Unit cell: (224.64, 267.84, 220.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 380 16.00 P 2 15.00 O 13405 8.00 N 12205 7.00 C 45606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS U 371 " - pdb=" SG CYS U 418 " distance=2.03 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 Links applied NAG-ASN " NAG R 901 " - " ASN R 488 " " NAG S 101 " - " ASN S 70 " " NAG U 501 " - " ASN U 350 " " NAG U 503 " - " ASN U 261 " " NAG U 506 " - " ASN U 273 " Time building additional restraints: 22.66 Conformation dependent library (CDL) restraints added in 10.1 seconds 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 336 helices and 46 sheets defined 55.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.87 Creating SS restraints... Processing helix chain 'R' and resid 19 through 32 removed outlier: 4.000A pdb=" N CYS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 48 No H-bonds generated for 'chain 'R' and resid 46 through 48' Processing helix chain 'R' and resid 52 through 75 Processing helix chain 'R' and resid 92 through 133 removed outlier: 5.060A pdb=" N GLU R 116 " --> pdb=" O THR R 113 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 118 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE R 131 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU R 132 " --> pdb=" O LYS R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 190 Processing helix chain 'R' and resid 227 through 239 Processing helix chain 'R' and resid 252 through 308 removed outlier: 3.797A pdb=" N ILE R 290 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG R 291 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 343 removed outlier: 5.685A pdb=" N ASP R 331 " --> pdb=" O THR R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 379 Processing helix chain 'R' and resid 392 through 395 No H-bonds generated for 'chain 'R' and resid 392 through 395' Processing helix chain 'R' and resid 398 through 406 Processing helix chain 'R' and resid 410 through 431 removed outlier: 3.951A pdb=" N GLU R 427 " --> pdb=" O MET R 423 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER R 428 " --> pdb=" O VAL R 424 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ARG R 429 " --> pdb=" O LEU R 425 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 463 removed outlier: 4.255A pdb=" N VAL R 443 " --> pdb=" O MET R 439 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY R 446 " --> pdb=" O THR R 442 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG R 447 " --> pdb=" O VAL R 443 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR R 448 " --> pdb=" O PHE R 444 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE R 449 " --> pdb=" O SER R 445 " (cutoff:3.500A) Processing helix chain 'R' and resid 481 through 487 removed outlier: 3.674A pdb=" N TYR R 487 " --> pdb=" O MET R 484 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 496 Processing helix chain 'R' and resid 520 through 524 Processing helix chain 'R' and resid 528 through 562 removed outlier: 5.010A pdb=" N ASN R 533 " --> pdb=" O LEU R 529 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL R 541 " --> pdb=" O MET R 537 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 554 " --> pdb=" O PHE R 550 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER R 555 " --> pdb=" O GLY R 551 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU R 556 " --> pdb=" O VAL R 552 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE R 557 " --> pdb=" O SER R 553 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN R 558 " --> pdb=" O LEU R 554 " (cutoff:3.500A) Processing helix chain 'R' and resid 565 through 569 removed outlier: 3.822A pdb=" N TYR R 569 " --> pdb=" O LEU R 566 " (cutoff:3.500A) Processing helix chain 'R' and resid 572 through 596 removed outlier: 4.423A pdb=" N TYR R 585 " --> pdb=" O SER R 581 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU R 586 " --> pdb=" O LEU R 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL R 587 " --> pdb=" O PHE R 583 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE R 588 " --> pdb=" O GLY R 584 " (cutoff:3.500A) Processing helix chain 'R' and resid 602 through 604 No H-bonds generated for 'chain 'R' and resid 602 through 604' Processing helix chain 'R' and resid 608 through 617 removed outlier: 3.793A pdb=" N PHE R 612 " --> pdb=" O LEU R 608 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE R 616 " --> pdb=" O PHE R 612 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU R 617 " --> pdb=" O ILE R 613 " (cutoff:3.500A) Processing helix chain 'R' and resid 632 through 651 removed outlier: 3.743A pdb=" N VAL R 647 " --> pdb=" O ALA R 643 " (cutoff:3.500A) Proline residue: R 648 - end of helix Processing helix chain 'R' and resid 653 through 665 Processing helix chain 'R' and resid 713 through 757 removed outlier: 4.068A pdb=" N THR R 735 " --> pdb=" O CYS R 731 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA R 736 " --> pdb=" O ILE R 732 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU R 739 " --> pdb=" O THR R 735 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG R 740 " --> pdb=" O ALA R 736 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU R 741 " --> pdb=" O SER R 737 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP R 742 " --> pdb=" O TYR R 738 " (cutoff:3.500A) Processing helix chain 'R' and resid 760 through 763 No H-bonds generated for 'chain 'R' and resid 760 through 763' Processing helix chain 'R' and resid 768 through 788 removed outlier: 3.598A pdb=" N GLY R 772 " --> pdb=" O SER R 768 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU R 775 " --> pdb=" O GLY R 771 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE R 776 " --> pdb=" O GLY R 772 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE R 777 " --> pdb=" O LEU R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 793 through 808 removed outlier: 4.304A pdb=" N PHE R 799 " --> pdb=" O GLY R 795 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 22 removed outlier: 5.733A pdb=" N GLU O 20 " --> pdb=" O GLN O 17 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS O 21 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU O 22 " --> pdb=" O TRP O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 79 removed outlier: 3.971A pdb=" N ASP O 56 " --> pdb=" O VAL O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 103 Processing helix chain 'O' and resid 118 through 156 Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 194 through 204 removed outlier: 4.111A pdb=" N GLU O 202 " --> pdb=" O ILE O 198 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR O 203 " --> pdb=" O LYS O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 234 through 242 Processing helix chain 'O' and resid 255 through 310 Proline residue: O 278 - end of helix removed outlier: 4.364A pdb=" N ARG O 281 " --> pdb=" O GLY O 277 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 339 Processing helix chain 'J' and resid 7 through 106 removed outlier: 3.759A pdb=" N GLN J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS J 13 " --> pdb=" O GLN J 9 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS J 14 " --> pdb=" O LYS J 10 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN J 39 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU J 51 " --> pdb=" O GLN J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 127 Processing helix chain 'J' and resid 138 through 157 removed outlier: 3.949A pdb=" N PHE J 141 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Proline residue: J 142 - end of helix removed outlier: 3.537A pdb=" N GLN J 149 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Proline residue: J 153 - end of helix removed outlier: 3.508A pdb=" N ILE J 157 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 removed outlier: 4.436A pdb=" N MET J 207 " --> pdb=" O ILE J 203 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'M' and resid 5 through 103 removed outlier: 3.830A pdb=" N GLN M 9 " --> pdb=" O SER M 5 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA M 19 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL M 73 " --> pdb=" O CYS M 69 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR M 82 " --> pdb=" O GLN M 78 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU M 84 " --> pdb=" O LYS M 80 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN M 90 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN M 91 " --> pdb=" O TYR M 87 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG M 92 " --> pdb=" O PHE M 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP M 93 " --> pdb=" O ARG M 89 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 106 removed outlier: 3.791A pdb=" N LYS I 42 " --> pdb=" O PHE I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 127 Processing helix chain 'I' and resid 141 through 157 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 205 Processing helix chain 'I' and resid 208 through 216 Processing helix chain 'L' and resid 5 through 103 removed outlier: 3.848A pdb=" N GLU L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASP L 93 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL L 95 " --> pdb=" O ASN L 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 104 removed outlier: 3.655A pdb=" N GLU H 22 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN H 100 " --> pdb=" O ASN H 96 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG H 101 " --> pdb=" O GLU H 97 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 127 Processing helix chain 'H' and resid 141 through 157 Proline residue: H 153 - end of helix Processing helix chain 'H' and resid 196 through 205 Processing helix chain 'H' and resid 208 through 215 Processing helix chain 'K' and resid 4 through 103 removed outlier: 4.253A pdb=" N GLN K 13 " --> pdb=" O GLN K 9 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA K 14 " --> pdb=" O GLN K 10 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS K 16 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP K 93 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU K 94 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 22 removed outlier: 3.598A pdb=" N LEU S 10 " --> pdb=" O LEU S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 27 Processing helix chain 'S' and resid 34 through 58 removed outlier: 3.684A pdb=" N ALA S 58 " --> pdb=" O ILE S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 78 removed outlier: 3.684A pdb=" N LYS S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR S 78 " --> pdb=" O TRP S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 74 removed outlier: 3.595A pdb=" N CYS T 53 " --> pdb=" O LYS T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 128 Processing helix chain 'U' and resid 286 through 288 No H-bonds generated for 'chain 'U' and resid 286 through 288' Processing helix chain 'U' and resid 424 through 448 Processing helix chain 'V' and resid 303 through 329 Processing helix chain '0' and resid 3 through 27 Processing helix chain '0' and resid 32 through 34 No H-bonds generated for 'chain '0' and resid 32 through 34' Processing helix chain '0' and resid 37 through 43 Processing helix chain '0' and resid 47 through 81 removed outlier: 4.416A pdb=" N SER 0 75 " --> pdb=" O ILE 0 71 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL 0 81 " --> pdb=" O ILE 0 77 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 88 No H-bonds generated for 'chain '0' and resid 86 through 88' Processing helix chain '0' and resid 91 through 114 removed outlier: 3.653A pdb=" N ALA 0 101 " --> pdb=" O CYS 0 97 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET 0 114 " --> pdb=" O VAL 0 110 " (cutoff:3.500A) Processing helix chain '0' and resid 131 through 166 Processing helix chain '0' and resid 178 through 197 removed outlier: 4.018A pdb=" N ILE 0 186 " --> pdb=" O PHE 0 182 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY 0 187 " --> pdb=" O GLY 0 183 " (cutoff:3.500A) Processing helix chain '1' and resid 11 through 45 removed outlier: 3.969A pdb=" N ALA 1 15 " --> pdb=" O ALA 1 11 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 1 21 " --> pdb=" O MET 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 51 No H-bonds generated for 'chain '1' and resid 49 through 51' Processing helix chain '1' and resid 53 through 55 No H-bonds generated for 'chain '1' and resid 53 through 55' Processing helix chain '1' and resid 57 through 79 removed outlier: 3.918A pdb=" N SER 1 79 " --> pdb=" O LEU 1 75 " (cutoff:3.500A) Processing helix chain '1' and resid 88 through 121 Processing helix chain '1' and resid 127 through 153 removed outlier: 3.994A pdb=" N GLY 1 142 " --> pdb=" O ALA 1 138 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU 1 143 " --> pdb=" O GLU 1 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL 1 148 " --> pdb=" O TYR 1 144 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 44 removed outlier: 3.807A pdb=" N ALA 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA 2 21 " --> pdb=" O MET 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 49 through 54 removed outlier: 3.536A pdb=" N ILE 2 52 " --> pdb=" O PRO 2 49 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET 2 53 " --> pdb=" O GLU 2 50 " (cutoff:3.500A) Processing helix chain '2' and resid 57 through 78 removed outlier: 3.557A pdb=" N ILE 2 65 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA 2 66 " --> pdb=" O ALA 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 88 through 123 removed outlier: 3.550A pdb=" N ALA 2 122 " --> pdb=" O VAL 2 118 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN 2 123 " --> pdb=" O ARG 2 119 " (cutoff:3.500A) Processing helix chain '2' and resid 125 through 154 removed outlier: 3.768A pdb=" N PHE 2 128 " --> pdb=" O PRO 2 125 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL 2 129 " --> pdb=" O ARG 2 126 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER 2 153 " --> pdb=" O LEU 2 150 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR 2 154 " --> pdb=" O ILE 2 151 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 43 Processing helix chain '3' and resid 49 through 55 removed outlier: 6.182A pdb=" N MET 3 53 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 78 Processing helix chain '3' and resid 88 through 122 removed outlier: 3.900A pdb=" N ALA 3 122 " --> pdb=" O VAL 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 125 through 153 removed outlier: 3.772A pdb=" N PHE 3 128 " --> pdb=" O PRO 3 125 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL 3 129 " --> pdb=" O ARG 3 126 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 44 Processing helix chain '4' and resid 53 through 55 No H-bonds generated for 'chain '4' and resid 53 through 55' Processing helix chain '4' and resid 57 through 78 Processing helix chain '4' and resid 87 through 120 Processing helix chain '4' and resid 128 through 154 removed outlier: 3.583A pdb=" N LEU 4 141 " --> pdb=" O PHE 4 137 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY 4 142 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) Processing helix chain '5' and resid 11 through 42 removed outlier: 3.738A pdb=" N ALA 5 15 " --> pdb=" O ALA 5 11 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA 5 21 " --> pdb=" O MET 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 51 No H-bonds generated for 'chain '5' and resid 49 through 51' Processing helix chain '5' and resid 53 through 55 No H-bonds generated for 'chain '5' and resid 53 through 55' Processing helix chain '5' and resid 57 through 78 removed outlier: 3.858A pdb=" N ALA 5 66 " --> pdb=" O ALA 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 88 through 122 removed outlier: 3.511A pdb=" N ALA 5 122 " --> pdb=" O VAL 5 118 " (cutoff:3.500A) Processing helix chain '5' and resid 125 through 153 removed outlier: 4.441A pdb=" N PHE 5 128 " --> pdb=" O PRO 5 125 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL 5 129 " --> pdb=" O ARG 5 126 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL 5 140 " --> pdb=" O PHE 5 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER 5 153 " --> pdb=" O LEU 5 150 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 47 removed outlier: 4.679A pdb=" N VAL 6 46 " --> pdb=" O ALA 6 42 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET 6 47 " --> pdb=" O ALA 6 43 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 55 No H-bonds generated for 'chain '6' and resid 53 through 55' Processing helix chain '6' and resid 57 through 79 Processing helix chain '6' and resid 88 through 122 Processing helix chain '6' and resid 125 through 153 removed outlier: 3.625A pdb=" N PHE 6 128 " --> pdb=" O PRO 6 125 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL 6 129 " --> pdb=" O ARG 6 126 " (cutoff:3.500A) Processing helix chain '7' and resid 11 through 44 Processing helix chain '7' and resid 49 through 51 No H-bonds generated for 'chain '7' and resid 49 through 51' Processing helix chain '7' and resid 53 through 55 No H-bonds generated for 'chain '7' and resid 53 through 55' Processing helix chain '7' and resid 57 through 78 Processing helix chain '7' and resid 88 through 122 removed outlier: 3.504A pdb=" N ALA 7 122 " --> pdb=" O VAL 7 118 " (cutoff:3.500A) Processing helix chain '7' and resid 125 through 154 removed outlier: 3.551A pdb=" N PHE 7 128 " --> pdb=" O PRO 7 125 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL 7 129 " --> pdb=" O ARG 7 126 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR 7 154 " --> pdb=" O ILE 7 151 " (cutoff:3.500A) Processing helix chain '8' and resid 11 through 44 Processing helix chain '8' and resid 49 through 51 No H-bonds generated for 'chain '8' and resid 49 through 51' Processing helix chain '8' and resid 53 through 55 No H-bonds generated for 'chain '8' and resid 53 through 55' Processing helix chain '8' and resid 57 through 78 removed outlier: 3.802A pdb=" N ILE 8 65 " --> pdb=" O MET 8 61 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA 8 66 " --> pdb=" O ALA 8 62 " (cutoff:3.500A) Processing helix chain '8' and resid 88 through 122 removed outlier: 3.527A pdb=" N ALA 8 122 " --> pdb=" O VAL 8 118 " (cutoff:3.500A) Processing helix chain '8' and resid 125 through 154 removed outlier: 4.000A pdb=" N PHE 8 128 " --> pdb=" O PRO 8 125 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL 8 129 " --> pdb=" O ARG 8 126 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL 8 140 " --> pdb=" O PHE 8 137 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR 8 154 " --> pdb=" O ILE 8 151 " (cutoff:3.500A) Processing helix chain '9' and resid 11 through 44 Processing helix chain '9' and resid 53 through 55 No H-bonds generated for 'chain '9' and resid 53 through 55' Processing helix chain '9' and resid 57 through 78 Processing helix chain '9' and resid 88 through 121 Processing helix chain '9' and resid 125 through 154 removed outlier: 3.754A pdb=" N PHE 9 128 " --> pdb=" O PRO 9 125 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL 9 129 " --> pdb=" O ARG 9 126 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR 9 154 " --> pdb=" O ILE 9 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 26 removed outlier: 6.357A pdb=" N TYR Q 15 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU Q 16 " --> pdb=" O ASP Q 12 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY Q 26 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 37 Processing helix chain 'Q' and resid 42 through 51 removed outlier: 3.759A pdb=" N SER Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 88 removed outlier: 3.932A pdb=" N HIS Q 88 " --> pdb=" O HIS Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 112 removed outlier: 4.093A pdb=" N PHE Q 96 " --> pdb=" O PRO Q 92 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER Q 103 " --> pdb=" O PHE Q 99 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR Q 104 " --> pdb=" O ILE Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 128 Proline residue: Q 127 - end of helix Processing helix chain 'Q' and resid 147 through 157 Processing helix chain 'Q' and resid 159 through 165 removed outlier: 3.853A pdb=" N ALA Q 162 " --> pdb=" O PRO Q 159 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN Q 165 " --> pdb=" O ALA Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 175 No H-bonds generated for 'chain 'Q' and resid 172 through 175' Processing helix chain 'Q' and resid 178 through 199 Processing helix chain 'Q' and resid 203 through 227 Proline residue: Q 210 - end of helix Processing helix chain 'Q' and resid 234 through 240 removed outlier: 4.033A pdb=" N LEU Q 240 " --> pdb=" O ASP Q 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 256 Processing helix chain 'Q' and resid 261 through 270 removed outlier: 4.777A pdb=" N TYR Q 270 " --> pdb=" O ASN Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 272 through 279 Processing helix chain 'Q' and resid 290 through 307 removed outlier: 4.057A pdb=" N PHE Q 306 " --> pdb=" O ASN Q 302 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU Q 307 " --> pdb=" O LYS Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 312 through 337 removed outlier: 3.698A pdb=" N PHE Q 315 " --> pdb=" O PHE Q 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 344 through 346 No H-bonds generated for 'chain 'Q' and resid 344 through 346' Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 281 through 290 removed outlier: 3.719A pdb=" N SER C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 320 through 339 removed outlier: 4.715A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 378 through 386 Processing helix chain 'C' and resid 420 through 428 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 472 through 496 removed outlier: 4.324A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 518 Processing helix chain 'C' and resid 534 through 557 Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 575 through 586 removed outlier: 4.624A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 284 through 293 removed outlier: 3.635A pdb=" N ARG A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 379 through 388 removed outlier: 4.443A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 472 through 496 Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 534 through 558 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 321 through 339 removed outlier: 3.535A pdb=" N GLU B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 327 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 378 through 388 removed outlier: 4.472A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 Processing helix chain 'B' and resid 437 through 442 removed outlier: 3.946A pdb=" N ARG B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 472 through 495 Processing helix chain 'B' and resid 503 through 518 Processing helix chain 'B' and resid 534 through 558 removed outlier: 3.998A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 573 Processing helix chain 'B' and resid 575 through 586 removed outlier: 4.703A pdb=" N LYS B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE B 586 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 238 through 249 Processing helix chain 'D' and resid 254 through 256 No H-bonds generated for 'chain 'D' and resid 254 through 256' Processing helix chain 'D' and resid 268 through 289 Proline residue: D 275 - end of helix Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 364 through 372 Processing helix chain 'D' and resid 381 through 386 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 415 through 439 Processing helix chain 'D' and resid 446 through 461 Processing helix chain 'D' and resid 473 through 486 removed outlier: 4.220A pdb=" N ILE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 219 through 225 Processing helix chain 'E' and resid 238 through 249 Processing helix chain 'E' and resid 269 through 289 removed outlier: 4.025A pdb=" N THR E 274 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Proline residue: E 275 - end of helix removed outlier: 4.011A pdb=" N TYR E 287 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN E 288 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N CYS E 289 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 314 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 Processing helix chain 'E' and resid 382 through 385 No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 402 through 405 No H-bonds generated for 'chain 'E' and resid 402 through 405' Processing helix chain 'E' and resid 415 through 439 Processing helix chain 'E' and resid 441 through 443 No H-bonds generated for 'chain 'E' and resid 441 through 443' Processing helix chain 'E' and resid 446 through 461 Processing helix chain 'E' and resid 473 through 486 removed outlier: 4.369A pdb=" N ILE E 486 " --> pdb=" O GLN E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'Z' and resid 15 through 36 Processing helix chain 'Z' and resid 43 through 48 Processing helix chain 'Z' and resid 50 through 55 removed outlier: 5.471A pdb=" N TRP Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 71 Processing helix chain 'Z' and resid 78 through 98 removed outlier: 4.085A pdb=" N ILE Z 98 " --> pdb=" O LEU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 116 Processing helix chain 'Z' and resid 121 through 123 No H-bonds generated for 'chain 'Z' and resid 121 through 123' Processing helix chain 'Z' and resid 125 through 141 Processing helix chain 'Z' and resid 147 through 165 Processing helix chain 'Z' and resid 174 through 186 Processing helix chain 'Z' and resid 194 through 205 Processing helix chain 'Z' and resid 219 through 234 Processing helix chain 'Z' and resid 240 through 251 removed outlier: 4.379A pdb=" N SER Z 251 " --> pdb=" O SER Z 247 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 273 removed outlier: 3.601A pdb=" N LYS Z 272 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU Z 273 " --> pdb=" O GLU Z 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 36 Processing helix chain 'X' and resid 43 through 48 Processing helix chain 'X' and resid 50 through 55 removed outlier: 5.515A pdb=" N TRP X 55 " --> pdb=" O ASP X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 71 Processing helix chain 'X' and resid 78 through 98 removed outlier: 4.100A pdb=" N ILE X 98 " --> pdb=" O LEU X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 116 Processing helix chain 'X' and resid 121 through 123 No H-bonds generated for 'chain 'X' and resid 121 through 123' Processing helix chain 'X' and resid 125 through 142 removed outlier: 3.681A pdb=" N LEU X 140 " --> pdb=" O LEU X 136 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS X 141 " --> pdb=" O THR X 137 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN X 142 " --> pdb=" O ASP X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 174 through 186 Processing helix chain 'X' and resid 194 through 206 Processing helix chain 'X' and resid 219 through 234 Processing helix chain 'X' and resid 240 through 251 removed outlier: 4.541A pdb=" N SER X 251 " --> pdb=" O SER X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 273 Processing helix chain 'Y' and resid 15 through 36 Processing helix chain 'Y' and resid 43 through 46 No H-bonds generated for 'chain 'Y' and resid 43 through 46' Processing helix chain 'Y' and resid 50 through 53 No H-bonds generated for 'chain 'Y' and resid 50 through 53' Processing helix chain 'Y' and resid 63 through 70 Processing helix chain 'Y' and resid 78 through 98 removed outlier: 4.135A pdb=" N ILE Y 98 " --> pdb=" O LEU Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 116 Processing helix chain 'Y' and resid 125 through 141 Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 173 through 186 Processing helix chain 'Y' and resid 194 through 205 Processing helix chain 'Y' and resid 219 through 236 Proline residue: Y 235 - end of helix Processing helix chain 'Y' and resid 240 through 251 removed outlier: 4.253A pdb=" N SER Y 251 " --> pdb=" O SER Y 247 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 273 removed outlier: 3.757A pdb=" N LYS Y 272 " --> pdb=" O LYS Y 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU Y 273 " --> pdb=" O GLU Y 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 75 removed outlier: 3.608A pdb=" N GLU G 60 " --> pdb=" O MET G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'G' and resid 129 through 174 Processing helix chain 'G' and resid 176 through 214 Processing helix chain 'N' and resid 14 through 23 Processing helix chain 'N' and resid 45 through 57 Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'N' and resid 75 through 80 Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 104 through 108 removed outlier: 4.053A pdb=" N ARG N 108 " --> pdb=" O SER N 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 104 through 108' Processing helix chain 'P' and resid 18 through 28 removed outlier: 4.155A pdb=" N ALA P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 36 No H-bonds generated for 'chain 'P' and resid 34 through 36' Processing helix chain 'P' and resid 48 through 54 removed outlier: 3.777A pdb=" N ARG P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE P 53 " --> pdb=" O PHE P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 68 Processing helix chain 'P' and resid 75 through 83 removed outlier: 3.549A pdb=" N ASN P 79 " --> pdb=" O LYS P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 103 removed outlier: 4.107A pdb=" N ILE P 93 " --> pdb=" O THR P 89 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP P 99 " --> pdb=" O THR P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 108 No H-bonds generated for 'chain 'P' and resid 106 through 108' Processing helix chain 'P' and resid 112 through 114 No H-bonds generated for 'chain 'P' and resid 112 through 114' Processing helix chain 'P' and resid 127 through 129 No H-bonds generated for 'chain 'P' and resid 127 through 129' Processing helix chain 'P' and resid 136 through 145 Processing helix chain 'P' and resid 158 through 161 No H-bonds generated for 'chain 'P' and resid 158 through 161' Processing helix chain 'P' and resid 170 through 172 No H-bonds generated for 'chain 'P' and resid 170 through 172' Processing helix chain 'P' and resid 195 through 210 removed outlier: 3.842A pdb=" N CYS P 200 " --> pdb=" O GLN P 196 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG P 210 " --> pdb=" O GLN P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 220 Processing helix chain 'P' and resid 224 through 232 Processing helix chain 'P' and resid 237 through 250 Processing helix chain 'P' and resid 254 through 260 removed outlier: 3.530A pdb=" N HIS P 259 " --> pdb=" O GLN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 274 Processing helix chain 'P' and resid 281 through 295 Processing helix chain 'P' and resid 301 through 309 removed outlier: 3.533A pdb=" N GLU P 304 " --> pdb=" O THR P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 329 through 349 Processing helix chain 'P' and resid 352 through 361 Processing helix chain 'P' and resid 374 through 376 No H-bonds generated for 'chain 'P' and resid 374 through 376' Processing helix chain 'P' and resid 380 through 383 No H-bonds generated for 'chain 'P' and resid 380 through 383' Processing helix chain 'P' and resid 386 through 399 removed outlier: 5.770A pdb=" N LEU P 390 " --> pdb=" O ASN P 387 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE P 393 " --> pdb=" O LEU P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 419 removed outlier: 4.220A pdb=" N VAL P 409 " --> pdb=" O GLN P 405 " (cutoff:3.500A) Processing helix chain 'P' and resid 424 through 431 Processing helix chain 'P' and resid 433 through 442 removed outlier: 3.536A pdb=" N HIS P 442 " --> pdb=" O MET P 438 " (cutoff:3.500A) Processing helix chain 'P' and resid 446 through 460 removed outlier: 4.006A pdb=" N ASN P 451 " --> pdb=" O GLN P 447 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU P 454 " --> pdb=" O TYR P 450 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 33 Processing helix chain 'W' and resid 47 through 57 removed outlier: 6.134A pdb=" N GLU W 56 " --> pdb=" O ASN W 52 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA W 57 " --> pdb=" O HIS W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 71 Processing helix chain 'W' and resid 88 through 99 Processing helix chain 'W' and resid 103 through 114 Processing helix chain 'W' and resid 123 through 144 Processing helix chain 'W' and resid 160 through 172 removed outlier: 4.386A pdb=" N ASP W 172 " --> pdb=" O GLN W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 188 Processing helix chain 'W' and resid 193 through 202 Processing helix chain 'W' and resid 204 through 218 Processing helix chain 'W' and resid 248 through 257 removed outlier: 3.907A pdb=" N GLN W 257 " --> pdb=" O TYR W 253 " (cutoff:3.500A) Processing helix chain 'W' and resid 260 through 262 No H-bonds generated for 'chain 'W' and resid 260 through 262' Processing helix chain 'W' and resid 272 through 275 No H-bonds generated for 'chain 'W' and resid 272 through 275' Processing helix chain 'W' and resid 279 through 286 Processing helix chain 'W' and resid 431 through 440 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 219 through 226 removed outlier: 3.940A pdb=" N GLU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 225 " --> pdb=" O ASP F 221 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASN F 226 " --> pdb=" O TYR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 251 removed outlier: 4.309A pdb=" N ASN F 251 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 288 removed outlier: 3.847A pdb=" N THR F 274 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Proline residue: F 275 - end of helix removed outlier: 3.640A pdb=" N ALA F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN F 288 " --> pdb=" O LEU F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 removed outlier: 3.511A pdb=" N TYR F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 402 through 405 No H-bonds generated for 'chain 'F' and resid 402 through 405' Processing helix chain 'F' and resid 415 through 439 removed outlier: 3.819A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 439 " --> pdb=" O MET F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 461 Processing helix chain 'F' and resid 473 through 482 Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 497 through 503 Processing sheet with id= A, first strand: chain 'R' and resid 319 through 326 removed outlier: 4.138A pdb=" N LEU R 12 " --> pdb=" O MET R 355 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 197 through 202 Processing sheet with id= C, first strand: chain 'O' and resid 373 through 375 Processing sheet with id= D, first strand: chain 'O' and resid 247 through 249 removed outlier: 3.915A pdb=" N LEU O 186 " --> pdb=" O ARG O 249 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS O 225 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL O 189 " --> pdb=" O TYR O 223 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR O 223 " --> pdb=" O VAL O 189 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN O 226 " --> pdb=" O VAL O 215 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL O 215 " --> pdb=" O ASN O 226 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 164 through 167 Processing sheet with id= F, first strand: chain 'I' and resid 164 through 167 Processing sheet with id= G, first strand: chain 'H' and resid 164 through 167 Processing sheet with id= H, first strand: chain 'U' and resid 258 through 260 removed outlier: 3.930A pdb=" N ILE U 267 " --> pdb=" O TYR U 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'U' and resid 273 through 277 removed outlier: 3.727A pdb=" N ASN U 273 " --> pdb=" O GLN U 398 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'U' and resid 301 through 303 removed outlier: 3.618A pdb=" N PHE U 306 " --> pdb=" O ASN U 303 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG U 344 " --> pdb=" O ILE U 326 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA U 328 " --> pdb=" O MET U 342 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N MET U 342 " --> pdb=" O ALA U 328 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG U 330 " --> pdb=" O PHE U 340 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE U 340 " --> pdb=" O ARG U 330 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR U 332 " --> pdb=" O HIS U 338 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS U 338 " --> pdb=" O TYR U 332 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU U 343 " --> pdb=" O ALA U 358 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA U 358 " --> pdb=" O GLU U 343 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.522A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 23 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= M, first strand: chain 'C' and resid 183 through 186 removed outlier: 5.503A pdb=" N ASP C 134 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 157 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.200A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 245 through 247 removed outlier: 8.675A pdb=" N THR C 246 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASP C 349 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 275 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= Q, first strand: chain 'A' and resid 79 through 81 Processing sheet with id= R, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= S, first strand: chain 'A' and resid 183 through 186 removed outlier: 5.481A pdb=" N ASP A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 157 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 166 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 155 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS A 164 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.150A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 245 through 247 removed outlier: 8.452A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 348 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 295 through 298 Processing sheet with id= W, first strand: chain 'A' and resid 21 through 25 removed outlier: 6.729A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.574A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= Z, first strand: chain 'B' and resid 98 through 100 removed outlier: 8.779A pdb=" N PHE B 99 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 311 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 272 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL B 312 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR B 274 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASN B 314 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY B 276 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 271 " --> pdb=" O HIS B 343 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER B 403 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET B 346 " --> pdb=" O SER B 403 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N SER B 405 " --> pdb=" O MET B 346 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA B 348 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 407 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 183 through 185 removed outlier: 6.638A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.320A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= AD, first strand: chain 'D' and resid 111 through 114 Processing sheet with id= AE, first strand: chain 'D' and resid 120 through 123 Processing sheet with id= AF, first strand: chain 'D' and resid 131 through 133 removed outlier: 8.388A pdb=" N PHE D 132 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU D 259 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N CYS D 258 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N HIS D 292 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL D 230 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU D 294 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA D 232 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE D 296 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET D 234 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR D 298 " --> pdb=" O MET D 234 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL D 236 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N SER D 347 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL D 295 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR D 349 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU D 297 " --> pdb=" O THR D 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'D' and resid 191 through 193 Processing sheet with id= AH, first strand: chain 'E' and resid 111 through 114 Processing sheet with id= AI, first strand: chain 'E' and resid 120 through 123 Processing sheet with id= AJ, first strand: chain 'E' and resid 131 through 133 removed outlier: 8.424A pdb=" N PHE E 132 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 259 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL E 230 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU E 294 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA E 232 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE E 296 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET E 234 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR E 298 " --> pdb=" O MET E 234 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL E 236 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'E' and resid 191 through 193 Processing sheet with id= AL, first strand: chain 'G' and resid 92 through 101 Processing sheet with id= AM, first strand: chain 'N' and resid 36 through 38 removed outlier: 6.683A pdb=" N VAL N 10 " --> pdb=" O LEU N 37 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA N 87 " --> pdb=" O ILE N 64 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE N 66 " --> pdb=" O ALA N 87 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU N 89 " --> pdb=" O ILE N 66 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'W' and resid 233 through 235 removed outlier: 6.804A pdb=" N VAL W 408 " --> pdb=" O LEU W 269 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER W 271 " --> pdb=" O MET W 406 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N MET W 406 " --> pdb=" O SER W 271 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP W 404 " --> pdb=" O GLU W 297 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU W 297 " --> pdb=" O ASP W 404 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET W 406 " --> pdb=" O VAL W 295 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL W 295 " --> pdb=" O MET W 406 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL W 408 " --> pdb=" O VAL W 293 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL W 293 " --> pdb=" O VAL W 408 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'W' and resid 347 through 349 Processing sheet with id= AP, first strand: chain 'W' and resid 378 through 380 Processing sheet with id= AQ, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.381A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA F 94 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AS, first strand: chain 'F' and resid 131 through 133 removed outlier: 8.635A pdb=" N PHE F 132 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU F 259 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N CYS F 258 " --> pdb=" O PHE F 227 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N HIS F 292 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL F 230 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU F 294 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA F 232 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE F 296 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET F 234 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR F 298 " --> pdb=" O MET F 234 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL F 236 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER F 347 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL F 295 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR F 349 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU F 297 " --> pdb=" O THR F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'F' and resid 191 through 193 4152 hydrogen bonds defined for protein. 11232 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.48 Time building geometry restraints manager: 24.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18192 1.33 - 1.45: 14528 1.45 - 1.58: 39462 1.58 - 1.70: 15 1.70 - 1.82: 662 Bond restraints: 72859 Sorted by residual: bond pdb=" C ARG F 120 " pdb=" N THR F 121 " ideal model delta sigma weight residual 1.331 1.274 0.057 2.07e-02 2.33e+03 7.65e+00 bond pdb=" CB PRO O 313 " pdb=" CG PRO O 313 " ideal model delta sigma weight residual 1.506 1.614 -0.108 3.90e-02 6.57e+02 7.60e+00 bond pdb=" CB PRO W 38 " pdb=" CG PRO W 38 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.62e+00 bond pdb=" CB CYS S 47 " pdb=" SG CYS S 47 " ideal model delta sigma weight residual 1.808 1.730 0.078 3.30e-02 9.18e+02 5.52e+00 bond pdb=" CB PRO R 248 " pdb=" CG PRO R 248 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.01e+00 ... (remaining 72854 not shown) Histogram of bond angle deviations from ideal: 92.22 - 100.86: 172 100.86 - 109.50: 6508 109.50 - 118.14: 49117 118.14 - 126.78: 42375 126.78 - 135.42: 655 Bond angle restraints: 98827 Sorted by residual: angle pdb=" CA PRO F 496 " pdb=" N PRO F 496 " pdb=" CD PRO F 496 " ideal model delta sigma weight residual 112.00 103.59 8.41 1.40e+00 5.10e-01 3.61e+01 angle pdb=" N ILE T 97 " pdb=" CA ILE T 97 " pdb=" C ILE T 97 " ideal model delta sigma weight residual 112.96 107.14 5.82 1.00e+00 1.00e+00 3.38e+01 angle pdb=" CA PRO U 390 " pdb=" N PRO U 390 " pdb=" CD PRO U 390 " ideal model delta sigma weight residual 112.00 104.40 7.60 1.40e+00 5.10e-01 2.95e+01 angle pdb=" N LYS O 111 " pdb=" CA LYS O 111 " pdb=" C LYS O 111 " ideal model delta sigma weight residual 114.04 107.58 6.46 1.24e+00 6.50e-01 2.72e+01 angle pdb=" CA PRO R 181 " pdb=" N PRO R 181 " pdb=" CD PRO R 181 " ideal model delta sigma weight residual 112.00 105.40 6.60 1.40e+00 5.10e-01 2.23e+01 ... (remaining 98822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 42591 30.32 - 60.63: 1269 60.63 - 90.95: 119 90.95 - 121.27: 0 121.27 - 151.58: 1 Dihedral angle restraints: 43980 sinusoidal: 16221 harmonic: 27759 Sorted by residual: dihedral pdb=" O2A ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PA ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 148.42 151.58 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" CA PHE I 224 " pdb=" C PHE I 224 " pdb=" N LEU I 225 " pdb=" CA LEU I 225 " ideal model delta harmonic sigma weight residual -180.00 -148.40 -31.60 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA THR A 295 " pdb=" C THR A 295 " pdb=" N MET A 296 " pdb=" CA MET A 296 " ideal model delta harmonic sigma weight residual 180.00 148.53 31.47 0 5.00e+00 4.00e-02 3.96e+01 ... (remaining 43977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 10255 0.075 - 0.150: 1178 0.150 - 0.225: 39 0.225 - 0.300: 3 0.300 - 0.375: 1 Chirality restraints: 11476 Sorted by residual: chirality pdb=" C1 NAG U 501 " pdb=" ND2 ASN U 350 " pdb=" C2 NAG U 501 " pdb=" O5 NAG U 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB VAL A 75 " pdb=" CA VAL A 75 " pdb=" CG1 VAL A 75 " pdb=" CG2 VAL A 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE A 118 " pdb=" CA ILE A 118 " pdb=" CG1 ILE A 118 " pdb=" CG2 ILE A 118 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 11473 not shown) Planarity restraints: 12785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 495 " 0.095 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO F 496 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO F 496 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO F 496 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO W 59 " -0.073 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO W 60 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO W 60 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO W 60 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 37 " -0.072 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO W 38 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO W 38 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO W 38 " -0.058 5.00e-02 4.00e+02 ... (remaining 12782 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 421 2.52 - 3.11: 58319 3.11 - 3.71: 110491 3.71 - 4.30: 149156 4.30 - 4.90: 251158 Nonbonded interactions: 569545 Sorted by model distance: nonbonded pdb=" O TYR J 155 " pdb=" O ALA J 158 " model vdw 1.919 3.040 nonbonded pdb=" OH TYR F 426 " pdb=" OE2 GLU F 459 " model vdw 2.090 2.440 nonbonded pdb=" O SER A 71 " pdb=" NH1 ARG A 120 " model vdw 2.099 2.520 nonbonded pdb=" O THR U 298 " pdb=" OG SER U 310 " model vdw 2.115 2.440 nonbonded pdb=" OG SER C 316 " pdb=" OE2 GLU F 336 " model vdw 2.116 2.440 ... (remaining 569540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 17 through 616) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = (chain 'I' and ((resid 7 through 58 and (name N or name CA or name C or name O o \ r name CB )) or resid 59 through 226)) selection = (chain 'J' and ((resid 7 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 or (resid 44 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 226)) } ncs_group { reference = (chain 'K' and resid 4 through 116) selection = (chain 'L' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 or (resid 65 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 116)) selection = (chain 'M' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 or (resid 65 through 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 116)) } ncs_group { reference = (chain 'X' and (resid 14 through 235 or (resid 236 and (name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ )) or resid 237 throu \ gh 275)) selection = (chain 'Y' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 235 or (resid 2 \ 36 and (name CA or name C or name O or name CB or name CG or name CD or name CE \ or name NZ )) or resid 237 through 275)) selection = (chain 'Z' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 275)) } 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.010 Check model and map are aligned: 0.780 Set scattering table: 0.490 Process input model: 149.200 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 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 : 0.006 0.119 72859 Z= 0.425 Angle : 0.762 11.810 98827 Z= 0.408 Chirality : 0.047 0.375 11476 Planarity : 0.006 0.138 12780 Dihedral : 14.147 151.583 26105 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.33 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.29 (0.09), residues: 9526 helix: 1.01 (0.07), residues: 5422 sheet: -0.90 (0.18), residues: 801 loop : -2.06 (0.10), residues: 3303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 450 HIS 0.017 0.001 HIS R 801 PHE 0.063 0.002 PHE S 16 TYR 0.042 0.002 TYR 0 70 ARG 0.016 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1622 time to evaluate : 6.198 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: R 9 GLU cc_start: 0.2056 (tm-30) cc_final: 0.1267 (mm-30) REVERT: R 35 VAL cc_start: 0.7372 (t) cc_final: 0.7022 (t) REVERT: R 80 MET cc_start: 0.5882 (mpp) cc_final: 0.5444 (mtt) REVERT: R 294 PHE cc_start: 0.7444 (t80) cc_final: 0.7211 (t80) REVERT: R 358 ASN cc_start: 0.5258 (p0) cc_final: 0.4807 (m110) REVERT: R 383 ILE cc_start: 0.6147 (mp) cc_final: 0.5935 (mt) REVERT: R 421 VAL cc_start: 0.6799 (t) cc_final: 0.6536 (p) REVERT: R 439 MET cc_start: 0.3992 (ppp) cc_final: 0.2135 (tpp) REVERT: R 479 TRP cc_start: 0.5311 (m100) cc_final: 0.4666 (m100) REVERT: R 492 GLU cc_start: 0.7486 (tp30) cc_final: 0.7015 (pp20) REVERT: R 808 VAL cc_start: 0.6799 (t) cc_final: 0.6370 (t) REVERT: O 313 PRO cc_start: 0.6480 (Cg_endo) cc_final: 0.6087 (Cg_exo) REVERT: J 53 ILE cc_start: 0.1408 (pt) cc_final: 0.0432 (pt) REVERT: J 65 GLU cc_start: 0.7898 (tt0) cc_final: 0.7371 (mm-30) REVERT: J 72 MET cc_start: 0.6768 (mmp) cc_final: 0.5744 (tmm) REVERT: J 182 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8096 (mt-10) REVERT: M 56 LYS cc_start: 0.6790 (mptt) cc_final: 0.6589 (ttmt) REVERT: M 63 LEU cc_start: 0.6670 (mp) cc_final: 0.6366 (mt) REVERT: M 86 THR cc_start: 0.5151 (p) cc_final: 0.4931 (p) REVERT: M 105 ASP cc_start: 0.6502 (t0) cc_final: 0.5876 (p0) REVERT: I 52 LYS cc_start: 0.8316 (tttp) cc_final: 0.8110 (tmtt) REVERT: I 59 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7848 (tmmt) REVERT: I 77 ASN cc_start: 0.7800 (t0) cc_final: 0.7430 (t0) REVERT: I 172 TYR cc_start: 0.6786 (m-80) cc_final: 0.6477 (m-10) REVERT: L 58 LYS cc_start: 0.7829 (mptt) cc_final: 0.7371 (mttt) REVERT: L 63 LEU cc_start: 0.5936 (mp) cc_final: 0.5704 (tt) REVERT: L 78 GLN cc_start: 0.7451 (tp-100) cc_final: 0.7134 (mm-40) REVERT: L 85 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7652 (mp10) REVERT: H 66 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7564 (mm-40) REVERT: H 117 ASP cc_start: 0.7532 (t0) cc_final: 0.7079 (m-30) REVERT: H 168 ASP cc_start: 0.7481 (m-30) cc_final: 0.6614 (t70) REVERT: H 184 TYR cc_start: 0.7033 (m-10) cc_final: 0.6730 (m-80) REVERT: K 83 ILE cc_start: 0.8262 (tt) cc_final: 0.7971 (mm) REVERT: S 40 MET cc_start: 0.8269 (ptp) cc_final: 0.7384 (ppp) REVERT: U 342 MET cc_start: 0.5374 (ttm) cc_final: 0.5086 (tpp) REVERT: U 401 GLN cc_start: 0.5386 (tp40) cc_final: 0.5080 (mt0) REVERT: U 408 MET cc_start: 0.6537 (mpp) cc_final: 0.6006 (mtt) REVERT: 1 124 GLN cc_start: 0.5350 (tm-30) cc_final: 0.4982 (tt0) REVERT: 1 146 LEU cc_start: 0.7407 (tt) cc_final: 0.7103 (mm) REVERT: 2 61 MET cc_start: 0.5460 (mtp) cc_final: 0.5006 (mtp) REVERT: 3 53 MET cc_start: 0.1733 (mmp) cc_final: 0.1139 (ptm) REVERT: 6 47 MET cc_start: 0.6122 (mpp) cc_final: 0.4340 (tmm) REVERT: 6 53 MET cc_start: 0.6538 (mmm) cc_final: 0.5831 (mtp) REVERT: 7 76 ILE cc_start: 0.7125 (mm) cc_final: 0.6917 (mt) REVERT: 9 14 PHE cc_start: 0.6759 (m-80) cc_final: 0.6262 (m-80) REVERT: 9 70 LEU cc_start: 0.7445 (tp) cc_final: 0.7171 (tp) REVERT: Q 3 PHE cc_start: 0.5466 (t80) cc_final: 0.5027 (m-10) REVERT: Q 208 MET cc_start: 0.7045 (mmm) cc_final: 0.6835 (mmp) REVERT: C 438 LYS cc_start: 0.7403 (tmtt) cc_final: 0.7155 (tptm) REVERT: C 478 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7993 (tppt) REVERT: C 498 LYS cc_start: 0.7163 (tttt) cc_final: 0.6850 (tmmt) REVERT: C 591 LYS cc_start: 0.7116 (mmtt) cc_final: 0.6327 (ptpp) REVERT: C 608 MET cc_start: 0.4403 (ptm) cc_final: 0.4126 (ptm) REVERT: A 39 MET cc_start: 0.8473 (mpp) cc_final: 0.8255 (mpp) REVERT: A 296 MET cc_start: 0.4979 (mpp) cc_final: 0.3813 (ptm) REVERT: A 349 ASP cc_start: 0.7994 (t70) cc_final: 0.7666 (t0) REVERT: A 353 ARG cc_start: 0.7198 (mmt-90) cc_final: 0.6792 (mmp80) REVERT: A 367 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7644 (mt-10) REVERT: A 443 LYS cc_start: 0.8376 (tttm) cc_final: 0.8083 (mmtm) REVERT: A 600 ASP cc_start: 0.6681 (m-30) cc_final: 0.6384 (m-30) REVERT: B 193 GLU cc_start: 0.7550 (tp30) cc_final: 0.7230 (tp30) REVERT: B 299 ASP cc_start: 0.6896 (p0) cc_final: 0.6480 (p0) REVERT: B 436 ASP cc_start: 0.8276 (t70) cc_final: 0.8017 (t0) REVERT: B 550 MET cc_start: 0.6842 (mtm) cc_final: 0.6589 (mtt) REVERT: D 141 ARG cc_start: 0.7536 (tpt170) cc_final: 0.7121 (tpt90) REVERT: D 214 LYS cc_start: 0.8310 (pptt) cc_final: 0.7244 (ptpp) REVERT: D 247 ASP cc_start: 0.8551 (t0) cc_final: 0.8095 (t0) REVERT: D 309 GLU cc_start: 0.7240 (tt0) cc_final: 0.6913 (mt-10) REVERT: D 456 GLN cc_start: 0.7552 (tp40) cc_final: 0.6980 (tt0) REVERT: E 141 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7891 (ttp80) REVERT: E 456 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7314 (tp-100) REVERT: Z 54 ILE cc_start: 0.8495 (tp) cc_final: 0.8279 (tp) REVERT: Z 59 ASN cc_start: 0.7225 (m-40) cc_final: 0.6467 (p0) REVERT: Z 74 CYS cc_start: 0.7975 (p) cc_final: 0.7638 (p) REVERT: Z 184 HIS cc_start: 0.7720 (t70) cc_final: 0.7416 (t70) REVERT: X 139 TYR cc_start: 0.7610 (t80) cc_final: 0.7245 (t80) REVERT: X 180 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7491 (tppt) REVERT: X 251 SER cc_start: 0.7572 (t) cc_final: 0.7330 (p) REVERT: Y 39 GLU cc_start: 0.7298 (pt0) cc_final: 0.6969 (pm20) REVERT: Y 125 ASP cc_start: 0.6994 (p0) cc_final: 0.6153 (m-30) REVERT: Y 137 THR cc_start: 0.6788 (t) cc_final: 0.6399 (p) REVERT: Y 196 GLN cc_start: 0.3594 (mt0) cc_final: 0.3343 (tt0) REVERT: G 45 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7495 (mmm-85) REVERT: G 58 MET cc_start: 0.4982 (tmm) cc_final: 0.4623 (ttp) REVERT: G 85 GLN cc_start: 0.7934 (pp30) cc_final: 0.7191 (pp30) REVERT: N 33 HIS cc_start: 0.7302 (m170) cc_final: 0.7033 (m-70) REVERT: N 69 TYR cc_start: 0.8071 (p90) cc_final: 0.6900 (p90) REVERT: N 72 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6916 (mm-30) REVERT: N 93 SER cc_start: 0.5906 (p) cc_final: 0.3652 (t) REVERT: N 102 LYS cc_start: 0.6474 (ttmm) cc_final: 0.5603 (tppt) REVERT: N 107 ARG cc_start: 0.7021 (mtt180) cc_final: 0.6208 (mtt180) REVERT: N 110 ARG cc_start: 0.5619 (mpt180) cc_final: 0.4810 (ttm170) REVERT: W 333 MET cc_start: 0.6331 (mmt) cc_final: 0.5975 (mmm) REVERT: W 336 TYR cc_start: 0.6872 (m-80) cc_final: 0.6422 (m-80) REVERT: W 345 TYR cc_start: 0.7451 (m-80) cc_final: 0.6918 (m-10) REVERT: W 378 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8293 (mmtm) REVERT: F 239 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7458 (tm-30) REVERT: F 423 TYR cc_start: 0.7309 (t80) cc_final: 0.6967 (t80) REVERT: F 435 MET cc_start: 0.7132 (mmm) cc_final: 0.5944 (mmm) outliers start: 0 outliers final: 0 residues processed: 1622 average time/residue: 0.6714 time to fit residues: 1837.9014 Evaluate side-chains 1035 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1035 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 803 optimal weight: 1.9990 chunk 720 optimal weight: 9.9990 chunk 399 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 486 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 745 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 453 optimal weight: 3.9990 chunk 554 optimal weight: 4.9990 chunk 863 optimal weight: 50.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 359 GLN ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 719 HIS ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN ** I 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 GLN ** T 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** V 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 81 ASN ** 1 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 78 ASN ** 3 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 92 GLN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 ASN Q 137 GLN Q 266 ASN ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN C 430 GLN A 317 ASN A 449 ASN D 265 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 118 HIS ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 160 GLN N 33 HIS N 46 ASN W 281 GLN ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 72859 Z= 0.459 Angle : 0.742 12.633 98827 Z= 0.388 Chirality : 0.047 0.339 11476 Planarity : 0.006 0.086 12780 Dihedral : 5.786 149.917 10472 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.63 % Favored : 94.36 % Rotamer: Outliers : 2.36 % Allowed : 10.62 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 9526 helix: 1.06 (0.07), residues: 5435 sheet: -1.13 (0.18), residues: 814 loop : -2.14 (0.10), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 52 HIS 0.011 0.002 HIS R 801 PHE 0.049 0.003 PHE S 16 TYR 0.053 0.003 TYR D 68 ARG 0.011 0.001 ARG 7 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1113 time to evaluate : 6.027 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: R 59 GLU cc_start: 0.7851 (mm-30) cc_final: 0.6983 (pp20) REVERT: R 71 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: R 80 MET cc_start: 0.5828 (mpp) cc_final: 0.5372 (mmt) REVERT: R 358 ASN cc_start: 0.5577 (p0) cc_final: 0.4952 (m110) REVERT: R 439 MET cc_start: 0.4212 (ppp) cc_final: 0.3479 (tmm) REVERT: R 479 TRP cc_start: 0.5438 (m100) cc_final: 0.4748 (m100) REVERT: R 492 GLU cc_start: 0.7324 (tp30) cc_final: 0.6862 (pp20) REVERT: R 539 MET cc_start: 0.8374 (tmm) cc_final: 0.8082 (tmm) REVERT: R 572 PHE cc_start: 0.4105 (t80) cc_final: 0.2931 (t80) REVERT: J 72 MET cc_start: 0.7314 (mmp) cc_final: 0.6015 (tmm) REVERT: J 76 MET cc_start: 0.8302 (mmt) cc_final: 0.8064 (mmt) REVERT: M 30 ASN cc_start: 0.7148 (t0) cc_final: 0.6903 (m-40) REVERT: M 63 LEU cc_start: 0.6548 (mp) cc_final: 0.6254 (mt) REVERT: M 87 TYR cc_start: 0.6564 (m-80) cc_final: 0.6323 (m-80) REVERT: M 105 ASP cc_start: 0.6439 (t0) cc_final: 0.5932 (p0) REVERT: I 52 LYS cc_start: 0.8357 (tttp) cc_final: 0.8145 (tmtt) REVERT: L 58 LYS cc_start: 0.7836 (mptt) cc_final: 0.7371 (mttt) REVERT: L 63 LEU cc_start: 0.6325 (mp) cc_final: 0.5916 (tt) REVERT: L 75 LYS cc_start: 0.9123 (tptt) cc_final: 0.8575 (pttp) REVERT: L 85 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7819 (mp10) REVERT: L 94 GLU cc_start: 0.6873 (pm20) cc_final: 0.6547 (pm20) REVERT: H 117 ASP cc_start: 0.7751 (t0) cc_final: 0.7336 (m-30) REVERT: H 139 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8288 (pp30) REVERT: K 75 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7583 (ttpp) REVERT: K 83 ILE cc_start: 0.8417 (tt) cc_final: 0.8050 (mt) REVERT: S 40 MET cc_start: 0.8084 (ptp) cc_final: 0.7316 (ppp) REVERT: T 50 LEU cc_start: 0.3211 (tp) cc_final: 0.2878 (mt) REVERT: T 67 MET cc_start: 0.7279 (mtt) cc_final: 0.6488 (tpt) REVERT: T 71 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5636 (t80) REVERT: U 395 MET cc_start: 0.3171 (tpp) cc_final: 0.2516 (tpt) REVERT: U 453 MET cc_start: 0.2314 (mmm) cc_final: 0.1666 (mmt) REVERT: 1 47 MET cc_start: 0.5758 (ppp) cc_final: 0.4813 (mmt) REVERT: 1 146 LEU cc_start: 0.7465 (tt) cc_final: 0.6902 (mm) REVERT: 2 44 MET cc_start: 0.4579 (mpp) cc_final: 0.4283 (mpp) REVERT: 2 61 MET cc_start: 0.5774 (mtp) cc_final: 0.5559 (mtp) REVERT: 3 28 LEU cc_start: 0.7257 (mm) cc_final: 0.6992 (tp) REVERT: 3 53 MET cc_start: 0.1840 (mmp) cc_final: 0.1078 (ptm) REVERT: 5 10 TYR cc_start: 0.5415 (p90) cc_final: 0.4160 (m-80) REVERT: 6 119 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7406 (ttp80) REVERT: 6 123 GLN cc_start: 0.6591 (pm20) cc_final: 0.5984 (mm-40) REVERT: 6 155 LYS cc_start: 0.5388 (OUTLIER) cc_final: 0.3314 (mmtm) REVERT: 9 14 PHE cc_start: 0.6865 (m-80) cc_final: 0.6478 (m-80) REVERT: 9 70 LEU cc_start: 0.7356 (tp) cc_final: 0.7108 (tp) REVERT: 9 93 LEU cc_start: 0.4249 (tt) cc_final: 0.4049 (tt) REVERT: 9 131 MET cc_start: 0.5260 (tmm) cc_final: 0.5056 (tmm) REVERT: Q 3 PHE cc_start: 0.5949 (t80) cc_final: 0.4875 (m-10) REVERT: Q 208 MET cc_start: 0.6846 (mmm) cc_final: 0.6349 (mmm) REVERT: C 142 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7684 (mtm-85) REVERT: C 266 TYR cc_start: 0.7115 (m-10) cc_final: 0.6699 (m-10) REVERT: C 432 PHE cc_start: 0.8148 (t80) cc_final: 0.7931 (t80) REVERT: C 438 LYS cc_start: 0.7443 (tmtt) cc_final: 0.7184 (tttm) REVERT: C 462 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7921 (t0) REVERT: C 498 LYS cc_start: 0.7099 (tttt) cc_final: 0.6882 (tmmt) REVERT: C 586 PHE cc_start: 0.7538 (m-80) cc_final: 0.7306 (m-80) REVERT: C 608 MET cc_start: 0.4553 (ptm) cc_final: 0.4279 (ptm) REVERT: A 81 ARG cc_start: 0.6124 (mtm-85) cc_final: 0.4762 (ptp-170) REVERT: A 314 ASN cc_start: 0.8092 (t0) cc_final: 0.7705 (t0) REVERT: A 349 ASP cc_start: 0.7928 (t70) cc_final: 0.7674 (t0) REVERT: A 353 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6880 (mmp80) REVERT: A 367 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7689 (mt-10) REVERT: A 442 ARG cc_start: 0.7809 (mtm110) cc_final: 0.6922 (ttt180) REVERT: A 443 LYS cc_start: 0.8166 (tttm) cc_final: 0.7921 (tptp) REVERT: A 463 GLU cc_start: 0.8019 (mp0) cc_final: 0.7752 (tp30) REVERT: A 570 ILE cc_start: 0.5300 (mm) cc_final: 0.5004 (mm) REVERT: B 193 GLU cc_start: 0.7586 (tp30) cc_final: 0.7284 (tp30) REVERT: B 203 PHE cc_start: 0.6884 (t80) cc_final: 0.5909 (t80) REVERT: B 299 ASP cc_start: 0.6957 (p0) cc_final: 0.6616 (p0) REVERT: B 550 MET cc_start: 0.6861 (mtm) cc_final: 0.6530 (mtt) REVERT: B 594 GLU cc_start: 0.6675 (tm-30) cc_final: 0.6172 (tm-30) REVERT: D 141 ARG cc_start: 0.7534 (tpt170) cc_final: 0.7159 (tpt90) REVERT: D 214 LYS cc_start: 0.8360 (pptt) cc_final: 0.7382 (ptpp) REVERT: D 309 GLU cc_start: 0.7235 (tt0) cc_final: 0.6940 (mt-10) REVERT: D 456 GLN cc_start: 0.7629 (tp40) cc_final: 0.7101 (tt0) REVERT: E 80 THR cc_start: 0.8878 (m) cc_final: 0.8352 (p) REVERT: Z 59 ASN cc_start: 0.7109 (m-40) cc_final: 0.6300 (p0) REVERT: Z 74 CYS cc_start: 0.8095 (p) cc_final: 0.7804 (p) REVERT: Z 170 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6126 (pm20) REVERT: Z 184 HIS cc_start: 0.7700 (t70) cc_final: 0.7442 (t70) REVERT: Z 271 GLU cc_start: 0.3980 (OUTLIER) cc_final: 0.3445 (mm-30) REVERT: X 139 TYR cc_start: 0.8094 (t80) cc_final: 0.7850 (t80) REVERT: X 161 MET cc_start: 0.7864 (tpt) cc_final: 0.7559 (tpt) REVERT: X 166 TYR cc_start: 0.7315 (m-10) cc_final: 0.7112 (m-10) REVERT: X 180 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7504 (tppt) REVERT: X 188 MET cc_start: 0.8185 (tpp) cc_final: 0.7881 (tpp) REVERT: Y 137 THR cc_start: 0.6789 (t) cc_final: 0.6537 (p) REVERT: Y 139 TYR cc_start: 0.7408 (t80) cc_final: 0.7097 (t80) REVERT: Y 213 PHE cc_start: 0.7571 (m-80) cc_final: 0.7325 (m-80) REVERT: G 45 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7510 (mmm-85) REVERT: G 56 MET cc_start: 0.4770 (mmp) cc_final: 0.2944 (ptp) REVERT: G 58 MET cc_start: 0.4789 (tmm) cc_final: 0.4388 (ttp) REVERT: G 85 GLN cc_start: 0.8109 (pp30) cc_final: 0.7323 (pp30) REVERT: W 144 ARG cc_start: 0.7321 (mtt-85) cc_final: 0.6983 (ttm-80) REVERT: W 174 LYS cc_start: 0.4806 (OUTLIER) cc_final: 0.4361 (mtmm) REVERT: W 333 MET cc_start: 0.6610 (mmt) cc_final: 0.6391 (mmm) REVERT: W 345 TYR cc_start: 0.7476 (m-80) cc_final: 0.7072 (m-10) REVERT: W 378 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8270 (mmtt) REVERT: W 391 ASN cc_start: 0.8407 (m110) cc_final: 0.8053 (p0) REVERT: F 54 ASN cc_start: 0.8071 (t0) cc_final: 0.7852 (t0) REVERT: F 88 GLU cc_start: 0.7882 (tp30) cc_final: 0.7414 (tp30) REVERT: F 239 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7427 (tm-30) REVERT: F 299 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7798 (t0) REVERT: F 387 GLN cc_start: 0.7439 (mm110) cc_final: 0.7191 (mt0) REVERT: F 402 MET cc_start: 0.5158 (ptm) cc_final: 0.4909 (pmm) REVERT: F 435 MET cc_start: 0.7336 (mmm) cc_final: 0.6540 (mmm) outliers start: 167 outliers final: 102 residues processed: 1218 average time/residue: 0.6741 time to fit residues: 1394.4104 Evaluate side-chains 1074 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 963 time to evaluate : 5.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 367 THR Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 617 LEU Chi-restraints excluded: chain R residue 784 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain H residue 139 GLN Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain U residue 396 MET Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 0 residue 149 LEU Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 81 ASN Chi-restraints excluded: chain 1 residue 102 SER Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 143 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 4 residue 46 VAL Chi-restraints excluded: chain 4 residue 47 MET Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 5 residue 59 VAL Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 98 SER Chi-restraints excluded: chain 6 residue 140 VAL Chi-restraints excluded: chain 6 residue 155 LYS Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 140 VAL Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 47 MET Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 102 SER Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 137 GLN Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 170 GLU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 207 CYS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 345 ASN Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 479 optimal weight: 0.7980 chunk 268 optimal weight: 20.0000 chunk 718 optimal weight: 0.8980 chunk 588 optimal weight: 0.4980 chunk 238 optimal weight: 30.0000 chunk 865 optimal weight: 40.0000 chunk 934 optimal weight: 0.6980 chunk 770 optimal weight: 1.9990 chunk 857 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 694 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 316 GLN ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN S 61 ASN T 125 GLN U 338 HIS U 348 HIS 1 92 GLN 2 78 ASN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 346 ASN A 317 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 72859 Z= 0.176 Angle : 0.582 10.399 98827 Z= 0.303 Chirality : 0.042 0.523 11476 Planarity : 0.004 0.067 12780 Dihedral : 5.210 148.397 10472 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.48 % Favored : 95.51 % Rotamer: Outliers : 2.11 % Allowed : 13.45 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.17 (0.09), residues: 9526 helix: 1.45 (0.07), residues: 5443 sheet: -0.82 (0.18), residues: 800 loop : -1.98 (0.10), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 567 HIS 0.007 0.001 HIS R 801 PHE 0.032 0.001 PHE S 16 TYR 0.040 0.002 TYR 5 68 ARG 0.007 0.000 ARG J 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1084 time to evaluate : 6.061 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: R 71 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: R 80 MET cc_start: 0.5651 (mpp) cc_final: 0.5174 (mmt) REVERT: R 94 MET cc_start: 0.7311 (ppp) cc_final: 0.6272 (mmm) REVERT: R 355 MET cc_start: 0.6453 (tpt) cc_final: 0.5610 (ptm) REVERT: R 358 ASN cc_start: 0.5096 (p0) cc_final: 0.4606 (m-40) REVERT: R 439 MET cc_start: 0.4385 (ppp) cc_final: 0.3624 (tmm) REVERT: R 479 TRP cc_start: 0.5127 (m100) cc_final: 0.4632 (m100) REVERT: R 492 GLU cc_start: 0.7341 (tp30) cc_final: 0.6944 (tm-30) REVERT: R 539 MET cc_start: 0.8302 (tmm) cc_final: 0.8081 (tmm) REVERT: R 572 PHE cc_start: 0.3970 (t80) cc_final: 0.2823 (t80) REVERT: R 615 MET cc_start: 0.7842 (tmm) cc_final: 0.7525 (tmm) REVERT: R 727 TYR cc_start: 0.6549 (t80) cc_final: 0.6318 (t80) REVERT: J 72 MET cc_start: 0.7275 (mmp) cc_final: 0.5945 (tmm) REVERT: J 83 VAL cc_start: 0.7735 (t) cc_final: 0.7220 (p) REVERT: J 131 ARG cc_start: 0.7684 (mtp-110) cc_final: 0.7418 (mtp85) REVERT: M 30 ASN cc_start: 0.7162 (t0) cc_final: 0.6940 (m-40) REVERT: M 63 LEU cc_start: 0.6225 (mp) cc_final: 0.5947 (mt) REVERT: M 81 MET cc_start: 0.6443 (mtt) cc_final: 0.6126 (tmm) REVERT: M 105 ASP cc_start: 0.6380 (t0) cc_final: 0.5906 (p0) REVERT: I 59 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7842 (tmmt) REVERT: I 74 ASN cc_start: 0.7985 (t0) cc_final: 0.7667 (m-40) REVERT: I 149 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: I 172 TYR cc_start: 0.6596 (m-80) cc_final: 0.6232 (m-80) REVERT: L 58 LYS cc_start: 0.7811 (mptt) cc_final: 0.7351 (mttt) REVERT: L 63 LEU cc_start: 0.6322 (mp) cc_final: 0.5921 (tt) REVERT: L 75 LYS cc_start: 0.9089 (tptt) cc_final: 0.8518 (pttp) REVERT: L 85 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7853 (mt0) REVERT: H 117 ASP cc_start: 0.7682 (t0) cc_final: 0.7145 (m-30) REVERT: K 83 ILE cc_start: 0.8363 (tt) cc_final: 0.8046 (mt) REVERT: S 40 MET cc_start: 0.8266 (ptp) cc_final: 0.7507 (ppp) REVERT: T 67 MET cc_start: 0.7513 (mtt) cc_final: 0.6827 (tpt) REVERT: T 71 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.5334 (t80) REVERT: U 342 MET cc_start: 0.4863 (ttm) cc_final: 0.4524 (tmm) REVERT: U 379 LYS cc_start: 0.7273 (mttp) cc_final: 0.6924 (pptt) REVERT: U 395 MET cc_start: 0.3192 (tpp) cc_final: 0.2941 (tpt) REVERT: U 428 MET cc_start: 0.3562 (mtt) cc_final: 0.3277 (mtm) REVERT: U 453 MET cc_start: 0.2203 (mmm) cc_final: 0.1722 (mmt) REVERT: V 299 TYR cc_start: 0.1151 (OUTLIER) cc_final: -0.0099 (t80) REVERT: 1 23 MET cc_start: 0.7225 (tpt) cc_final: 0.6924 (tpt) REVERT: 1 34 THR cc_start: 0.7713 (p) cc_final: 0.7085 (t) REVERT: 1 44 MET cc_start: 0.6536 (tmm) cc_final: 0.6129 (tmm) REVERT: 1 47 MET cc_start: 0.5829 (ppp) cc_final: 0.4892 (mmt) REVERT: 1 146 LEU cc_start: 0.7411 (tt) cc_final: 0.6792 (mm) REVERT: 2 61 MET cc_start: 0.5870 (mtp) cc_final: 0.5546 (mtp) REVERT: 2 137 PHE cc_start: 0.6105 (m-80) cc_final: 0.5864 (t80) REVERT: 3 53 MET cc_start: 0.2238 (mmp) cc_final: 0.1190 (ptm) REVERT: 3 68 TYR cc_start: 0.6639 (m-80) cc_final: 0.6263 (m-80) REVERT: 3 141 LEU cc_start: 0.6625 (mm) cc_final: 0.6090 (mp) REVERT: 4 44 MET cc_start: 0.5443 (tmm) cc_final: 0.4388 (ppp) REVERT: 5 10 TYR cc_start: 0.5627 (p90) cc_final: 0.4409 (m-80) REVERT: 5 44 MET cc_start: 0.5978 (ppp) cc_final: 0.5693 (ttp) REVERT: 6 155 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.3062 (mmtm) REVERT: 7 45 SER cc_start: 0.7799 (t) cc_final: 0.7596 (t) REVERT: 7 82 ASP cc_start: 0.5808 (OUTLIER) cc_final: 0.5513 (t0) REVERT: 8 23 MET cc_start: 0.6341 (tpt) cc_final: 0.6102 (tpt) REVERT: 8 44 MET cc_start: 0.6797 (tpp) cc_final: 0.6452 (tpp) REVERT: 9 13 PHE cc_start: 0.6817 (t80) cc_final: 0.6570 (t80) REVERT: 9 14 PHE cc_start: 0.6757 (m-80) cc_final: 0.6429 (m-80) REVERT: Q 85 MET cc_start: 0.5850 (tpp) cc_final: 0.5610 (ttm) REVERT: Q 208 MET cc_start: 0.6635 (mmm) cc_final: 0.6387 (mmp) REVERT: Q 306 PHE cc_start: 0.6140 (m-80) cc_final: 0.5844 (t80) REVERT: C 142 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7751 (mtm-85) REVERT: C 193 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6665 (mm-30) REVERT: C 283 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7592 (tt0) REVERT: C 432 PHE cc_start: 0.8181 (t80) cc_final: 0.7812 (t80) REVERT: C 462 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7798 (t0) REVERT: C 586 PHE cc_start: 0.7479 (m-80) cc_final: 0.7194 (m-80) REVERT: A 81 ARG cc_start: 0.5866 (mtm-85) cc_final: 0.4666 (ptp-170) REVERT: A 296 MET cc_start: 0.5297 (mpp) cc_final: 0.3711 (ptm) REVERT: A 314 ASN cc_start: 0.7692 (t0) cc_final: 0.7342 (t0) REVERT: A 349 ASP cc_start: 0.7992 (t70) cc_final: 0.7675 (t0) REVERT: A 399 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 442 ARG cc_start: 0.7774 (mtm110) cc_final: 0.6956 (ttt180) REVERT: A 443 LYS cc_start: 0.8159 (tttm) cc_final: 0.7947 (tptp) REVERT: A 570 ILE cc_start: 0.5398 (mm) cc_final: 0.5193 (mm) REVERT: B 136 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (t) REVERT: B 193 GLU cc_start: 0.7510 (tp30) cc_final: 0.7171 (tp30) REVERT: B 203 PHE cc_start: 0.6664 (t80) cc_final: 0.6023 (t80) REVERT: B 299 ASP cc_start: 0.6827 (p0) cc_final: 0.6480 (p0) REVERT: B 347 MET cc_start: 0.8121 (mmm) cc_final: 0.7537 (mmm) REVERT: B 485 GLU cc_start: 0.7958 (mp0) cc_final: 0.7740 (mp0) REVERT: B 577 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7290 (tt) REVERT: D 141 ARG cc_start: 0.7556 (tpt170) cc_final: 0.7114 (mmm160) REVERT: D 214 LYS cc_start: 0.8161 (pptt) cc_final: 0.7111 (ptpp) REVERT: D 309 GLU cc_start: 0.7149 (tt0) cc_final: 0.6860 (mt-10) REVERT: D 456 GLN cc_start: 0.7509 (tp40) cc_final: 0.6993 (tt0) REVERT: E 80 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8400 (p) REVERT: Z 59 ASN cc_start: 0.7038 (m-40) cc_final: 0.6430 (p0) REVERT: Z 74 CYS cc_start: 0.8113 (p) cc_final: 0.7832 (p) REVERT: Z 271 GLU cc_start: 0.3696 (OUTLIER) cc_final: 0.3222 (mm-30) REVERT: X 139 TYR cc_start: 0.8179 (t80) cc_final: 0.7892 (t80) REVERT: X 161 MET cc_start: 0.7780 (tpt) cc_final: 0.7574 (mmm) REVERT: X 180 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7202 (tppt) REVERT: X 243 GLN cc_start: 0.7399 (mt0) cc_final: 0.6995 (mm-40) REVERT: Y 137 THR cc_start: 0.6921 (t) cc_final: 0.6604 (p) REVERT: Y 139 TYR cc_start: 0.7426 (t80) cc_final: 0.7210 (t80) REVERT: Y 210 GLU cc_start: 0.7182 (tp30) cc_final: 0.6921 (pp20) REVERT: G 45 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7502 (mmm-85) REVERT: G 56 MET cc_start: 0.4865 (mmp) cc_final: 0.3404 (ptm) REVERT: G 58 MET cc_start: 0.4632 (tmm) cc_final: 0.4215 (ttp) REVERT: G 85 GLN cc_start: 0.8033 (pp30) cc_final: 0.7385 (pp30) REVERT: W 333 MET cc_start: 0.6586 (mmt) cc_final: 0.5778 (mmm) REVERT: W 345 TYR cc_start: 0.7295 (m-80) cc_final: 0.7069 (m-10) REVERT: W 378 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8120 (mmtm) REVERT: F 239 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7319 (tm-30) REVERT: F 299 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7559 (t0) REVERT: F 387 GLN cc_start: 0.7293 (mm110) cc_final: 0.7010 (mt0) REVERT: F 435 MET cc_start: 0.7042 (mmm) cc_final: 0.6586 (mmm) REVERT: F 462 PHE cc_start: 0.8064 (t80) cc_final: 0.7553 (t80) outliers start: 149 outliers final: 74 residues processed: 1178 average time/residue: 0.6889 time to fit residues: 1383.2977 Evaluate side-chains 1039 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 952 time to evaluate : 5.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 367 THR Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 71 PHE Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 113 VAL Chi-restraints excluded: chain 2 residue 143 LEU Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 155 LYS Chi-restraints excluded: chain 7 residue 20 SER Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 854 optimal weight: 50.0000 chunk 650 optimal weight: 2.9990 chunk 449 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 412 optimal weight: 20.0000 chunk 580 optimal weight: 1.9990 chunk 868 optimal weight: 40.0000 chunk 919 optimal weight: 7.9990 chunk 453 optimal weight: 0.0980 chunk 822 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 overall best weight: 1.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN M 50 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 78 ASN 4 92 GLN ** 7 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 209 GLN E 421 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 207 GLN ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 72859 Z= 0.209 Angle : 0.576 10.627 98827 Z= 0.299 Chirality : 0.042 0.504 11476 Planarity : 0.004 0.061 12780 Dihedral : 5.070 146.163 10472 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.43 % Allowed : 14.98 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 9526 helix: 1.52 (0.07), residues: 5448 sheet: -0.77 (0.18), residues: 801 loop : -1.95 (0.10), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP W 199 HIS 0.008 0.001 HIS R 801 PHE 0.028 0.001 PHE 1 137 TYR 0.052 0.002 TYR 9 144 ARG 0.008 0.000 ARG 8 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1029 time to evaluate : 7.164 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: R 71 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: R 74 LYS cc_start: 0.5472 (pptt) cc_final: 0.5105 (ptmt) REVERT: R 80 MET cc_start: 0.5620 (mpp) cc_final: 0.5151 (mmt) REVERT: R 94 MET cc_start: 0.7166 (ppp) cc_final: 0.6190 (mmm) REVERT: R 358 ASN cc_start: 0.5248 (p0) cc_final: 0.4669 (m-40) REVERT: R 423 MET cc_start: 0.4807 (tpp) cc_final: 0.4043 (tpp) REVERT: R 439 MET cc_start: 0.4327 (ppp) cc_final: 0.3599 (tmm) REVERT: R 450 ILE cc_start: 0.7369 (pt) cc_final: 0.7104 (pt) REVERT: R 453 MET cc_start: 0.6617 (mmt) cc_final: 0.6347 (mmm) REVERT: R 479 TRP cc_start: 0.5135 (m100) cc_final: 0.4655 (m100) REVERT: R 484 MET cc_start: 0.5044 (mmm) cc_final: 0.4467 (mmt) REVERT: R 492 GLU cc_start: 0.7312 (tp30) cc_final: 0.6913 (tm-30) REVERT: R 572 PHE cc_start: 0.4094 (t80) cc_final: 0.2909 (t80) REVERT: R 615 MET cc_start: 0.7727 (tmm) cc_final: 0.6699 (tmm) REVERT: R 727 TYR cc_start: 0.6538 (t80) cc_final: 0.6326 (t80) REVERT: R 756 TRP cc_start: 0.3501 (t60) cc_final: 0.3243 (t60) REVERT: R 764 LEU cc_start: 0.3358 (OUTLIER) cc_final: 0.2866 (tt) REVERT: J 72 MET cc_start: 0.7437 (mmp) cc_final: 0.6052 (tmm) REVERT: J 111 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7804 (mtm180) REVERT: J 131 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7406 (mtp85) REVERT: M 30 ASN cc_start: 0.6957 (t0) cc_final: 0.6721 (m-40) REVERT: M 81 MET cc_start: 0.6316 (mtt) cc_final: 0.5838 (tmm) REVERT: M 105 ASP cc_start: 0.6405 (t0) cc_final: 0.5893 (p0) REVERT: I 52 LYS cc_start: 0.7884 (tmtt) cc_final: 0.7300 (pttm) REVERT: I 74 ASN cc_start: 0.8007 (t0) cc_final: 0.7688 (m-40) REVERT: I 149 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: L 58 LYS cc_start: 0.7842 (mptt) cc_final: 0.7374 (mttt) REVERT: L 63 LEU cc_start: 0.6310 (mp) cc_final: 0.5922 (tt) REVERT: L 75 LYS cc_start: 0.9092 (tptt) cc_final: 0.8552 (pttp) REVERT: L 85 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7514 (mp10) REVERT: H 117 ASP cc_start: 0.7708 (t0) cc_final: 0.7197 (m-30) REVERT: H 197 GLU cc_start: 0.7815 (mp0) cc_final: 0.7519 (mp0) REVERT: K 74 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7367 (tp30) REVERT: K 83 ILE cc_start: 0.8357 (tt) cc_final: 0.8070 (mt) REVERT: S 40 MET cc_start: 0.8194 (ptp) cc_final: 0.7355 (ppp) REVERT: T 67 MET cc_start: 0.7408 (mtt) cc_final: 0.6787 (tpt) REVERT: U 342 MET cc_start: 0.5028 (ttm) cc_final: 0.4597 (tmm) REVERT: U 395 MET cc_start: 0.3376 (tpp) cc_final: 0.3073 (tpt) REVERT: U 428 MET cc_start: 0.3116 (mtt) cc_final: 0.2759 (mtm) REVERT: U 453 MET cc_start: 0.2350 (mmm) cc_final: 0.1844 (mmt) REVERT: V 299 TYR cc_start: 0.0680 (OUTLIER) cc_final: -0.0310 (t80) REVERT: 0 71 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6332 (tt) REVERT: 1 44 MET cc_start: 0.6473 (tmm) cc_final: 0.5932 (tmm) REVERT: 1 47 MET cc_start: 0.6182 (ppp) cc_final: 0.5244 (mmt) REVERT: 1 146 LEU cc_start: 0.7505 (tt) cc_final: 0.6887 (mm) REVERT: 2 61 MET cc_start: 0.5945 (mtp) cc_final: 0.5564 (mtp) REVERT: 2 146 LEU cc_start: 0.5974 (tp) cc_final: 0.5717 (tp) REVERT: 2 150 LEU cc_start: 0.6469 (mm) cc_final: 0.5945 (tp) REVERT: 3 17 MET cc_start: 0.4024 (mmp) cc_final: 0.3600 (mmt) REVERT: 3 53 MET cc_start: 0.2517 (mmp) cc_final: 0.1427 (ptm) REVERT: 4 44 MET cc_start: 0.5580 (tmm) cc_final: 0.4635 (ppp) REVERT: 5 10 TYR cc_start: 0.5502 (p90) cc_final: 0.4247 (m-80) REVERT: 5 44 MET cc_start: 0.6122 (ppp) cc_final: 0.5877 (ttp) REVERT: 6 101 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8673 (mp) REVERT: 6 155 LYS cc_start: 0.5286 (OUTLIER) cc_final: 0.3004 (mmtm) REVERT: 7 17 MET cc_start: 0.7938 (ttt) cc_final: 0.7668 (ttt) REVERT: 7 82 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5738 (t0) REVERT: 8 119 ARG cc_start: 0.6515 (mtt90) cc_final: 0.6268 (mtt90) REVERT: 9 14 PHE cc_start: 0.6666 (m-80) cc_final: 0.6418 (m-80) REVERT: C 142 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7797 (mtm-85) REVERT: C 266 TYR cc_start: 0.7083 (m-10) cc_final: 0.6570 (m-10) REVERT: C 283 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7741 (tt0) REVERT: C 432 PHE cc_start: 0.8156 (t80) cc_final: 0.7821 (t80) REVERT: C 462 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7859 (t0) REVERT: C 586 PHE cc_start: 0.7482 (m-80) cc_final: 0.7230 (m-80) REVERT: A 81 ARG cc_start: 0.6243 (mtm-85) cc_final: 0.4987 (ptp-170) REVERT: A 314 ASN cc_start: 0.7824 (t0) cc_final: 0.7443 (t0) REVERT: A 349 ASP cc_start: 0.8044 (t70) cc_final: 0.7679 (t0) REVERT: A 353 ARG cc_start: 0.7151 (mmt-90) cc_final: 0.6850 (mmp80) REVERT: A 399 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: A 442 ARG cc_start: 0.7798 (mtm110) cc_final: 0.6957 (ttt180) REVERT: A 443 LYS cc_start: 0.8172 (tttm) cc_final: 0.7944 (tptp) REVERT: A 570 ILE cc_start: 0.5522 (mm) cc_final: 0.5230 (mm) REVERT: A 600 ASP cc_start: 0.6656 (m-30) cc_final: 0.6315 (m-30) REVERT: B 136 THR cc_start: 0.7675 (OUTLIER) cc_final: 0.7406 (t) REVERT: B 142 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.7977 (mtm110) REVERT: B 193 GLU cc_start: 0.7632 (tp30) cc_final: 0.7244 (tp30) REVERT: B 203 PHE cc_start: 0.6687 (t80) cc_final: 0.6016 (t80) REVERT: B 299 ASP cc_start: 0.6903 (p0) cc_final: 0.6523 (p0) REVERT: B 347 MET cc_start: 0.8309 (mmm) cc_final: 0.7472 (mmm) REVERT: B 459 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.8000 (mmm-85) REVERT: D 141 ARG cc_start: 0.7586 (tpt170) cc_final: 0.7159 (mmm160) REVERT: D 214 LYS cc_start: 0.8140 (pptt) cc_final: 0.7100 (ptpp) REVERT: D 309 GLU cc_start: 0.7142 (tt0) cc_final: 0.6877 (mt-10) REVERT: D 435 MET cc_start: 0.7153 (tmm) cc_final: 0.6801 (tmm) REVERT: D 456 GLN cc_start: 0.7524 (tp40) cc_final: 0.6997 (tt0) REVERT: E 80 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8424 (p) REVERT: E 201 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: Z 59 ASN cc_start: 0.7115 (m-40) cc_final: 0.6292 (p0) REVERT: Z 74 CYS cc_start: 0.8074 (p) cc_final: 0.7733 (p) REVERT: Z 184 HIS cc_start: 0.7685 (t70) cc_final: 0.7286 (t-90) REVERT: Z 271 GLU cc_start: 0.3606 (OUTLIER) cc_final: 0.3128 (mm-30) REVERT: X 139 TYR cc_start: 0.8166 (t80) cc_final: 0.7886 (t80) REVERT: X 161 MET cc_start: 0.7787 (tpt) cc_final: 0.7397 (tpt) REVERT: X 180 LYS cc_start: 0.7825 (ttpp) cc_final: 0.7192 (tppt) REVERT: X 243 GLN cc_start: 0.7484 (mt0) cc_final: 0.7117 (mm-40) REVERT: Y 137 THR cc_start: 0.6964 (t) cc_final: 0.6649 (p) REVERT: Y 139 TYR cc_start: 0.7415 (t80) cc_final: 0.7174 (t80) REVERT: Y 188 MET cc_start: 0.6905 (ptm) cc_final: 0.5790 (ptp) REVERT: G 45 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7538 (mmm-85) REVERT: G 56 MET cc_start: 0.4902 (mmp) cc_final: 0.3295 (ptm) REVERT: G 58 MET cc_start: 0.4672 (tmm) cc_final: 0.4292 (ttp) REVERT: G 85 GLN cc_start: 0.8047 (pp30) cc_final: 0.7439 (pp30) REVERT: W 333 MET cc_start: 0.6638 (mmt) cc_final: 0.5934 (mmt) REVERT: W 345 TYR cc_start: 0.7529 (m-80) cc_final: 0.6944 (m-10) REVERT: W 378 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8237 (mmtt) REVERT: W 391 ASN cc_start: 0.7988 (m-40) cc_final: 0.7511 (p0) REVERT: F 239 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7283 (tm-30) REVERT: F 299 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7644 (t0) REVERT: F 387 GLN cc_start: 0.7354 (mm110) cc_final: 0.7030 (mt0) REVERT: F 402 MET cc_start: 0.5142 (pmm) cc_final: 0.4867 (ttt) REVERT: F 435 MET cc_start: 0.6985 (mmm) cc_final: 0.6697 (mmt) outliers start: 172 outliers final: 105 residues processed: 1147 average time/residue: 0.6619 time to fit residues: 1302.1728 Evaluate side-chains 1063 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 943 time to evaluate : 6.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 764 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 71 ILE Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 143 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 147 ILE Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 101 LEU Chi-restraints excluded: chain 6 residue 155 LYS Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 9 residue 34 THR Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 369 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 765 optimal weight: 4.9990 chunk 521 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 684 optimal weight: 4.9990 chunk 379 optimal weight: 4.9990 chunk 784 optimal weight: 1.9990 chunk 635 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 469 optimal weight: 0.6980 chunk 825 optimal weight: 50.0000 chunk 231 optimal weight: 40.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 GLN U 348 HIS U 403 GLN ** U 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 78 ASN 6 123 GLN 8 51 GLN Q 266 ASN ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 209 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 184 HIS ** Z 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN F 265 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 72859 Z= 0.295 Angle : 0.613 12.482 98827 Z= 0.317 Chirality : 0.043 0.452 11476 Planarity : 0.005 0.060 12780 Dihedral : 5.183 146.921 10472 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.14 % Allowed : 16.36 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.19 (0.09), residues: 9526 helix: 1.48 (0.07), residues: 5433 sheet: -0.85 (0.18), residues: 807 loop : -1.98 (0.10), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP W 199 HIS 0.008 0.001 HIS R 801 PHE 0.027 0.002 PHE 1 137 TYR 0.032 0.002 TYR 3 68 ARG 0.008 0.001 ARG K 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 995 time to evaluate : 6.447 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: R 71 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: R 80 MET cc_start: 0.5644 (mpp) cc_final: 0.5165 (mmt) REVERT: R 94 MET cc_start: 0.6849 (ppp) cc_final: 0.5954 (mmm) REVERT: R 355 MET cc_start: 0.5717 (tpt) cc_final: 0.4963 (ptm) REVERT: R 358 ASN cc_start: 0.5236 (p0) cc_final: 0.4660 (m-40) REVERT: R 439 MET cc_start: 0.4311 (ppp) cc_final: 0.3612 (tmm) REVERT: R 479 TRP cc_start: 0.5156 (m100) cc_final: 0.4686 (m100) REVERT: R 484 MET cc_start: 0.4941 (mmm) cc_final: 0.4481 (tpt) REVERT: R 492 GLU cc_start: 0.7394 (tp30) cc_final: 0.6986 (tm-30) REVERT: R 539 MET cc_start: 0.8225 (tmm) cc_final: 0.7546 (ttt) REVERT: R 572 PHE cc_start: 0.4055 (t80) cc_final: 0.2849 (t80) REVERT: R 615 MET cc_start: 0.7673 (tmm) cc_final: 0.6681 (tmm) REVERT: R 727 TYR cc_start: 0.6602 (t80) cc_final: 0.6383 (t80) REVERT: R 756 TRP cc_start: 0.3609 (t60) cc_final: 0.3408 (t60) REVERT: R 758 MET cc_start: 0.4908 (tpt) cc_final: 0.4258 (tpt) REVERT: R 764 LEU cc_start: 0.3389 (OUTLIER) cc_final: 0.2764 (tt) REVERT: J 72 MET cc_start: 0.7470 (mmp) cc_final: 0.6018 (tmm) REVERT: J 111 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7942 (mtm180) REVERT: J 131 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.7449 (mtp85) REVERT: M 81 MET cc_start: 0.6399 (mtt) cc_final: 0.5935 (tmm) REVERT: M 105 ASP cc_start: 0.6700 (t0) cc_final: 0.6041 (p0) REVERT: I 74 ASN cc_start: 0.8096 (t0) cc_final: 0.7741 (m-40) REVERT: I 149 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: I 172 TYR cc_start: 0.6687 (m-10) cc_final: 0.5922 (m-10) REVERT: L 58 LYS cc_start: 0.7835 (mptt) cc_final: 0.7371 (mttt) REVERT: L 63 LEU cc_start: 0.6220 (mp) cc_final: 0.5904 (tt) REVERT: L 75 LYS cc_start: 0.9125 (tptt) cc_final: 0.8553 (pttp) REVERT: L 85 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7490 (mp10) REVERT: H 117 ASP cc_start: 0.7725 (t0) cc_final: 0.7258 (m-30) REVERT: K 74 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7455 (tp30) REVERT: K 83 ILE cc_start: 0.8338 (tt) cc_final: 0.8005 (mt) REVERT: K 94 GLU cc_start: 0.8190 (pm20) cc_final: 0.7839 (pm20) REVERT: S 34 ARG cc_start: 0.3846 (tpt90) cc_final: 0.3477 (tpt90) REVERT: S 40 MET cc_start: 0.8195 (ptp) cc_final: 0.7494 (ppp) REVERT: T 67 MET cc_start: 0.7165 (mtt) cc_final: 0.6717 (tpt) REVERT: U 428 MET cc_start: 0.3298 (mtt) cc_final: 0.2866 (mtm) REVERT: U 453 MET cc_start: 0.2354 (mmm) cc_final: 0.1927 (mmt) REVERT: V 299 TYR cc_start: 0.0522 (OUTLIER) cc_final: -0.0550 (t80) REVERT: 0 71 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6421 (tt) REVERT: 1 44 MET cc_start: 0.6124 (tmm) cc_final: 0.5740 (tmm) REVERT: 1 47 MET cc_start: 0.6353 (ppp) cc_final: 0.5222 (mmt) REVERT: 1 101 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7884 (tt) REVERT: 2 61 MET cc_start: 0.5768 (mtp) cc_final: 0.5560 (mtp) REVERT: 2 150 LEU cc_start: 0.6312 (mm) cc_final: 0.5750 (tp) REVERT: 2 155 LYS cc_start: 0.2346 (mtpt) cc_final: 0.2102 (mtpt) REVERT: 3 53 MET cc_start: 0.3057 (mmp) cc_final: 0.1699 (ptm) REVERT: 3 68 TYR cc_start: 0.5757 (m-80) cc_final: 0.5375 (m-80) REVERT: 3 82 ASP cc_start: 0.4277 (t0) cc_final: 0.4040 (t0) REVERT: 4 44 MET cc_start: 0.5665 (tmm) cc_final: 0.4844 (ppp) REVERT: 4 139 GLU cc_start: 0.4326 (tp30) cc_final: 0.4034 (tp30) REVERT: 5 10 TYR cc_start: 0.5640 (p90) cc_final: 0.4293 (m-80) REVERT: 5 44 MET cc_start: 0.6195 (ppp) cc_final: 0.5767 (ttp) REVERT: 6 155 LYS cc_start: 0.5189 (OUTLIER) cc_final: 0.3070 (mmtm) REVERT: 7 82 ASP cc_start: 0.6244 (OUTLIER) cc_final: 0.5943 (t0) REVERT: 9 14 PHE cc_start: 0.6865 (m-80) cc_final: 0.6582 (m-80) REVERT: Q 176 MET cc_start: 0.5360 (ptp) cc_final: 0.5082 (ptp) REVERT: C 142 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7857 (mtm-85) REVERT: C 266 TYR cc_start: 0.7016 (m-10) cc_final: 0.6575 (m-10) REVERT: C 432 PHE cc_start: 0.8224 (t80) cc_final: 0.7891 (t80) REVERT: C 462 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7927 (t0) REVERT: C 586 PHE cc_start: 0.7486 (m-80) cc_final: 0.7263 (m-80) REVERT: A 39 MET cc_start: 0.8991 (mmm) cc_final: 0.8484 (mmm) REVERT: A 81 ARG cc_start: 0.6276 (mtm-85) cc_final: 0.5057 (ptp-170) REVERT: A 314 ASN cc_start: 0.8007 (t0) cc_final: 0.7626 (t0) REVERT: A 349 ASP cc_start: 0.8035 (t70) cc_final: 0.7674 (t0) REVERT: A 353 ARG cc_start: 0.7172 (mmt-90) cc_final: 0.6960 (mmp80) REVERT: A 399 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: A 443 LYS cc_start: 0.8180 (tttm) cc_final: 0.7924 (tptp) REVERT: A 518 ASP cc_start: 0.7808 (t0) cc_final: 0.7587 (t0) REVERT: B 136 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7434 (t) REVERT: B 142 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.8033 (mtm110) REVERT: B 193 GLU cc_start: 0.7554 (tp30) cc_final: 0.7182 (tp30) REVERT: B 203 PHE cc_start: 0.6707 (t80) cc_final: 0.5951 (t80) REVERT: B 299 ASP cc_start: 0.6924 (p0) cc_final: 0.6612 (p0) REVERT: B 577 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7315 (tt) REVERT: D 141 ARG cc_start: 0.7619 (tpt170) cc_final: 0.7204 (mmm160) REVERT: D 214 LYS cc_start: 0.8151 (pptt) cc_final: 0.7117 (ptpp) REVERT: D 309 GLU cc_start: 0.7156 (tt0) cc_final: 0.6863 (mt-10) REVERT: D 358 ASN cc_start: 0.8348 (t0) cc_final: 0.8144 (t0) REVERT: D 435 MET cc_start: 0.7199 (tmm) cc_final: 0.6793 (tmm) REVERT: D 456 GLN cc_start: 0.7589 (tp40) cc_final: 0.7045 (tt0) REVERT: E 44 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7394 (mtt90) REVERT: E 80 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8377 (p) REVERT: E 154 MET cc_start: 0.8640 (mmm) cc_final: 0.8349 (mmt) REVERT: Z 59 ASN cc_start: 0.7061 (m-40) cc_final: 0.6307 (p0) REVERT: Z 74 CYS cc_start: 0.8062 (p) cc_final: 0.7754 (p) REVERT: Z 170 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6125 (pt0) REVERT: Z 271 GLU cc_start: 0.3682 (OUTLIER) cc_final: 0.3119 (mm-30) REVERT: X 161 MET cc_start: 0.7704 (tpt) cc_final: 0.7447 (tpt) REVERT: X 180 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7315 (tppt) REVERT: X 243 GLN cc_start: 0.7511 (mt0) cc_final: 0.7138 (mm-40) REVERT: Y 137 THR cc_start: 0.6961 (t) cc_final: 0.6629 (p) REVERT: G 45 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7512 (mmm-85) REVERT: G 56 MET cc_start: 0.4987 (mmp) cc_final: 0.3250 (ptm) REVERT: G 58 MET cc_start: 0.4687 (tmm) cc_final: 0.4257 (ttp) REVERT: G 85 GLN cc_start: 0.8006 (pp30) cc_final: 0.7409 (pp30) REVERT: W 333 MET cc_start: 0.6609 (mmt) cc_final: 0.5808 (mmt) REVERT: W 345 TYR cc_start: 0.7533 (m-80) cc_final: 0.7011 (m-10) REVERT: W 378 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8321 (mttm) REVERT: F 54 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7573 (p0) REVERT: F 239 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 297 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8319 (mt) REVERT: F 299 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7816 (t0) REVERT: F 376 GLN cc_start: 0.7568 (mt0) cc_final: 0.7057 (pm20) REVERT: F 387 GLN cc_start: 0.7476 (mm110) cc_final: 0.7208 (mt0) REVERT: F 435 MET cc_start: 0.6678 (mmm) cc_final: 0.6194 (tpt) outliers start: 222 outliers final: 144 residues processed: 1151 average time/residue: 0.6668 time to fit residues: 1318.5392 Evaluate side-chains 1105 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 942 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 GLU Chi-restraints excluded: chain R residue 367 THR Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 764 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 108 ASP Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 124 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 380 LYS Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 71 ILE Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 143 LEU Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 155 LYS Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 8 residue 143 LEU Chi-restraints excluded: chain 9 residue 34 THR Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 170 GLU Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 225 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 67 GLU Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain W residue 373 ASP Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 309 optimal weight: 5.9990 chunk 827 optimal weight: 50.0000 chunk 181 optimal weight: 5.9990 chunk 539 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 920 optimal weight: 0.9990 chunk 763 optimal weight: 2.9990 chunk 426 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 304 optimal weight: 2.9990 chunk 483 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 523 ASN ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 GLN S 67 GLN U 348 HIS ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 90 ASN 1 81 ASN 2 78 ASN ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN Z 207 GLN ** X 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 72859 Z= 0.296 Angle : 0.615 12.276 98827 Z= 0.318 Chirality : 0.043 0.428 11476 Planarity : 0.005 0.058 12780 Dihedral : 5.157 145.777 10472 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.38 % Allowed : 16.97 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.09), residues: 9526 helix: 1.49 (0.07), residues: 5425 sheet: -0.89 (0.18), residues: 807 loop : -1.98 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 52 HIS 0.010 0.001 HIS R 801 PHE 0.049 0.002 PHE 3 25 TYR 0.033 0.002 TYR 5 68 ARG 0.008 0.001 ARG 8 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 982 time to evaluate : 6.248 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: R 80 MET cc_start: 0.5658 (mpp) cc_final: 0.5151 (mmt) REVERT: R 94 MET cc_start: 0.6571 (ppp) cc_final: 0.5890 (mmt) REVERT: R 358 ASN cc_start: 0.5513 (p0) cc_final: 0.4695 (m-40) REVERT: R 439 MET cc_start: 0.4304 (ppp) cc_final: 0.3624 (tmm) REVERT: R 479 TRP cc_start: 0.5138 (m100) cc_final: 0.4694 (m100) REVERT: R 484 MET cc_start: 0.4638 (mmm) cc_final: 0.4188 (tpt) REVERT: R 492 GLU cc_start: 0.7321 (tp30) cc_final: 0.6920 (tm-30) REVERT: R 539 MET cc_start: 0.8289 (tmm) cc_final: 0.7603 (ttt) REVERT: R 572 PHE cc_start: 0.4012 (t80) cc_final: 0.2983 (t80) REVERT: R 588 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8389 (tp) REVERT: R 615 MET cc_start: 0.7601 (tmm) cc_final: 0.6586 (tmm) REVERT: R 764 LEU cc_start: 0.3499 (OUTLIER) cc_final: 0.2819 (tt) REVERT: R 801 HIS cc_start: 0.5537 (OUTLIER) cc_final: 0.5131 (m-70) REVERT: O 313 PRO cc_start: 0.7275 (Cg_endo) cc_final: 0.6960 (Cg_exo) REVERT: J 72 MET cc_start: 0.7539 (mmp) cc_final: 0.6206 (tmm) REVERT: J 73 SER cc_start: 0.7557 (t) cc_final: 0.6934 (p) REVERT: J 111 ARG cc_start: 0.8307 (mtm180) cc_final: 0.7993 (mtm180) REVERT: J 131 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.7449 (mtp85) REVERT: M 53 LYS cc_start: 0.8101 (pttt) cc_final: 0.7699 (tttt) REVERT: M 75 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8156 (mmmm) REVERT: M 79 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: M 81 MET cc_start: 0.6391 (mtt) cc_final: 0.5908 (tmm) REVERT: M 105 ASP cc_start: 0.6696 (t0) cc_final: 0.5954 (p0) REVERT: I 74 ASN cc_start: 0.8250 (t0) cc_final: 0.7931 (m-40) REVERT: I 92 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8624 (p) REVERT: I 149 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: I 172 TYR cc_start: 0.6661 (m-10) cc_final: 0.5985 (m-10) REVERT: L 58 LYS cc_start: 0.7831 (mptt) cc_final: 0.7353 (mttt) REVERT: L 63 LEU cc_start: 0.6201 (mp) cc_final: 0.5908 (tt) REVERT: L 75 LYS cc_start: 0.9114 (tptt) cc_final: 0.8661 (pttp) REVERT: L 85 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7481 (mp10) REVERT: L 112 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7753 (pp20) REVERT: H 117 ASP cc_start: 0.7736 (t0) cc_final: 0.7240 (m-30) REVERT: H 197 GLU cc_start: 0.7847 (mp0) cc_final: 0.7551 (mp0) REVERT: K 74 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7572 (tp30) REVERT: K 75 LYS cc_start: 0.7909 (pttp) cc_final: 0.7513 (pttm) REVERT: K 94 GLU cc_start: 0.8197 (pm20) cc_final: 0.7868 (pm20) REVERT: S 34 ARG cc_start: 0.3882 (tpt90) cc_final: 0.3394 (tpt90) REVERT: S 40 MET cc_start: 0.8181 (ptp) cc_final: 0.7483 (ppp) REVERT: T 67 MET cc_start: 0.7116 (mtt) cc_final: 0.6721 (tpt) REVERT: T 129 ASN cc_start: 0.4661 (p0) cc_final: 0.4142 (t0) REVERT: U 342 MET cc_start: 0.5768 (tmm) cc_final: 0.5114 (tmm) REVERT: U 396 MET cc_start: 0.4934 (ppp) cc_final: 0.4379 (ppp) REVERT: U 428 MET cc_start: 0.3046 (mtt) cc_final: 0.2605 (mtm) REVERT: U 453 MET cc_start: 0.2580 (mmm) cc_final: 0.2140 (mmt) REVERT: V 299 TYR cc_start: 0.0441 (OUTLIER) cc_final: -0.0569 (t80) REVERT: 0 51 ASN cc_start: 0.4444 (m-40) cc_final: 0.4001 (t0) REVERT: 0 71 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6517 (tt) REVERT: 1 44 MET cc_start: 0.6222 (tmm) cc_final: 0.5738 (tmm) REVERT: 1 47 MET cc_start: 0.6650 (ppp) cc_final: 0.5435 (mmt) REVERT: 2 61 MET cc_start: 0.5775 (mtp) cc_final: 0.5433 (mtp) REVERT: 2 137 PHE cc_start: 0.5993 (m-10) cc_final: 0.5790 (m-10) REVERT: 3 47 MET cc_start: 0.6253 (ppp) cc_final: 0.5077 (ttp) REVERT: 3 53 MET cc_start: 0.3312 (mmp) cc_final: 0.1776 (ptm) REVERT: 5 10 TYR cc_start: 0.5588 (p90) cc_final: 0.4206 (m-80) REVERT: 5 44 MET cc_start: 0.6147 (ppp) cc_final: 0.5839 (ttt) REVERT: 6 155 LYS cc_start: 0.5045 (OUTLIER) cc_final: 0.2978 (mmtm) REVERT: 7 10 TYR cc_start: 0.5149 (p90) cc_final: 0.4667 (p90) REVERT: 7 82 ASP cc_start: 0.6223 (OUTLIER) cc_final: 0.5911 (t0) REVERT: 8 23 MET cc_start: 0.6118 (tpt) cc_final: 0.5908 (tpt) REVERT: Q 176 MET cc_start: 0.5439 (ptp) cc_final: 0.5199 (ptp) REVERT: C 193 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6848 (mm-30) REVERT: C 432 PHE cc_start: 0.8266 (t80) cc_final: 0.7933 (t80) REVERT: C 451 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8768 (mt) REVERT: C 462 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7834 (t0) REVERT: C 586 PHE cc_start: 0.7476 (m-80) cc_final: 0.7238 (m-80) REVERT: A 81 ARG cc_start: 0.6419 (mtm-85) cc_final: 0.5140 (ptp-170) REVERT: A 314 ASN cc_start: 0.7984 (t0) cc_final: 0.7641 (t0) REVERT: A 349 ASP cc_start: 0.7964 (t70) cc_final: 0.7649 (t0) REVERT: A 353 ARG cc_start: 0.7213 (mmt-90) cc_final: 0.6991 (mmp80) REVERT: A 399 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 443 LYS cc_start: 0.8180 (tttm) cc_final: 0.7880 (mmtm) REVERT: A 463 GLU cc_start: 0.7927 (mp0) cc_final: 0.7649 (tp30) REVERT: B 136 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7479 (t) REVERT: B 142 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8086 (mtm110) REVERT: B 193 GLU cc_start: 0.7543 (tp30) cc_final: 0.7190 (tp30) REVERT: B 203 PHE cc_start: 0.6725 (t80) cc_final: 0.5938 (t80) REVERT: B 299 ASP cc_start: 0.6916 (p0) cc_final: 0.6609 (p0) REVERT: B 436 ASP cc_start: 0.8110 (t70) cc_final: 0.7872 (t0) REVERT: B 577 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7204 (tt) REVERT: B 588 ASP cc_start: 0.8196 (t0) cc_final: 0.7975 (t0) REVERT: B 594 GLU cc_start: 0.6617 (tm-30) cc_final: 0.6023 (tm-30) REVERT: D 141 ARG cc_start: 0.7540 (tpt170) cc_final: 0.7130 (mmm160) REVERT: D 214 LYS cc_start: 0.8137 (pptt) cc_final: 0.7107 (ptpp) REVERT: D 309 GLU cc_start: 0.7169 (tt0) cc_final: 0.6864 (mt-10) REVERT: D 358 ASN cc_start: 0.8365 (t0) cc_final: 0.8143 (t0) REVERT: D 435 MET cc_start: 0.7321 (tmm) cc_final: 0.6833 (tmm) REVERT: D 456 GLN cc_start: 0.7668 (tp40) cc_final: 0.7080 (tt0) REVERT: E 44 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7490 (mtt90) REVERT: E 80 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8376 (p) REVERT: E 154 MET cc_start: 0.8636 (mmm) cc_final: 0.8363 (mmt) REVERT: Z 59 ASN cc_start: 0.7107 (m-40) cc_final: 0.6363 (p0) REVERT: Z 74 CYS cc_start: 0.8004 (p) cc_final: 0.7686 (p) REVERT: Z 271 GLU cc_start: 0.3696 (OUTLIER) cc_final: 0.3167 (mm-30) REVERT: X 180 LYS cc_start: 0.7860 (ttpp) cc_final: 0.7327 (tppt) REVERT: X 243 GLN cc_start: 0.7517 (mt0) cc_final: 0.7057 (mm-40) REVERT: Y 137 THR cc_start: 0.6877 (t) cc_final: 0.6574 (p) REVERT: G 45 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7529 (mmm-85) REVERT: G 56 MET cc_start: 0.4934 (mmp) cc_final: 0.3173 (ptm) REVERT: G 58 MET cc_start: 0.4690 (tmm) cc_final: 0.4275 (ttp) REVERT: G 85 GLN cc_start: 0.8040 (pp30) cc_final: 0.7794 (pp30) REVERT: N 73 MET cc_start: 0.7145 (tmm) cc_final: 0.6859 (tmm) REVERT: W 333 MET cc_start: 0.6652 (mmt) cc_final: 0.5818 (mmt) REVERT: W 345 TYR cc_start: 0.7385 (m-80) cc_final: 0.6924 (m-10) REVERT: W 378 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8171 (mmtm) REVERT: F 239 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7342 (tm-30) REVERT: F 297 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8314 (mt) REVERT: F 299 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.7812 (t0) REVERT: F 321 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8143 (tpp80) REVERT: F 376 GLN cc_start: 0.7472 (mt0) cc_final: 0.7002 (pm20) REVERT: F 387 GLN cc_start: 0.7496 (mm110) cc_final: 0.7234 (mt0) REVERT: F 435 MET cc_start: 0.6512 (mmm) cc_final: 0.6185 (tpt) REVERT: F 456 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7046 (mp-120) REVERT: F 462 PHE cc_start: 0.8045 (t80) cc_final: 0.7566 (t80) outliers start: 239 outliers final: 158 residues processed: 1151 average time/residue: 0.6597 time to fit residues: 1304.7329 Evaluate side-chains 1115 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 935 time to evaluate : 6.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 367 THR Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 735 THR Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain R residue 764 LEU Chi-restraints excluded: chain R residue 784 THR Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 0 residue 71 ILE Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 81 ASN Chi-restraints excluded: chain 1 residue 102 SER Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 143 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 155 LYS Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 143 LEU Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 34 THR Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 112 LEU Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 225 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 887 optimal weight: 10.0000 chunk 103 optimal weight: 50.0000 chunk 524 optimal weight: 1.9990 chunk 671 optimal weight: 1.9990 chunk 520 optimal weight: 0.7980 chunk 774 optimal weight: 10.0000 chunk 513 optimal weight: 0.8980 chunk 916 optimal weight: 0.9980 chunk 573 optimal weight: 0.9980 chunk 558 optimal weight: 7.9990 chunk 423 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS U 403 GLN ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 51 GLN 2 78 ASN ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 123 GLN ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 449 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 270 ASN ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 72859 Z= 0.189 Angle : 0.582 13.997 98827 Z= 0.298 Chirality : 0.042 0.421 11476 Planarity : 0.004 0.055 12780 Dihedral : 4.952 143.671 10472 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.55 % Allowed : 18.27 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.39 (0.09), residues: 9526 helix: 1.60 (0.07), residues: 5441 sheet: -0.73 (0.19), residues: 798 loop : -1.85 (0.10), residues: 3287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 0 49 HIS 0.008 0.001 HIS R 801 PHE 0.036 0.001 PHE 1 137 TYR 0.034 0.001 TYR 0 70 ARG 0.007 0.000 ARG 8 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1002 time to evaluate : 6.124 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: R 80 MET cc_start: 0.5700 (mpp) cc_final: 0.5177 (mmt) REVERT: R 94 MET cc_start: 0.6778 (ppp) cc_final: 0.6059 (mmm) REVERT: R 355 MET cc_start: 0.5997 (tpt) cc_final: 0.4551 (ttt) REVERT: R 358 ASN cc_start: 0.5377 (p0) cc_final: 0.4663 (m-40) REVERT: R 439 MET cc_start: 0.4254 (ppp) cc_final: 0.3454 (tmm) REVERT: R 479 TRP cc_start: 0.5066 (m100) cc_final: 0.4606 (m100) REVERT: R 484 MET cc_start: 0.4800 (mmm) cc_final: 0.4398 (tpt) REVERT: R 492 GLU cc_start: 0.7209 (tp30) cc_final: 0.6805 (tm-30) REVERT: R 539 MET cc_start: 0.8310 (tmm) cc_final: 0.7632 (ttt) REVERT: R 615 MET cc_start: 0.7616 (tmm) cc_final: 0.6602 (tmm) REVERT: R 756 TRP cc_start: 0.3551 (t60) cc_final: 0.3327 (t60) REVERT: R 764 LEU cc_start: 0.3498 (OUTLIER) cc_final: 0.2826 (tt) REVERT: O 313 PRO cc_start: 0.7284 (Cg_endo) cc_final: 0.6959 (Cg_exo) REVERT: J 72 MET cc_start: 0.7416 (mmp) cc_final: 0.6118 (tmm) REVERT: J 73 SER cc_start: 0.7506 (t) cc_final: 0.6855 (p) REVERT: J 111 ARG cc_start: 0.8301 (mtm180) cc_final: 0.8002 (mtm180) REVERT: J 131 ARG cc_start: 0.7634 (mtp-110) cc_final: 0.7423 (mtp85) REVERT: J 177 ILE cc_start: 0.7463 (tp) cc_final: 0.7224 (mm) REVERT: J 208 MET cc_start: 0.8712 (mmt) cc_final: 0.8436 (mmt) REVERT: M 53 LYS cc_start: 0.8101 (pttt) cc_final: 0.7730 (tttt) REVERT: M 81 MET cc_start: 0.6327 (mtt) cc_final: 0.5914 (tmm) REVERT: M 105 ASP cc_start: 0.6652 (t0) cc_final: 0.5951 (p0) REVERT: I 52 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7171 (pttm) REVERT: I 74 ASN cc_start: 0.8035 (t0) cc_final: 0.7697 (m-40) REVERT: I 149 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: L 58 LYS cc_start: 0.7811 (mptt) cc_final: 0.7344 (mttt) REVERT: L 63 LEU cc_start: 0.6079 (mp) cc_final: 0.5811 (tt) REVERT: L 85 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7506 (mp10) REVERT: L 92 ARG cc_start: 0.7265 (ttm170) cc_final: 0.7056 (ttm170) REVERT: L 112 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: H 117 ASP cc_start: 0.7712 (t0) cc_final: 0.7231 (m-30) REVERT: H 197 GLU cc_start: 0.7824 (mp0) cc_final: 0.7561 (mp0) REVERT: K 74 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7474 (tp30) REVERT: K 83 ILE cc_start: 0.8433 (tt) cc_final: 0.8097 (mt) REVERT: K 94 GLU cc_start: 0.8183 (pm20) cc_final: 0.7800 (pm20) REVERT: S 34 ARG cc_start: 0.3889 (tpt90) cc_final: 0.3365 (tpt90) REVERT: S 40 MET cc_start: 0.8139 (ptp) cc_final: 0.7535 (ppp) REVERT: T 67 MET cc_start: 0.7114 (mtt) cc_final: 0.6601 (tpt) REVERT: U 342 MET cc_start: 0.5726 (tmm) cc_final: 0.5141 (tmm) REVERT: U 428 MET cc_start: 0.3227 (mtt) cc_final: 0.2809 (mtm) REVERT: U 453 MET cc_start: 0.2595 (mmm) cc_final: 0.2210 (mmt) REVERT: V 299 TYR cc_start: 0.0486 (OUTLIER) cc_final: -0.0520 (t80) REVERT: 0 51 ASN cc_start: 0.4363 (m-40) cc_final: 0.4109 (t0) REVERT: 0 86 ILE cc_start: 0.3486 (OUTLIER) cc_final: 0.3270 (mm) REVERT: 1 47 MET cc_start: 0.6810 (ppp) cc_final: 0.5356 (mmt) REVERT: 2 137 PHE cc_start: 0.6151 (m-10) cc_final: 0.5949 (m-10) REVERT: 3 47 MET cc_start: 0.6241 (ppp) cc_final: 0.4876 (ttp) REVERT: 3 53 MET cc_start: 0.3423 (mmp) cc_final: 0.1801 (ptm) REVERT: 3 81 ASN cc_start: 0.4521 (OUTLIER) cc_final: 0.4145 (m110) REVERT: 5 10 TYR cc_start: 0.5478 (p90) cc_final: 0.4044 (m-80) REVERT: 6 155 LYS cc_start: 0.4928 (OUTLIER) cc_final: 0.3062 (mmtm) REVERT: 7 82 ASP cc_start: 0.6484 (OUTLIER) cc_final: 0.6142 (t0) REVERT: 8 53 MET cc_start: 0.6980 (mpp) cc_final: 0.4737 (mmm) REVERT: 8 119 ARG cc_start: 0.6509 (mtt90) cc_final: 0.6264 (mmt-90) REVERT: Q 176 MET cc_start: 0.5383 (ptp) cc_final: 0.5154 (ptp) REVERT: C 193 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6835 (mm-30) REVERT: C 432 PHE cc_start: 0.8208 (t80) cc_final: 0.7849 (t80) REVERT: C 462 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7783 (t0) REVERT: C 586 PHE cc_start: 0.7500 (m-80) cc_final: 0.7249 (m-80) REVERT: C 608 MET cc_start: 0.3756 (ptt) cc_final: 0.3384 (ptt) REVERT: A 317 ASN cc_start: 0.8457 (t0) cc_final: 0.8235 (t0) REVERT: A 349 ASP cc_start: 0.7986 (t70) cc_final: 0.7675 (t0) REVERT: A 353 ARG cc_start: 0.7140 (mmt-90) cc_final: 0.6898 (mmp80) REVERT: A 367 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7581 (mt-10) REVERT: A 399 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: A 443 LYS cc_start: 0.8188 (tttm) cc_final: 0.7883 (mmtm) REVERT: A 463 GLU cc_start: 0.7868 (mp0) cc_final: 0.7590 (tp30) REVERT: A 574 MET cc_start: 0.4442 (pmm) cc_final: 0.3909 (ptt) REVERT: A 600 ASP cc_start: 0.6715 (m-30) cc_final: 0.6456 (m-30) REVERT: B 136 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7457 (t) REVERT: B 142 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8088 (mtm110) REVERT: B 193 GLU cc_start: 0.7622 (tp30) cc_final: 0.7381 (tt0) REVERT: B 203 PHE cc_start: 0.6653 (t80) cc_final: 0.5933 (t80) REVERT: B 299 ASP cc_start: 0.6817 (p0) cc_final: 0.6602 (p0) REVERT: B 347 MET cc_start: 0.8284 (mmm) cc_final: 0.7299 (mmm) REVERT: B 436 ASP cc_start: 0.8031 (t70) cc_final: 0.7765 (t0) REVERT: B 459 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8002 (mmm-85) REVERT: B 577 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7136 (tt) REVERT: B 588 ASP cc_start: 0.8190 (t0) cc_final: 0.7959 (t0) REVERT: B 608 MET cc_start: 0.7135 (mtp) cc_final: 0.6849 (mtm) REVERT: D 141 ARG cc_start: 0.7590 (tpt170) cc_final: 0.7153 (mmm160) REVERT: D 214 LYS cc_start: 0.8066 (pptt) cc_final: 0.7074 (ptpp) REVERT: D 309 GLU cc_start: 0.7131 (tt0) cc_final: 0.6869 (mt-10) REVERT: D 435 MET cc_start: 0.7382 (tmm) cc_final: 0.6845 (tmm) REVERT: D 456 GLN cc_start: 0.7574 (tp40) cc_final: 0.6990 (tt0) REVERT: E 44 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7556 (mtt90) REVERT: E 80 THR cc_start: 0.8834 (m) cc_final: 0.8362 (p) REVERT: E 154 MET cc_start: 0.8648 (mmm) cc_final: 0.8398 (mmt) REVERT: Z 59 ASN cc_start: 0.7129 (m-40) cc_final: 0.6425 (p0) REVERT: Z 74 CYS cc_start: 0.7967 (p) cc_final: 0.7622 (p) REVERT: Z 188 MET cc_start: 0.6894 (tpp) cc_final: 0.6687 (mmp) REVERT: Z 271 GLU cc_start: 0.3579 (OUTLIER) cc_final: 0.3208 (mm-30) REVERT: X 115 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7574 (ttp) REVERT: X 139 TYR cc_start: 0.8252 (t80) cc_final: 0.8017 (t80) REVERT: X 161 MET cc_start: 0.7432 (mmm) cc_final: 0.7228 (mmm) REVERT: X 180 LYS cc_start: 0.7812 (ttpp) cc_final: 0.7199 (tppt) REVERT: X 243 GLN cc_start: 0.7524 (mt0) cc_final: 0.7080 (mm-40) REVERT: Y 137 THR cc_start: 0.6908 (t) cc_final: 0.6585 (p) REVERT: G 45 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7511 (mmm-85) REVERT: G 56 MET cc_start: 0.4902 (mmp) cc_final: 0.3294 (ptm) REVERT: G 58 MET cc_start: 0.4645 (tmm) cc_final: 0.4251 (ttp) REVERT: G 85 GLN cc_start: 0.7841 (pp30) cc_final: 0.7356 (pp30) REVERT: N 73 MET cc_start: 0.6946 (tmm) cc_final: 0.6707 (tmm) REVERT: W 333 MET cc_start: 0.6642 (mmt) cc_final: 0.5802 (mmt) REVERT: W 345 TYR cc_start: 0.7278 (m-80) cc_final: 0.6887 (m-10) REVERT: W 378 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8128 (mmtm) REVERT: F 299 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7796 (t0) REVERT: F 321 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8104 (tpp80) REVERT: F 376 GLN cc_start: 0.7353 (mt0) cc_final: 0.6969 (pm20) REVERT: F 378 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6932 (t80) REVERT: F 387 GLN cc_start: 0.7444 (mm110) cc_final: 0.7163 (mt0) REVERT: F 456 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7004 (mp-120) outliers start: 180 outliers final: 132 residues processed: 1129 average time/residue: 0.6563 time to fit residues: 1271.8140 Evaluate side-chains 1092 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 942 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain R residue 764 LEU Chi-restraints excluded: chain R residue 784 THR Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 27 THR Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 0 residue 86 ILE Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 1 residue 146 LEU Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 143 LEU Chi-restraints excluded: chain 3 residue 24 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 155 LYS Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 150 LEU Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain Q residue 278 PHE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 378 TYR Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 567 optimal weight: 3.9990 chunk 366 optimal weight: 30.0000 chunk 547 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 180 optimal weight: 40.0000 chunk 177 optimal weight: 6.9990 chunk 582 optimal weight: 4.9990 chunk 624 optimal weight: 2.9990 chunk 453 optimal weight: 4.9990 chunk 85 optimal weight: 50.0000 chunk 720 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 GLN M 90 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 128 HIS 2 78 ASN ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN ** B 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 ASN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 72859 Z= 0.456 Angle : 0.723 11.302 98827 Z= 0.374 Chirality : 0.047 0.388 11476 Planarity : 0.005 0.080 12780 Dihedral : 5.424 146.162 10472 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.21 % Favored : 93.77 % Rotamer: Outliers : 3.45 % Allowed : 18.75 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.08 (0.09), residues: 9526 helix: 1.26 (0.07), residues: 5448 sheet: -1.09 (0.18), residues: 833 loop : -2.08 (0.10), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP 0 49 HIS 0.014 0.002 HIS R 801 PHE 0.036 0.002 PHE I 224 TYR 0.038 0.002 TYR 9 144 ARG 0.008 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 950 time to evaluate : 6.107 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: R 80 MET cc_start: 0.6223 (mpp) cc_final: 0.5407 (mmt) REVERT: R 94 MET cc_start: 0.6848 (ppp) cc_final: 0.6121 (mmm) REVERT: R 355 MET cc_start: 0.5725 (tpt) cc_final: 0.4075 (ttt) REVERT: R 358 ASN cc_start: 0.5357 (p0) cc_final: 0.4604 (m-40) REVERT: R 439 MET cc_start: 0.4227 (ppp) cc_final: 0.3413 (tmm) REVERT: R 479 TRP cc_start: 0.5094 (m100) cc_final: 0.4686 (m100) REVERT: R 484 MET cc_start: 0.4819 (mmm) cc_final: 0.4505 (mmt) REVERT: R 492 GLU cc_start: 0.7279 (tp30) cc_final: 0.6849 (tm-30) REVERT: R 539 MET cc_start: 0.8363 (tmm) cc_final: 0.7849 (ttt) REVERT: R 588 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8337 (tp) REVERT: R 756 TRP cc_start: 0.3790 (t60) cc_final: 0.3533 (t60) REVERT: R 764 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2681 (tt) REVERT: O 313 PRO cc_start: 0.7327 (Cg_endo) cc_final: 0.6971 (Cg_exo) REVERT: J 65 GLU cc_start: 0.8001 (tt0) cc_final: 0.7335 (tp30) REVERT: M 53 LYS cc_start: 0.8056 (pttt) cc_final: 0.7567 (tttt) REVERT: M 79 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: M 105 ASP cc_start: 0.6729 (t0) cc_final: 0.5953 (p0) REVERT: I 74 ASN cc_start: 0.8344 (t0) cc_final: 0.7974 (m-40) REVERT: I 149 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: L 58 LYS cc_start: 0.7828 (mptt) cc_final: 0.7347 (mttt) REVERT: L 63 LEU cc_start: 0.6007 (mp) cc_final: 0.5728 (tt) REVERT: L 75 LYS cc_start: 0.9113 (tptt) cc_final: 0.8593 (pttp) REVERT: L 81 MET cc_start: 0.7183 (mtp) cc_final: 0.6855 (mtt) REVERT: L 85 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7549 (mp10) REVERT: L 112 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7812 (pp20) REVERT: H 117 ASP cc_start: 0.7792 (t0) cc_final: 0.7211 (m-30) REVERT: H 187 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8266 (p0) REVERT: K 74 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7465 (tp30) REVERT: K 94 GLU cc_start: 0.8144 (pm20) cc_final: 0.7858 (pm20) REVERT: S 34 ARG cc_start: 0.3807 (tpt90) cc_final: 0.3561 (tpt90) REVERT: S 40 MET cc_start: 0.8297 (ptp) cc_final: 0.7662 (ppp) REVERT: T 67 MET cc_start: 0.6961 (mtt) cc_final: 0.6467 (tpt) REVERT: U 342 MET cc_start: 0.5614 (tmm) cc_final: 0.4910 (tmm) REVERT: U 396 MET cc_start: 0.5009 (ppp) cc_final: 0.4744 (ppp) REVERT: U 428 MET cc_start: 0.3750 (mtt) cc_final: 0.3333 (mtm) REVERT: U 453 MET cc_start: 0.2841 (mmm) cc_final: 0.2569 (mmt) REVERT: V 299 TYR cc_start: 0.0322 (OUTLIER) cc_final: -0.0668 (t80) REVERT: 0 51 ASN cc_start: 0.4468 (m-40) cc_final: 0.4170 (t0) REVERT: 0 86 ILE cc_start: 0.3576 (OUTLIER) cc_final: 0.3366 (mm) REVERT: 1 47 MET cc_start: 0.6827 (ppp) cc_final: 0.5369 (mmp) REVERT: 1 113 VAL cc_start: 0.7173 (p) cc_final: 0.6972 (p) REVERT: 2 137 PHE cc_start: 0.6337 (m-10) cc_final: 0.6116 (m-10) REVERT: 3 47 MET cc_start: 0.6042 (ppp) cc_final: 0.4728 (ttp) REVERT: 3 53 MET cc_start: 0.3731 (mmp) cc_final: 0.2101 (ptm) REVERT: 3 81 ASN cc_start: 0.4620 (OUTLIER) cc_final: 0.4249 (m110) REVERT: 6 136 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7300 (tp) REVERT: 7 82 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.6005 (t0) REVERT: 8 23 MET cc_start: 0.5912 (tpt) cc_final: 0.5667 (tpt) REVERT: 8 53 MET cc_start: 0.6747 (mpp) cc_final: 0.4640 (mmm) REVERT: 8 119 ARG cc_start: 0.6850 (mtt90) cc_final: 0.6476 (mpt180) REVERT: Q 85 MET cc_start: 0.6071 (tpp) cc_final: 0.5652 (mmm) REVERT: C 193 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6914 (mm-30) REVERT: C 203 PHE cc_start: 0.6264 (t80) cc_final: 0.5879 (t80) REVERT: C 266 TYR cc_start: 0.7176 (m-10) cc_final: 0.6816 (m-10) REVERT: C 432 PHE cc_start: 0.8246 (t80) cc_final: 0.7953 (t80) REVERT: C 462 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7976 (t0) REVERT: C 481 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 586 PHE cc_start: 0.7531 (m-80) cc_final: 0.7264 (m-80) REVERT: A 349 ASP cc_start: 0.7934 (t70) cc_final: 0.7670 (t0) REVERT: A 353 ARG cc_start: 0.7346 (mmt-90) cc_final: 0.7024 (mmp80) REVERT: A 367 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7756 (mt-10) REVERT: A 443 LYS cc_start: 0.8227 (tttm) cc_final: 0.7924 (tptp) REVERT: A 463 GLU cc_start: 0.7951 (mp0) cc_final: 0.7724 (tp30) REVERT: A 510 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7378 (tp30) REVERT: A 569 ILE cc_start: 0.8128 (tt) cc_final: 0.7918 (tp) REVERT: B 142 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8109 (mtm110) REVERT: B 203 PHE cc_start: 0.6934 (t80) cc_final: 0.6084 (t80) REVERT: B 213 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: B 459 ARG cc_start: 0.8501 (tpp-160) cc_final: 0.7979 (mmm-85) REVERT: B 588 ASP cc_start: 0.8303 (t0) cc_final: 0.8068 (t0) REVERT: B 594 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6120 (tm-30) REVERT: B 608 MET cc_start: 0.7262 (mtp) cc_final: 0.7057 (mtm) REVERT: D 54 ASN cc_start: 0.8299 (t0) cc_final: 0.8003 (t0) REVERT: D 141 ARG cc_start: 0.7612 (tpt170) cc_final: 0.7213 (mmm160) REVERT: D 214 LYS cc_start: 0.8167 (pptt) cc_final: 0.7140 (ptpp) REVERT: D 309 GLU cc_start: 0.7189 (tt0) cc_final: 0.6906 (mt-10) REVERT: D 362 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8631 (p) REVERT: D 435 MET cc_start: 0.7221 (tmm) cc_final: 0.6849 (tmm) REVERT: D 456 GLN cc_start: 0.7859 (tp40) cc_final: 0.7218 (tt0) REVERT: E 44 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7503 (mtt90) REVERT: E 80 THR cc_start: 0.8905 (m) cc_final: 0.8409 (p) REVERT: E 154 MET cc_start: 0.8658 (mmm) cc_final: 0.8400 (mmt) REVERT: Z 74 CYS cc_start: 0.7956 (p) cc_final: 0.7524 (p) REVERT: Z 188 MET cc_start: 0.6958 (tpp) cc_final: 0.6628 (ttm) REVERT: Z 271 GLU cc_start: 0.3544 (OUTLIER) cc_final: 0.3059 (mm-30) REVERT: X 161 MET cc_start: 0.7524 (mmm) cc_final: 0.7290 (mmm) REVERT: X 180 LYS cc_start: 0.7898 (ttpp) cc_final: 0.7353 (tppt) REVERT: X 243 GLN cc_start: 0.7473 (mt0) cc_final: 0.7060 (mm-40) REVERT: Y 137 THR cc_start: 0.6858 (t) cc_final: 0.6546 (p) REVERT: G 45 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7512 (mmm-85) REVERT: G 58 MET cc_start: 0.4802 (tmm) cc_final: 0.4503 (ttp) REVERT: G 85 GLN cc_start: 0.8004 (pp30) cc_final: 0.7497 (pp30) REVERT: G 215 LYS cc_start: 0.7003 (ttpt) cc_final: 0.6801 (ttpp) REVERT: N 67 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.7979 (t0) REVERT: N 103 ASP cc_start: 0.5148 (t70) cc_final: 0.4788 (m-30) REVERT: W 289 ARG cc_start: 0.6390 (mmt180) cc_final: 0.5552 (mpt180) REVERT: W 333 MET cc_start: 0.6398 (mmt) cc_final: 0.5703 (mmt) REVERT: W 345 TYR cc_start: 0.7036 (m-80) cc_final: 0.6747 (m-10) REVERT: W 378 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8057 (mttp) REVERT: F 54 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7455 (p0) REVERT: F 239 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7389 (tm-30) REVERT: F 297 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8408 (mt) REVERT: F 299 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8159 (t0) REVERT: F 321 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8069 (tpp80) REVERT: F 376 GLN cc_start: 0.7788 (mt0) cc_final: 0.7261 (pm20) REVERT: F 435 MET cc_start: 0.6226 (mmm) cc_final: 0.5642 (tpt) outliers start: 244 outliers final: 177 residues processed: 1120 average time/residue: 0.6633 time to fit residues: 1273.4097 Evaluate side-chains 1103 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 905 time to evaluate : 6.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 257 MET Chi-restraints excluded: chain R residue 367 THR Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 713 PHE Chi-restraints excluded: chain R residue 735 THR Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain R residue 764 LEU Chi-restraints excluded: chain R residue 784 THR Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 79 GLU Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 102 PHE Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain V residue 335 TYR Chi-restraints excluded: chain 0 residue 49 TRP Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 0 residue 72 THR Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 0 residue 86 ILE Chi-restraints excluded: chain 1 residue 61 MET Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 143 LEU Chi-restraints excluded: chain 3 residue 147 ILE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 65 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 147 ILE Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 6 residue 59 VAL Chi-restraints excluded: chain 6 residue 136 ILE Chi-restraints excluded: chain 7 residue 20 SER Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 60 VAL Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain Q residue 278 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain Z residue 54 ILE Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 221 ASP Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 168 ILE Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain Y residue 207 GLN Chi-restraints excluded: chain Y residue 256 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 833 optimal weight: 50.0000 chunk 878 optimal weight: 10.0000 chunk 801 optimal weight: 7.9990 chunk 854 optimal weight: 50.0000 chunk 877 optimal weight: 0.4980 chunk 514 optimal weight: 0.8980 chunk 372 optimal weight: 7.9990 chunk 670 optimal weight: 1.9990 chunk 262 optimal weight: 40.0000 chunk 771 optimal weight: 9.9990 chunk 807 optimal weight: 0.8980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 78 ASN ** 5 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 123 GLN ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 449 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 209 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 72859 Z= 0.275 Angle : 0.638 12.539 98827 Z= 0.327 Chirality : 0.043 0.391 11476 Planarity : 0.005 0.075 12780 Dihedral : 5.145 145.991 10472 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.90 % Allowed : 19.50 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.09), residues: 9526 helix: 1.40 (0.07), residues: 5435 sheet: -1.04 (0.18), residues: 806 loop : -2.00 (0.10), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP W 199 HIS 0.005 0.001 HIS D 199 PHE 0.039 0.002 PHE 1 137 TYR 0.047 0.002 TYR 9 144 ARG 0.007 0.000 ARG K 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 951 time to evaluate : 6.243 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: R 80 MET cc_start: 0.5896 (mpp) cc_final: 0.5221 (mmt) REVERT: R 94 MET cc_start: 0.6544 (ppp) cc_final: 0.5971 (mmm) REVERT: R 355 MET cc_start: 0.5637 (tpt) cc_final: 0.3937 (ttt) REVERT: R 358 ASN cc_start: 0.4755 (p0) cc_final: 0.4234 (m-40) REVERT: R 439 MET cc_start: 0.4192 (ppp) cc_final: 0.3371 (tmm) REVERT: R 479 TRP cc_start: 0.4966 (m100) cc_final: 0.4436 (m100) REVERT: R 484 MET cc_start: 0.4859 (mmm) cc_final: 0.4639 (mmt) REVERT: R 492 GLU cc_start: 0.7284 (tp30) cc_final: 0.6869 (tm-30) REVERT: R 539 MET cc_start: 0.8312 (tmm) cc_final: 0.7809 (ttt) REVERT: R 588 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8359 (tp) REVERT: R 756 TRP cc_start: 0.3786 (t60) cc_final: 0.3493 (t60) REVERT: R 764 LEU cc_start: 0.3335 (OUTLIER) cc_final: 0.2670 (tt) REVERT: O 313 PRO cc_start: 0.7235 (Cg_endo) cc_final: 0.6877 (Cg_exo) REVERT: J 65 GLU cc_start: 0.8024 (tt0) cc_final: 0.7328 (tp30) REVERT: J 111 ARG cc_start: 0.8296 (mtm180) cc_final: 0.8020 (mtm180) REVERT: J 207 MET cc_start: 0.8784 (mtp) cc_final: 0.8579 (mtp) REVERT: M 53 LYS cc_start: 0.8029 (pttt) cc_final: 0.7578 (tttt) REVERT: M 105 ASP cc_start: 0.6649 (t0) cc_final: 0.6009 (p0) REVERT: I 52 LYS cc_start: 0.7862 (tmtt) cc_final: 0.7282 (ttpt) REVERT: I 74 ASN cc_start: 0.8283 (t0) cc_final: 0.7923 (m-40) REVERT: I 132 MET cc_start: 0.8523 (mmt) cc_final: 0.7918 (mmt) REVERT: I 149 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7456 (mp10) REVERT: L 75 LYS cc_start: 0.9092 (tptt) cc_final: 0.8588 (pttp) REVERT: L 85 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7561 (mp10) REVERT: L 112 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: H 117 ASP cc_start: 0.7718 (t0) cc_final: 0.7158 (m-30) REVERT: H 187 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7939 (p0) REVERT: K 74 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7289 (tp30) REVERT: K 94 GLU cc_start: 0.8080 (pm20) cc_final: 0.7790 (pm20) REVERT: S 34 ARG cc_start: 0.3799 (tpt90) cc_final: 0.3563 (tpt90) REVERT: S 40 MET cc_start: 0.8237 (ptp) cc_final: 0.7725 (ppp) REVERT: T 67 MET cc_start: 0.6967 (mtt) cc_final: 0.6510 (tpt) REVERT: U 428 MET cc_start: 0.3508 (mtt) cc_final: 0.3184 (mtm) REVERT: U 453 MET cc_start: 0.3139 (mmm) cc_final: 0.2857 (mmt) REVERT: V 299 TYR cc_start: 0.0357 (OUTLIER) cc_final: -0.0527 (t80) REVERT: 0 51 ASN cc_start: 0.4407 (m-40) cc_final: 0.4170 (t0) REVERT: 1 23 MET cc_start: 0.7481 (tpp) cc_final: 0.7196 (tpt) REVERT: 1 47 MET cc_start: 0.6909 (ppp) cc_final: 0.5421 (mmt) REVERT: 3 47 MET cc_start: 0.5798 (ppp) cc_final: 0.4716 (ttp) REVERT: 3 53 MET cc_start: 0.3923 (mmp) cc_final: 0.2204 (ptm) REVERT: 3 81 ASN cc_start: 0.4497 (OUTLIER) cc_final: 0.4124 (m110) REVERT: 6 136 ILE cc_start: 0.7611 (mm) cc_final: 0.7320 (tp) REVERT: 7 10 TYR cc_start: 0.5052 (p90) cc_final: 0.4643 (p90) REVERT: 7 82 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.6126 (t0) REVERT: 8 53 MET cc_start: 0.6534 (mpp) cc_final: 0.4507 (mmm) REVERT: 8 119 ARG cc_start: 0.6938 (mtt90) cc_final: 0.6654 (mmt-90) REVERT: Q 85 MET cc_start: 0.6123 (tpp) cc_final: 0.5757 (mmm) REVERT: Q 176 MET cc_start: 0.5498 (ptp) cc_final: 0.5235 (ptp) REVERT: C 193 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6928 (mm-30) REVERT: C 432 PHE cc_start: 0.8238 (t80) cc_final: 0.7897 (t80) REVERT: C 451 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8739 (mt) REVERT: C 462 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7842 (t0) REVERT: C 481 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 586 PHE cc_start: 0.7526 (m-80) cc_final: 0.7216 (m-80) REVERT: A 34 MET cc_start: 0.1730 (ttp) cc_final: 0.1462 (ttp) REVERT: A 81 ARG cc_start: 0.5701 (mtt180) cc_final: 0.5320 (ttp-110) REVERT: A 317 ASN cc_start: 0.8446 (t0) cc_final: 0.8194 (t0) REVERT: A 349 ASP cc_start: 0.7958 (t70) cc_final: 0.7719 (t0) REVERT: A 353 ARG cc_start: 0.7247 (mmt-90) cc_final: 0.7005 (mmp80) REVERT: A 367 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7689 (mt-10) REVERT: A 443 LYS cc_start: 0.8127 (tttm) cc_final: 0.7874 (mmtm) REVERT: A 574 MET cc_start: 0.4532 (pmm) cc_final: 0.4002 (ptt) REVERT: B 136 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7478 (t) REVERT: B 142 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8087 (mtm110) REVERT: B 203 PHE cc_start: 0.6869 (t80) cc_final: 0.6089 (t80) REVERT: B 213 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7964 (mt0) REVERT: B 299 ASP cc_start: 0.6496 (p0) cc_final: 0.6210 (p0) REVERT: B 459 ARG cc_start: 0.8470 (tpp-160) cc_final: 0.7974 (mmm-85) REVERT: B 588 ASP cc_start: 0.8288 (t0) cc_final: 0.8062 (t0) REVERT: B 594 GLU cc_start: 0.6667 (tm-30) cc_final: 0.6072 (tm-30) REVERT: D 141 ARG cc_start: 0.7530 (tpt170) cc_final: 0.7129 (mmm160) REVERT: D 214 LYS cc_start: 0.8093 (pptt) cc_final: 0.7091 (ptpp) REVERT: D 309 GLU cc_start: 0.7154 (tt0) cc_final: 0.6848 (mt-10) REVERT: D 435 MET cc_start: 0.7458 (tmm) cc_final: 0.6921 (tmm) REVERT: D 456 GLN cc_start: 0.7778 (tp40) cc_final: 0.7116 (tt0) REVERT: E 44 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7568 (mtt90) REVERT: E 80 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8342 (p) REVERT: E 154 MET cc_start: 0.8631 (mmm) cc_final: 0.8383 (mmt) REVERT: Z 59 ASN cc_start: 0.7106 (m-40) cc_final: 0.6470 (p0) REVERT: Z 74 CYS cc_start: 0.7931 (p) cc_final: 0.7491 (p) REVERT: Z 188 MET cc_start: 0.7019 (tpp) cc_final: 0.6650 (mmp) REVERT: Z 271 GLU cc_start: 0.3477 (OUTLIER) cc_final: 0.3034 (mp0) REVERT: X 115 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7723 (ttp) REVERT: X 161 MET cc_start: 0.7513 (mmm) cc_final: 0.7067 (mmm) REVERT: X 180 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7355 (tppt) REVERT: X 243 GLN cc_start: 0.7421 (mt0) cc_final: 0.7026 (mm-40) REVERT: Y 137 THR cc_start: 0.6854 (t) cc_final: 0.6513 (p) REVERT: G 45 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7512 (mmm-85) REVERT: G 56 MET cc_start: 0.4954 (mmp) cc_final: 0.3189 (ptm) REVERT: G 58 MET cc_start: 0.4711 (tmm) cc_final: 0.4399 (ttp) REVERT: G 85 GLN cc_start: 0.8007 (pp30) cc_final: 0.7519 (pp30) REVERT: N 73 MET cc_start: 0.7038 (tmm) cc_final: 0.6751 (tmm) REVERT: N 103 ASP cc_start: 0.4831 (t70) cc_final: 0.4585 (m-30) REVERT: W 289 ARG cc_start: 0.6322 (mmt180) cc_final: 0.5309 (mpt180) REVERT: W 333 MET cc_start: 0.6393 (mmt) cc_final: 0.5755 (mmt) REVERT: W 345 TYR cc_start: 0.6884 (m-80) cc_final: 0.6682 (m-10) REVERT: W 378 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8066 (mttp) REVERT: F 299 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7809 (t0) REVERT: F 321 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8091 (tpp80) REVERT: F 376 GLN cc_start: 0.7570 (mt0) cc_final: 0.7123 (pm20) REVERT: F 410 MET cc_start: 0.4364 (ptp) cc_final: 0.3786 (ptp) REVERT: F 435 MET cc_start: 0.6283 (mmm) cc_final: 0.5642 (tpt) REVERT: F 456 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6967 (mp10) outliers start: 205 outliers final: 155 residues processed: 1099 average time/residue: 0.6730 time to fit residues: 1268.5613 Evaluate side-chains 1089 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 916 time to evaluate : 6.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 713 PHE Chi-restraints excluded: chain R residue 735 THR Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain R residue 764 LEU Chi-restraints excluded: chain R residue 784 THR Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 426 ILE Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 143 LEU Chi-restraints excluded: chain 3 residue 147 ILE Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 147 ILE Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 23 MET Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain Q residue 278 PHE Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 449 ASN Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 126 TYR Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 280 SER Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 378 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 851 optimal weight: 20.0000 chunk 560 optimal weight: 0.2980 chunk 903 optimal weight: 9.9990 chunk 551 optimal weight: 3.9990 chunk 428 optimal weight: 7.9990 chunk 627 optimal weight: 2.9990 chunk 947 optimal weight: 5.9990 chunk 872 optimal weight: 9.9990 chunk 754 optimal weight: 5.9990 chunk 78 optimal weight: 50.0000 chunk 582 optimal weight: 2.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 78 ASN ** 5 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 261 GLN B 449 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 72859 Z= 0.341 Angle : 0.670 11.184 98827 Z= 0.345 Chirality : 0.045 0.379 11476 Planarity : 0.005 0.083 12780 Dihedral : 5.210 144.668 10472 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.85 % Allowed : 19.55 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 9526 helix: 1.32 (0.07), residues: 5440 sheet: -1.05 (0.18), residues: 807 loop : -2.05 (0.10), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP W 199 HIS 0.007 0.001 HIS D 199 PHE 0.037 0.002 PHE 1 137 TYR 0.050 0.002 TYR 9 144 ARG 0.007 0.001 ARG 6 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19052 Ramachandran restraints generated. 9526 Oldfield, 0 Emsley, 9526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 925 time to evaluate : 6.158 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: R 80 MET cc_start: 0.6129 (mpp) cc_final: 0.5272 (mmt) REVERT: R 94 MET cc_start: 0.6348 (ppp) cc_final: 0.5802 (mmt) REVERT: R 355 MET cc_start: 0.5507 (tpt) cc_final: 0.3836 (ttt) REVERT: R 439 MET cc_start: 0.4337 (ppp) cc_final: 0.3507 (tmm) REVERT: R 453 MET cc_start: 0.6824 (mmp) cc_final: 0.6363 (mmp) REVERT: R 479 TRP cc_start: 0.4991 (m100) cc_final: 0.4453 (m100) REVERT: R 484 MET cc_start: 0.4907 (mmm) cc_final: 0.4670 (mmt) REVERT: R 492 GLU cc_start: 0.7321 (tp30) cc_final: 0.6861 (tm-30) REVERT: R 539 MET cc_start: 0.8313 (tmm) cc_final: 0.7816 (ttt) REVERT: R 588 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8363 (tp) REVERT: R 756 TRP cc_start: 0.3816 (t60) cc_final: 0.3501 (t60) REVERT: R 764 LEU cc_start: 0.3349 (OUTLIER) cc_final: 0.2678 (tt) REVERT: O 313 PRO cc_start: 0.7157 (Cg_endo) cc_final: 0.6810 (Cg_exo) REVERT: J 65 GLU cc_start: 0.8082 (tt0) cc_final: 0.7422 (tp30) REVERT: J 111 ARG cc_start: 0.8325 (mtm180) cc_final: 0.8057 (mtm180) REVERT: J 207 MET cc_start: 0.8762 (mtp) cc_final: 0.8553 (mtp) REVERT: M 53 LYS cc_start: 0.8050 (pttt) cc_final: 0.7627 (tttt) REVERT: M 105 ASP cc_start: 0.6667 (t0) cc_final: 0.6052 (p0) REVERT: I 52 LYS cc_start: 0.7874 (tmtt) cc_final: 0.7159 (pttm) REVERT: I 74 ASN cc_start: 0.8304 (t0) cc_final: 0.7943 (m-40) REVERT: I 132 MET cc_start: 0.8536 (mmt) cc_final: 0.7900 (mmt) REVERT: I 149 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: L 75 LYS cc_start: 0.9102 (tptt) cc_final: 0.8603 (pttp) REVERT: L 85 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7550 (mp10) REVERT: L 112 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: H 117 ASP cc_start: 0.7773 (t0) cc_final: 0.7164 (m-30) REVERT: H 187 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7746 (p0) REVERT: K 74 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7299 (tp30) REVERT: K 94 GLU cc_start: 0.8093 (pm20) cc_final: 0.7792 (pm20) REVERT: S 34 ARG cc_start: 0.3861 (tpt90) cc_final: 0.3598 (tpt90) REVERT: S 40 MET cc_start: 0.8378 (ptp) cc_final: 0.7718 (ppp) REVERT: T 67 MET cc_start: 0.6931 (mtt) cc_final: 0.6457 (tpt) REVERT: U 396 MET cc_start: 0.4570 (ppp) cc_final: 0.4255 (ppp) REVERT: U 428 MET cc_start: 0.3207 (mtt) cc_final: 0.2850 (mtm) REVERT: U 453 MET cc_start: 0.3372 (mmm) cc_final: 0.3092 (mmt) REVERT: U 456 PHE cc_start: 0.2419 (m-10) cc_final: 0.2160 (m-80) REVERT: V 299 TYR cc_start: 0.0357 (OUTLIER) cc_final: -0.0630 (t80) REVERT: 0 51 ASN cc_start: 0.4462 (m-40) cc_final: 0.4211 (t0) REVERT: 0 86 ILE cc_start: 0.3300 (OUTLIER) cc_final: 0.3024 (mm) REVERT: 1 23 MET cc_start: 0.7342 (tpp) cc_final: 0.7063 (tpt) REVERT: 1 47 MET cc_start: 0.6842 (ppp) cc_final: 0.5404 (mmp) REVERT: 3 81 ASN cc_start: 0.4592 (OUTLIER) cc_final: 0.4298 (m110) REVERT: 3 82 ASP cc_start: 0.4139 (t0) cc_final: 0.3800 (t0) REVERT: 5 44 MET cc_start: 0.5513 (ppp) cc_final: 0.5020 (ttt) REVERT: 6 119 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7348 (mtp85) REVERT: 6 136 ILE cc_start: 0.7645 (mm) cc_final: 0.7338 (tp) REVERT: 7 44 MET cc_start: 0.6856 (tmm) cc_final: 0.6532 (tmm) REVERT: 7 82 ASP cc_start: 0.6482 (OUTLIER) cc_final: 0.6146 (t0) REVERT: 8 23 MET cc_start: 0.5988 (tpt) cc_final: 0.5756 (tpt) REVERT: 8 53 MET cc_start: 0.6578 (mpp) cc_final: 0.4511 (mmm) REVERT: 8 119 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6718 (mmt-90) REVERT: Q 176 MET cc_start: 0.5370 (ptp) cc_final: 0.5103 (ptp) REVERT: C 193 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6920 (mm-30) REVERT: C 266 TYR cc_start: 0.7189 (m-10) cc_final: 0.6818 (m-10) REVERT: C 432 PHE cc_start: 0.8287 (t80) cc_final: 0.7951 (t80) REVERT: C 451 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8761 (mt) REVERT: C 462 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.7872 (t0) REVERT: C 481 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7377 (tm-30) REVERT: C 586 PHE cc_start: 0.7554 (m-80) cc_final: 0.7225 (m-80) REVERT: A 34 MET cc_start: 0.1816 (ttp) cc_final: 0.1476 (ttp) REVERT: A 81 ARG cc_start: 0.5808 (mtt180) cc_final: 0.5469 (ttp-110) REVERT: A 192 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7837 (tt) REVERT: A 317 ASN cc_start: 0.8478 (t0) cc_final: 0.8200 (t0) REVERT: A 349 ASP cc_start: 0.7990 (t70) cc_final: 0.7756 (t0) REVERT: A 353 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.7021 (mmp80) REVERT: A 367 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7781 (mt-10) REVERT: A 443 LYS cc_start: 0.8121 (tttm) cc_final: 0.7855 (mmtm) REVERT: A 463 GLU cc_start: 0.7911 (mp0) cc_final: 0.7706 (tp30) REVERT: A 510 GLU cc_start: 0.6912 (tp30) cc_final: 0.6568 (tm-30) REVERT: A 574 MET cc_start: 0.4574 (pmm) cc_final: 0.4173 (ptt) REVERT: B 136 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7542 (t) REVERT: B 142 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.8085 (mtm110) REVERT: B 203 PHE cc_start: 0.6903 (t80) cc_final: 0.6096 (t80) REVERT: B 213 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: B 299 ASP cc_start: 0.6569 (p0) cc_final: 0.6253 (p0) REVERT: B 459 ARG cc_start: 0.8481 (tpp-160) cc_final: 0.7991 (mmm-85) REVERT: B 588 ASP cc_start: 0.8304 (t0) cc_final: 0.8078 (t0) REVERT: B 594 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6087 (tm-30) REVERT: D 141 ARG cc_start: 0.7557 (tpt170) cc_final: 0.7161 (mmm160) REVERT: D 214 LYS cc_start: 0.8106 (pptt) cc_final: 0.7105 (ptpp) REVERT: D 309 GLU cc_start: 0.7143 (tt0) cc_final: 0.6862 (mt-10) REVERT: D 362 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8703 (p) REVERT: D 435 MET cc_start: 0.7395 (tmm) cc_final: 0.6887 (tmm) REVERT: D 456 GLN cc_start: 0.7812 (tp40) cc_final: 0.7149 (tt0) REVERT: E 44 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7482 (mtt90) REVERT: E 80 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8356 (p) REVERT: E 154 MET cc_start: 0.8621 (mmm) cc_final: 0.8365 (mmt) REVERT: Z 59 ASN cc_start: 0.7209 (m-40) cc_final: 0.6481 (p0) REVERT: Z 74 CYS cc_start: 0.7915 (p) cc_final: 0.7400 (p) REVERT: Z 188 MET cc_start: 0.7022 (tpp) cc_final: 0.6700 (ttm) REVERT: Z 271 GLU cc_start: 0.3462 (OUTLIER) cc_final: 0.3009 (mp0) REVERT: X 115 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7766 (ttp) REVERT: X 161 MET cc_start: 0.7528 (mmm) cc_final: 0.7085 (mmm) REVERT: X 180 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7244 (tppt) REVERT: X 243 GLN cc_start: 0.7419 (mt0) cc_final: 0.7042 (mm-40) REVERT: Y 137 THR cc_start: 0.6873 (t) cc_final: 0.6566 (p) REVERT: G 45 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7524 (mmm-85) REVERT: G 56 MET cc_start: 0.4979 (mmp) cc_final: 0.3187 (ptm) REVERT: G 58 MET cc_start: 0.4760 (tmm) cc_final: 0.4360 (ttp) REVERT: G 85 GLN cc_start: 0.8005 (pp30) cc_final: 0.7495 (pp30) REVERT: N 67 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7933 (t0) REVERT: W 289 ARG cc_start: 0.6053 (mmt180) cc_final: 0.5059 (mpt180) REVERT: W 333 MET cc_start: 0.6349 (mmt) cc_final: 0.5742 (mmt) REVERT: W 345 TYR cc_start: 0.6841 (m-80) cc_final: 0.6625 (m-10) REVERT: W 378 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8068 (mttp) REVERT: F 239 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7367 (tm-30) REVERT: F 299 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7935 (t0) REVERT: F 321 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8088 (tpp80) REVERT: F 376 GLN cc_start: 0.7632 (mt0) cc_final: 0.7196 (pm20) REVERT: F 435 MET cc_start: 0.6220 (mmm) cc_final: 0.5648 (tpt) REVERT: F 456 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7015 (mp-120) outliers start: 201 outliers final: 162 residues processed: 1071 average time/residue: 0.6581 time to fit residues: 1212.2455 Evaluate side-chains 1084 residues out of total 8154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 900 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 343 HIS Chi-restraints excluded: chain R residue 418 LEU Chi-restraints excluded: chain R residue 535 PHE Chi-restraints excluded: chain R residue 588 ILE Chi-restraints excluded: chain R residue 713 PHE Chi-restraints excluded: chain R residue 735 THR Chi-restraints excluded: chain R residue 751 LEU Chi-restraints excluded: chain R residue 764 LEU Chi-restraints excluded: chain R residue 784 THR Chi-restraints excluded: chain R residue 801 HIS Chi-restraints excluded: chain J residue 66 GLN Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain M residue 84 LEU Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 112 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 187 ASP Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain U residue 374 VAL Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 407 VAL Chi-restraints excluded: chain U residue 426 ILE Chi-restraints excluded: chain U residue 432 THR Chi-restraints excluded: chain V residue 299 TYR Chi-restraints excluded: chain 0 residue 59 SER Chi-restraints excluded: chain 0 residue 76 ILE Chi-restraints excluded: chain 0 residue 86 ILE Chi-restraints excluded: chain 1 residue 64 ILE Chi-restraints excluded: chain 1 residue 129 VAL Chi-restraints excluded: chain 2 residue 20 SER Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 57 ILE Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 39 THR Chi-restraints excluded: chain 3 residue 81 ASN Chi-restraints excluded: chain 3 residue 140 VAL Chi-restraints excluded: chain 3 residue 143 LEU Chi-restraints excluded: chain 3 residue 147 ILE Chi-restraints excluded: chain 4 residue 70 LEU Chi-restraints excluded: chain 4 residue 136 ILE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 147 ILE Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 23 MET Chi-restraints excluded: chain 6 residue 39 THR Chi-restraints excluded: chain 6 residue 57 ILE Chi-restraints excluded: chain 7 residue 20 SER Chi-restraints excluded: chain 7 residue 57 ILE Chi-restraints excluded: chain 7 residue 82 ASP Chi-restraints excluded: chain 7 residue 102 SER Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain 9 residue 39 THR Chi-restraints excluded: chain 9 residue 56 ILE Chi-restraints excluded: chain 9 residue 93 LEU Chi-restraints excluded: chain Q residue 12 ASP Chi-restraints excluded: chain Q residue 24 LYS Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 107 ASP Chi-restraints excluded: chain Q residue 110 ILE Chi-restraints excluded: chain Q residue 197 CYS Chi-restraints excluded: chain Q residue 278 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 462 ASP Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 299 ASP Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain Z residue 119 VAL Chi-restraints excluded: chain Z residue 146 THR Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain X residue 10 MET Chi-restraints excluded: chain X residue 74 CYS Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 177 GLN Chi-restraints excluded: chain X residue 241 VAL Chi-restraints excluded: chain Y residue 126 TYR Chi-restraints excluded: chain Y residue 169 THR Chi-restraints excluded: chain Y residue 179 PHE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain W residue 206 VAL Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 245 ILE Chi-restraints excluded: chain W residue 309 SER Chi-restraints excluded: chain W residue 337 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ASP Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 321 ARG Chi-restraints excluded: chain F residue 358 ASN Chi-restraints excluded: chain F residue 359 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 378 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 951 random chunks: chunk 462 optimal weight: 0.2980 chunk 599 optimal weight: 0.8980 chunk 803 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 695 optimal weight: 3.9990 chunk 111 optimal weight: 30.0000 chunk 209 optimal weight: 10.0000 chunk 755 optimal weight: 6.9990 chunk 316 optimal weight: 30.0000 chunk 775 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 348 HIS ** 0 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 78 ASN ** 5 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN B 65 GLN B 449 ASN D 358 ASN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 209 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.188864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.166946 restraints weight = 117453.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162573 restraints weight = 180043.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.159762 restraints weight = 174114.454| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 72859 Z= 0.236 Angle : 0.628 15.974 98827 Z= 0.321 Chirality : 0.043 0.376 11476 Planarity : 0.004 0.070 12780 Dihedral : 5.008 143.344 10472 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.66 % Allowed : 19.84 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.17 (0.09), residues: 9526 helix: 1.45 (0.07), residues: 5447 sheet: -0.90 (0.18), residues: 800 loop : -1.97 (0.10), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP W 199 HIS 0.009 0.001 HIS T 75 PHE 0.038 0.002 PHE 1 137 TYR 0.050 0.002 TYR T 101 ARG 0.007 0.000 ARG M 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18920.48 seconds wall clock time: 331 minutes 15.79 seconds (19875.79 seconds total)