Starting phenix.real_space_refine on Sat Feb 17 10:35:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2024/5xxu_6780_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2024/5xxu_6780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2024/5xxu_6780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2024/5xxu_6780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2024/5xxu_6780_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2024/5xxu_6780_neut.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 1619 5.49 5 S 171 5.16 5 C 37160 2.51 5 N 12701 2.21 5 O 17304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "H PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 7": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I ARG 175": "NH1" <-> "NH2" Residue "I ARG 181": "NH1" <-> "NH2" Residue "I TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 40": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J ARG 149": "NH1" <-> "NH2" Residue "J TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L ARG 139": "NH1" <-> "NH2" Residue "L PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 106": "NH1" <-> "NH2" Residue "N ARG 124": "NH1" <-> "NH2" Residue "O PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "O ARG 130": "NH1" <-> "NH2" Residue "O ARG 152": "NH1" <-> "NH2" Residue "P TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q ARG 127": "NH1" <-> "NH2" Residue "Q ARG 148": "NH1" <-> "NH2" Residue "R TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 123": "NH1" <-> "NH2" Residue "T ARG 15": "NH1" <-> "NH2" Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "T ARG 150": "NH1" <-> "NH2" Residue "U ARG 133": "NH1" <-> "NH2" Residue "V ARG 44": "NH1" <-> "NH2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 68": "NH1" <-> "NH2" Residue "W PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 117": "NH1" <-> "NH2" Residue "W TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 35": "NH1" <-> "NH2" Residue "X PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 34": "NH1" <-> "NH2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 96": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Z ARG 111": "NH1" <-> "NH2" Residue "Z ARG 134": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "a ARG 54": "NH1" <-> "NH2" Residue "a TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "m ARG 7": "NH1" <-> "NH2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 35": "NH1" <-> "NH2" Residue "m ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68955 Number of models: 1 Model: "" Number of chains: 34 Chain: "2" Number of atoms: 34513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1619, 34513 Classifications: {'RNA': 1619} Modifications used: {'rna2p_pur': 141, 'rna2p_pyr': 118, 'rna3p_pur': 717, 'rna3p_pyr': 643} Link IDs: {'rna2p': 258, 'rna3p': 1360} Chain breaks: 16 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1565 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1750 Classifications: {'peptide': 225} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 208} Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1568 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 1 Chain: "E" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2085 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1475 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "G" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1782 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1354 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 168} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1496 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "J" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1457 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "K" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 675 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 86} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "L" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1206 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain breaks: 1 Chain: "M" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 508 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 2 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1204 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 139} Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 966 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "P" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 939 Classifications: {'peptide': 115} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Chain: "Q" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1086 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1091 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1236 Classifications: {'peptide': 151} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 141} Chain: "U" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 823 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "V" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 618 Classifications: {'peptide': 80} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "W" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1040 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1040 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "Z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 576 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "a" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 794 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "b" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 605 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "c" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 448 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 1 Chain: "d" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 429 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "e" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain breaks: 1 Chain: "f" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 229 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 86 Chain: "m" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 348 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 28.68, per 1000 atoms: 0.42 Number of scatterers: 68955 At special positions: 0 Unit cell: (229.68, 217.8, 203.28, 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 171 16.00 P 1619 15.00 O 17304 8.00 N 12701 7.00 C 37160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 77 " distance=2.03 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 37 " distance=2.04 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 40 " distance=2.10 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 Atom "ATOM 27181 O4' U 21430 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.34 Conformation dependent library (CDL) restraints added in 4.9 seconds 8562 Ramachandran restraints generated. 4281 Oldfield, 0 Emsley, 4281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8146 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 46 sheets defined 37.6% alpha, 14.3% beta 371 base pairs and 862 stacking pairs defined. Time for finding SS restraints: 20.07 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.751A pdb=" N LEU A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 23 " --> pdb=" O MET A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.536A pdb=" N TRP A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 82 through 95 removed outlier: 4.595A pdb=" N ARG A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.799A pdb=" N VAL A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.184A pdb=" N ALA A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.596A pdb=" N LYS B 27 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.686A pdb=" N GLY B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.519A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 179 Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.752A pdb=" N LYS B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.539A pdb=" N LYS B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.506A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 3.508A pdb=" N ARG C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 removed outlier: 4.049A pdb=" N ILE C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.737A pdb=" N PHE C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.539A pdb=" N ALA C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 198 removed outlier: 3.648A pdb=" N ILE C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.587A pdb=" N LYS C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.717A pdb=" N TRP C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.528A pdb=" N TRP C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 removed outlier: 3.693A pdb=" N LEU C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 31 removed outlier: 3.509A pdb=" N GLN D 20 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.549A pdb=" N LEU D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 79 removed outlier: 3.622A pdb=" N ARG D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 76 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.727A pdb=" N LEU D 98 " --> pdb=" O ASN D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 99 through 114 removed outlier: 3.860A pdb=" N GLN D 103 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 132 removed outlier: 3.503A pdb=" N CYS D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 removed outlier: 4.242A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.825A pdb=" N TRP E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.574A pdb=" N LEU E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.574A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 239 through 243 removed outlier: 4.512A pdb=" N GLY E 243 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 260 removed outlier: 3.508A pdb=" N LEU E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 63 Processing helix chain 'F' and resid 73 through 91 removed outlier: 3.537A pdb=" N ARG F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 108 removed outlier: 4.542A pdb=" N GLY F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 150 Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 175 through 191 removed outlier: 3.614A pdb=" N ILE F 184 " --> pdb=" O LYS F 180 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 190 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.658A pdb=" N PHE G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 221 removed outlier: 3.616A pdb=" N LYS G 185 " --> pdb=" O ARG G 181 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 196 " --> pdb=" O GLN G 192 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS G 219 " --> pdb=" O HIS G 215 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 32 removed outlier: 4.039A pdb=" N PHE H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP H 29 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR H 32 " --> pdb=" O PHE H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.943A pdb=" N ARG H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 80 through 92 Processing helix chain 'H' and resid 105 through 110 removed outlier: 4.514A pdb=" N LYS H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 135 removed outlier: 3.587A pdb=" N LEU H 130 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 184 removed outlier: 4.128A pdb=" N GLU H 169 " --> pdb=" O LYS H 165 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU H 173 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 175 " --> pdb=" O LYS H 171 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 177 " --> pdb=" O GLU H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 87 through 93 removed outlier: 4.012A pdb=" N VAL I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 165 removed outlier: 3.709A pdb=" N ASN I 164 " --> pdb=" O GLU I 160 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR I 165 " --> pdb=" O GLU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 180 Processing helix chain 'I' and resid 189 through 201 removed outlier: 3.721A pdb=" N ARG I 197 " --> pdb=" O MET I 193 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS I 198 " --> pdb=" O PHE I 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 35 removed outlier: 3.716A pdb=" N GLN J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU J 30 " --> pdb=" O GLN J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 61 removed outlier: 4.106A pdb=" N VAL J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE J 52 " --> pdb=" O ALA J 48 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 83 removed outlier: 3.509A pdb=" N PHE J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR J 74 " --> pdb=" O VAL J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 removed outlier: 4.046A pdb=" N LEU J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 98' Processing helix chain 'J' and resid 100 through 106 removed outlier: 3.755A pdb=" N PHE J 104 " --> pdb=" O THR J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 117 Processing helix chain 'J' and resid 121 through 131 removed outlier: 3.534A pdb=" N ARG J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 180 Processing helix chain 'K' and resid 12 through 27 removed outlier: 3.661A pdb=" N LYS K 17 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 removed outlier: 3.515A pdb=" N VAL K 50 " --> pdb=" O PRO K 46 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR K 59 " --> pdb=" O ARG K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 89 removed outlier: 3.628A pdb=" N GLU K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE K 83 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG K 85 " --> pdb=" O ILE K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.960A pdb=" N LYS L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 39 removed outlier: 3.961A pdb=" N VAL M 31 " --> pdb=" O ALA M 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 33 " --> pdb=" O ARG M 29 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU M 36 " --> pdb=" O LEU M 32 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS M 38 " --> pdb=" O ASN M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 53 Processing helix chain 'M' and resid 68 through 83 removed outlier: 3.759A pdb=" N HIS M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 removed outlier: 3.991A pdb=" N TRP M 98 " --> pdb=" O LEU M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.987A pdb=" N ASN M 136 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS M 137 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS M 139 " --> pdb=" O GLN M 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.860A pdb=" N VAL N 33 " --> pdb=" O LYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 58 removed outlier: 3.897A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 removed outlier: 3.597A pdb=" N VAL N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 103 Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.618A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG N 131 " --> pdb=" O ARG N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 removed outlier: 3.585A pdb=" N LEU N 149 " --> pdb=" O THR N 145 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA N 151 " --> pdb=" O SER N 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 145 through 151' Processing helix chain 'O' and resid 63 through 67 Processing helix chain 'O' and resid 75 through 94 removed outlier: 3.731A pdb=" N ASP O 85 " --> pdb=" O MET O 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY O 94 " --> pdb=" O CYS O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 128 removed outlier: 4.220A pdb=" N GLN O 118 " --> pdb=" O GLY O 114 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER O 119 " --> pdb=" O PRO O 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA O 125 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 4.541A pdb=" N LEU P 31 " --> pdb=" O LEU P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 39 Processing helix chain 'P' and resid 44 through 53 removed outlier: 3.643A pdb=" N ARG P 48 " --> pdb=" O ALA P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 68 removed outlier: 3.581A pdb=" N LEU P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG P 66 " --> pdb=" O MET P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 49 through 54 removed outlier: 3.573A pdb=" N PHE Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 61 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.208A pdb=" N PHE Q 65 " --> pdb=" O GLY Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 101 removed outlier: 3.651A pdb=" N ILE Q 83 " --> pdb=" O TYR Q 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA Q 91 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN Q 99 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR Q 101 " --> pdb=" O PHE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 117 removed outlier: 4.207A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 104 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU Q 114 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.643A pdb=" N ALA R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.936A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.508A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.612A pdb=" N ARG R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE R 84 " --> pdb=" O ARG R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 110 removed outlier: 3.747A pdb=" N ASP R 104 " --> pdb=" O GLN R 100 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU R 106 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA R 108 " --> pdb=" O ASP R 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 32 Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 103 through 120 removed outlier: 3.551A pdb=" N LEU S 116 " --> pdb=" O ASP S 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS S 118 " --> pdb=" O GLU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 removed outlier: 3.563A pdb=" N HIS S 127 " --> pdb=" O ARG S 123 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 22 removed outlier: 3.622A pdb=" N ASP T 21 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 39 removed outlier: 3.502A pdb=" N ILE T 28 " --> pdb=" O ALA T 24 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 49 removed outlier: 4.479A pdb=" N ASP T 48 " --> pdb=" O LYS T 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 80 removed outlier: 3.528A pdb=" N ILE T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU T 74 " --> pdb=" O ALA T 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR T 78 " --> pdb=" O LEU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 92 removed outlier: 3.655A pdb=" N LYS T 90 " --> pdb=" O GLY T 86 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE T 92 " --> pdb=" O PHE T 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 124 removed outlier: 3.809A pdb=" N ILE T 113 " --> pdb=" O SER T 109 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE T 116 " --> pdb=" O ILE T 112 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU T 117 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 154 removed outlier: 3.546A pdb=" N ARG T 143 " --> pdb=" O LYS T 139 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE T 148 " --> pdb=" O GLU T 144 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG T 150 " --> pdb=" O ASP T 146 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN T 151 " --> pdb=" O VAL T 147 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA T 153 " --> pdb=" O ALA T 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 161 removed outlier: 3.521A pdb=" N ARG U 148 " --> pdb=" O LYS U 144 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL U 149 " --> pdb=" O SER U 145 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR U 151 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE U 154 " --> pdb=" O CYS U 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN U 155 " --> pdb=" O THR U 151 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS U 160 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 218 removed outlier: 3.789A pdb=" N VAL U 212 " --> pdb=" O PRO U 208 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS U 213 " --> pdb=" O SER U 209 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN U 214 " --> pdb=" O ASP U 210 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE U 215 " --> pdb=" O VAL U 211 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE U 218 " --> pdb=" O GLN U 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 62 removed outlier: 3.933A pdb=" N ARG V 61 " --> pdb=" O ALA V 57 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY V 62 " --> pdb=" O VAL V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 72 removed outlier: 3.581A pdb=" N CYS V 67 " --> pdb=" O GLU V 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG V 70 " --> pdb=" O ALA V 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.713A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS W 12 " --> pdb=" O ALA W 8 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA W 17 " --> pdb=" O THR W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 45 removed outlier: 4.214A pdb=" N ARG W 44 " --> pdb=" O CYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.543A pdb=" N ASN W 92 " --> pdb=" O GLN W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 removed outlier: 3.781A pdb=" N ARG W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 21 removed outlier: 3.504A pdb=" N LEU X 13 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG X 17 " --> pdb=" O LEU X 13 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG X 18 " --> pdb=" O ARG X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 32 removed outlier: 3.712A pdb=" N LYS X 28 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 38 removed outlier: 4.226A pdb=" N LYS X 37 " --> pdb=" O GLY X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 136 removed outlier: 3.967A pdb=" N LEU X 133 " --> pdb=" O SER X 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 51 removed outlier: 3.953A pdb=" N GLU Y 44 " --> pdb=" O LYS Y 40 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS Y 45 " --> pdb=" O GLU Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 89 removed outlier: 3.696A pdb=" N ALA Y 85 " --> pdb=" O ASN Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 98 removed outlier: 3.926A pdb=" N LEU Y 94 " --> pdb=" O ASN Y 90 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG Y 96 " --> pdb=" O PHE Y 92 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU Y 97 " --> pdb=" O ARG Y 93 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 121 removed outlier: 3.593A pdb=" N LYS Y 115 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG Y 117 " --> pdb=" O GLU Y 113 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS Y 120 " --> pdb=" O ASN Y 116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 132 removed outlier: 4.131A pdb=" N SER Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 110 removed outlier: 4.091A pdb=" N LYS Z 102 " --> pdb=" O ALA Z 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU Z 104 " --> pdb=" O TYR Z 100 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA Z 105 " --> pdb=" O ASP Z 101 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE Z 107 " --> pdb=" O LEU Z 103 " (cutoff:3.500A) Proline residue: Z 108 - end of helix Processing helix chain 'Z' and resid 114 through 122 removed outlier: 3.977A pdb=" N VAL Z 118 " --> pdb=" O THR Z 114 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS Z 119 " --> pdb=" O PRO Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 139 removed outlier: 4.004A pdb=" N ALA Z 129 " --> pdb=" O ASN Z 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN Z 131 " --> pdb=" O SER Z 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 50 through 57 Processing helix chain 'a' and resid 75 through 82 Processing helix chain 'a' and resid 90 through 94 removed outlier: 3.588A pdb=" N VAL a 94 " --> pdb=" O GLN a 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 16 removed outlier: 3.676A pdb=" N SER b 15 " --> pdb=" O LYS b 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 44 removed outlier: 4.309A pdb=" N GLU d 43 " --> pdb=" O GLN d 39 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG d 44 " --> pdb=" O CYS d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 49 Processing helix chain 'e' and resid 13 through 18 Processing helix chain 'e' and resid 32 through 45 removed outlier: 3.571A pdb=" N GLN e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG e 43 " --> pdb=" O GLN e 39 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE e 44 " --> pdb=" O PHE e 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 9 removed outlier: 4.419A pdb=" N TYR m 8 " --> pdb=" O ALA m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 38 removed outlier: 3.654A pdb=" N LYS m 33 " --> pdb=" O ARG m 29 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER m 38 " --> pdb=" O MET m 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.752A pdb=" N LEU A 49 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 removed outlier: 6.384A pdb=" N VAL A 75 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 100 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 77 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 47 removed outlier: 6.971A pdb=" N CYS B 96 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 91 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR B 98 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 100 " --> pdb=" O CYS B 87 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N CYS B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 102 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 47 Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 128 removed outlier: 6.213A pdb=" N ILE B 140 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 210 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 97 removed outlier: 5.314A pdb=" N ASP C 86 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY C 113 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL C 88 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 111 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 166 through 169 removed outlier: 7.084A pdb=" N VAL C 187 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N SER C 208 " --> pdb=" O VAL C 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 42 removed outlier: 4.170A pdb=" N GLY D 38 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 50 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 152 through 156 removed outlier: 3.792A pdb=" N GLY D 135 " --> pdb=" O MET D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.651A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 3.626A pdb=" N GLU E 97 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 137 through 141 removed outlier: 3.663A pdb=" N LYS E 128 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 171 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.540A pdb=" N ILE E 207 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE E 195 " --> pdb=" O ARG E 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 195 " --> pdb=" O ASN E 179 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN E 179 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 111 through 115 Processing sheet with id=AB7, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.573A pdb=" N LEU G 5 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G 109 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 73 through 77 removed outlier: 3.728A pdb=" N LYS G 93 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 50 through 53 removed outlier: 3.558A pdb=" N VAL H 53 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE H 63 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL H 98 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL H 65 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLN H 100 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL H 67 " --> pdb=" O GLN H 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 187 through 188 removed outlier: 6.458A pdb=" N LEU H 154 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP W 49 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS W 60 " --> pdb=" O VAL W 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.141A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 43 through 47 Processing sheet with id=AC4, first strand: chain 'I' and resid 62 through 67 removed outlier: 4.268A pdb=" N GLY I 80 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 135 through 136 removed outlier: 3.735A pdb=" N HIS J 139 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 28 through 30 removed outlier: 4.255A pdb=" N ILE K 29 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR K 74 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 72 through 79 removed outlier: 17.551A pdb=" N VAL L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 14.888A pdb=" N LEU L 93 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N LYS L 74 " --> pdb=" O ASN L 91 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN L 91 " --> pdb=" O LYS L 74 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL L 87 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE L 140 " --> pdb=" O THR L 110 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 41 through 42 removed outlier: 3.637A pdb=" N VAL M 119 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL M 59 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 38 through 40 removed outlier: 3.617A pdb=" N VAL O 59 " --> pdb=" O VAL O 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 97 through 102 removed outlier: 3.770A pdb=" N VAL O 100 " --> pdb=" O GLY O 132 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE O 134 " --> pdb=" O VAL O 100 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL O 102 " --> pdb=" O ILE O 134 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP O 136 " --> pdb=" O VAL O 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 81 through 83 removed outlier: 6.499A pdb=" N VAL P 81 " --> pdb=" O GLY P 100 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR P 102 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR P 83 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 11 through 16 removed outlier: 3.721A pdb=" N GLY Q 16 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Q 23 " --> pdb=" O GLY Q 16 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG Q 35 " --> pdb=" O VAL Q 72 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL Q 74 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 94 through 96 removed outlier: 3.512A pdb=" N CYS T 94 " --> pdb=" O SER T 106 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS T 104 " --> pdb=" O GLN T 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 126 through 127 removed outlier: 3.613A pdb=" N ARG T 136 " --> pdb=" O GLU T 127 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 165 through 169 removed outlier: 5.796A pdb=" N GLY U 166 " --> pdb=" O ASP U 204 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP U 204 " --> pdb=" O GLY U 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU U 227 " --> pdb=" O THR U 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 173 through 177 Processing sheet with id=AD8, first strand: chain 'V' and resid 32 through 37 Processing sheet with id=AD9, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.327A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET W 111 " --> pdb=" O LEU W 104 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 46 through 47 removed outlier: 6.398A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 8 through 17 removed outlier: 4.300A pdb=" N LEU Y 14 " --> pdb=" O GLN Y 24 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN Y 24 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR Y 16 " --> pdb=" O ARG Y 22 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG Y 22 " --> pdb=" O THR Y 16 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ARG Y 71 " --> pdb=" O THR Y 65 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR Y 65 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER Y 73 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU Y 63 " --> pdb=" O SER Y 73 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 112 through 113 removed outlier: 3.836A pdb=" N LYS Z 143 " --> pdb=" O THR Z 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AE5, first strand: chain 'a' and resid 37 through 42 removed outlier: 3.545A pdb=" N ILE a 69 " --> pdb=" O ASN a 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 42 through 45 Processing sheet with id=AE7, first strand: chain 'b' and resid 62 through 63 Processing sheet with id=AE8, first strand: chain 'c' and resid 41 through 45 removed outlier: 7.590A pdb=" N GLN c 24 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL c 12 " --> pdb=" O GLN c 24 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG c 26 " --> pdb=" O GLU c 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'd' and resid 28 through 29 Processing sheet with id=AF1, first strand: chain 'f' and resid 132 through 133 removed outlier: 3.634A pdb=" N TYR f 140 " --> pdb=" O ALA f 133 " (cutoff:3.500A) 1166 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 867 hydrogen bonds 1422 hydrogen bond angles 0 basepair planarities 371 basepair parallelities 862 stacking parallelities Total time for adding SS restraints: 47.04 Time building geometry restraints manager: 29.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 70095 1.56 - 1.91: 3495 1.91 - 2.26: 0 2.26 - 2.60: 0 2.60 - 2.95: 1 Bond restraints: 73591 Sorted by residual: bond pdb=" C SER H 135 " pdb=" N THR H 137 " ideal model delta sigma weight residual 1.329 2.950 -1.621 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C ILE B 189 " pdb=" N PRO B 190 " ideal model delta sigma weight residual 1.332 1.387 -0.055 8.90e-03 1.26e+04 3.80e+01 bond pdb=" C LEU K 90 " pdb=" N PRO K 91 " ideal model delta sigma weight residual 1.329 1.391 -0.062 1.18e-02 7.18e+03 2.74e+01 bond pdb=" C VAL H 55 " pdb=" N PRO H 56 " ideal model delta sigma weight residual 1.331 1.392 -0.061 1.20e-02 6.94e+03 2.55e+01 bond pdb=" C MET C 92 " pdb=" N PRO C 93 " ideal model delta sigma weight residual 1.334 1.388 -0.054 1.11e-02 8.12e+03 2.39e+01 ... (remaining 73586 not shown) Histogram of bond angle deviations from ideal: 41.02 - 65.05: 1 65.05 - 89.07: 0 89.07 - 113.10: 49408 113.10 - 137.13: 57613 137.13 - 161.15: 30 Bond angle restraints: 107052 Sorted by residual: angle pdb=" O SER H 135 " pdb=" C SER H 135 " pdb=" N THR H 137 " ideal model delta sigma weight residual 122.59 41.02 81.57 1.33e+00 5.65e-01 3.76e+03 angle pdb=" CA SER H 135 " pdb=" C SER H 135 " pdb=" N THR H 137 " ideal model delta sigma weight residual 116.84 161.15 -44.31 1.71e+00 3.42e-01 6.71e+02 angle pdb=" C SER H 135 " pdb=" N THR H 137 " pdb=" CA THR H 137 " ideal model delta sigma weight residual 121.70 141.48 -19.78 1.80e+00 3.09e-01 1.21e+02 angle pdb=" N ILE X 94 " pdb=" CA ILE X 94 " pdb=" C ILE X 94 " ideal model delta sigma weight residual 110.42 120.02 -9.60 9.60e-01 1.09e+00 1.00e+02 angle pdb=" N ALA a 35 " pdb=" CA ALA a 35 " pdb=" C ALA a 35 " ideal model delta sigma weight residual 111.28 120.91 -9.63 1.09e+00 8.42e-01 7.80e+01 ... (remaining 107047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 42400 35.95 - 71.91: 3719 71.91 - 107.86: 443 107.86 - 143.81: 17 143.81 - 179.77: 56 Dihedral angle restraints: 46635 sinusoidal: 34046 harmonic: 12589 Sorted by residual: dihedral pdb=" O4' U 2 827 " pdb=" C1' U 2 827 " pdb=" N1 U 2 827 " pdb=" C2 U 2 827 " ideal model delta sinusoidal sigma weight residual -160.00 18.34 -178.34 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 764 " pdb=" C1' U 2 764 " pdb=" N1 U 2 764 " pdb=" C2 U 2 764 " ideal model delta sinusoidal sigma weight residual -160.00 18.18 -178.18 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21151 " pdb=" C1' C 21151 " pdb=" N1 C 21151 " pdb=" C2 C 21151 " ideal model delta sinusoidal sigma weight residual 200.00 24.27 175.73 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 46632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 10767 0.117 - 0.234: 2464 0.234 - 0.351: 65 0.351 - 0.468: 7 0.468 - 0.585: 9 Chirality restraints: 13312 Sorted by residual: chirality pdb=" C3' A 2 541 " pdb=" C4' A 2 541 " pdb=" O3' A 2 541 " pdb=" C2' A 2 541 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" C3' A 2 135 " pdb=" C4' A 2 135 " pdb=" O3' A 2 135 " pdb=" C2' A 2 135 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" C3' U 2 154 " pdb=" C4' U 2 154 " pdb=" O3' U 2 154 " pdb=" C2' U 2 154 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 13309 not shown) Planarity restraints: 7623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 135 " -0.061 2.00e-02 2.50e+03 5.26e-02 2.76e+01 pdb=" C SER H 135 " 0.067 2.00e-02 2.50e+03 pdb=" O SER H 135 " 0.035 2.00e-02 2.50e+03 pdb=" N THR H 137 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 34 " -0.083 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO E 35 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO E 35 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 35 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 116 " -0.081 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO H 117 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO H 117 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 117 " -0.065 5.00e-02 4.00e+02 ... (remaining 7620 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 62 2.03 - 2.75: 6789 2.75 - 3.47: 88075 3.47 - 4.18: 194333 4.18 - 4.90: 285456 Nonbonded interactions: 574715 Sorted by model distance: nonbonded pdb=" O2' G 2 80 " pdb=" O5' C 2 81 " model vdw 1.315 2.440 nonbonded pdb=" O ILE X 94 " pdb=" OD2 ASP X 98 " model vdw 1.415 3.040 nonbonded pdb=" NZ LYS B 27 " pdb=" OE2 GLU O 56 " model vdw 1.464 2.520 nonbonded pdb=" O2' C 2 693 " pdb=" CE LYS H 111 " model vdw 1.465 3.440 nonbonded pdb=" O HIS J 155 " pdb=" OD1 ASP J 157 " model vdw 1.530 3.040 ... (remaining 574710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 9.450 Check model and map are aligned: 0.740 Set scattering table: 0.480 Process input model: 175.610 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.621 73591 Z= 0.648 Angle : 1.107 81.567 107052 Z= 0.745 Chirality : 0.091 0.585 13312 Planarity : 0.004 0.127 7623 Dihedral : 22.649 179.765 38480 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 2.62 % Allowed : 6.96 % Favored : 90.42 % Rotamer: Outliers : 3.58 % Allowed : 6.96 % Favored : 89.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.11), residues: 4281 helix: -1.87 (0.12), residues: 1328 sheet: -2.26 (0.18), residues: 629 loop : -2.15 (0.11), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP m 19 HIS 0.004 0.001 HIS X 110 PHE 0.013 0.001 PHE W 50 TYR 0.018 0.001 TYR P 128 ARG 0.006 0.000 ARG O 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8562 Ramachandran restraints generated. 4281 Oldfield, 0 Emsley, 4281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8562 Ramachandran restraints generated. 4281 Oldfield, 0 Emsley, 4281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1533 time to evaluate : 3.774 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: A 13 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7437 (mm-30) REVERT: A 14 ASP cc_start: 0.8165 (m-30) cc_final: 0.7955 (m-30) REVERT: A 48 HIS cc_start: 0.7674 (m-70) cc_final: 0.7041 (m90) REVERT: A 51 ASN cc_start: 0.7588 (m-40) cc_final: 0.6431 (t0) REVERT: A 81 ARG cc_start: 0.7813 (mmt180) cc_final: 0.7578 (mmm-85) REVERT: A 83 TYR cc_start: 0.7831 (m-80) cc_final: 0.7540 (m-80) REVERT: A 104 TRP cc_start: 0.7725 (t60) cc_final: 0.6128 (t60) REVERT: A 108 MET cc_start: 0.8051 (mmm) cc_final: 0.7615 (mmt) REVERT: A 118 MET cc_start: 0.8503 (mtp) cc_final: 0.7972 (mpp) REVERT: A 205 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.5628 (mt) REVERT: A 206 TRP cc_start: 0.7431 (t60) cc_final: 0.7110 (t60) REVERT: A 208 ASP cc_start: 0.8572 (m-30) cc_final: 0.8291 (m-30) REVERT: B 29 TRP cc_start: 0.7457 (m100) cc_final: 0.6592 (m-10) REVERT: B 84 ILE cc_start: 0.7003 (tp) cc_final: 0.6610 (tp) REVERT: B 99 ASP cc_start: 0.8428 (t0) cc_final: 0.8202 (t0) REVERT: B 103 MET cc_start: 0.7950 (ttm) cc_final: 0.7749 (ttm) REVERT: B 111 CYS cc_start: 0.8396 (t) cc_final: 0.7984 (m) REVERT: B 115 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7379 (mmt180) REVERT: B 178 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7828 (tppt) REVERT: B 217 MET cc_start: 0.8138 (mtt) cc_final: 0.7881 (mtp) REVERT: C 53 SER cc_start: 0.7527 (t) cc_final: 0.7047 (p) REVERT: C 67 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7017 (pm20) REVERT: C 68 TYR cc_start: 0.7699 (p90) cc_final: 0.7156 (p90) REVERT: C 89 MET cc_start: 0.8154 (mmt) cc_final: 0.7911 (mmm) REVERT: C 92 MET cc_start: 0.7654 (ttp) cc_final: 0.6887 (ptp) REVERT: C 99 ARG cc_start: 0.7121 (tpt170) cc_final: 0.6899 (tpp80) REVERT: C 134 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6695 (mtm-85) REVERT: C 151 TYR cc_start: 0.8050 (m-80) cc_final: 0.7513 (m-80) REVERT: C 169 ARG cc_start: 0.8759 (ptp90) cc_final: 0.8104 (ptt180) REVERT: C 194 LYS cc_start: 0.7304 (mttt) cc_final: 0.6938 (mmtm) REVERT: C 195 ILE cc_start: 0.8366 (pt) cc_final: 0.8127 (mp) REVERT: C 209 LYS cc_start: 0.8247 (tttt) cc_final: 0.7961 (ttpt) REVERT: C 215 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6911 (mtp85) REVERT: D 7 THR cc_start: 0.7960 (p) cc_final: 0.7636 (p) REVERT: D 15 LYS cc_start: 0.7611 (ttpt) cc_final: 0.7395 (ptmm) REVERT: D 22 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6416 (mm-30) REVERT: D 25 GLU cc_start: 0.7510 (tp30) cc_final: 0.6519 (mp0) REVERT: D 28 SER cc_start: 0.7435 (t) cc_final: 0.6909 (p) REVERT: D 49 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6256 (pt0) REVERT: D 87 GLU cc_start: 0.7490 (pt0) cc_final: 0.7155 (pm20) REVERT: D 101 MET cc_start: 0.8409 (mtp) cc_final: 0.8144 (mtp) REVERT: D 113 LYS cc_start: 0.7135 (tptt) cc_final: 0.6725 (tptt) REVERT: D 121 CYS cc_start: 0.8036 (m) cc_final: 0.7231 (p) REVERT: D 126 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7457 (tpp-160) REVERT: D 137 GLU cc_start: 0.7377 (pt0) cc_final: 0.6646 (pt0) REVERT: D 141 SER cc_start: 0.6763 (m) cc_final: 0.6062 (t) REVERT: D 143 LYS cc_start: 0.6712 (ptpt) cc_final: 0.6160 (pttt) REVERT: D 150 LYS cc_start: 0.7085 (ttpp) cc_final: 0.6263 (ttpp) REVERT: D 152 MET cc_start: 0.6582 (mmm) cc_final: 0.6198 (mpp) REVERT: D 153 LYS cc_start: 0.7046 (ttmt) cc_final: 0.6733 (mtmt) REVERT: D 154 PHE cc_start: 0.6641 (m-80) cc_final: 0.5845 (m-80) REVERT: D 175 ARG cc_start: 0.7759 (mmt-90) cc_final: 0.7071 (mmm-85) REVERT: D 180 ARG cc_start: 0.7660 (ptp90) cc_final: 0.7407 (ptp90) REVERT: D 184 LEU cc_start: 0.7009 (mt) cc_final: 0.6679 (mm) REVERT: D 189 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6796 (mtmm) REVERT: E 7 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7148 (mtmt) REVERT: E 19 MET cc_start: 0.6676 (mtt) cc_final: 0.6210 (mtt) REVERT: E 37 LYS cc_start: 0.7359 (mttm) cc_final: 0.7047 (mttp) REVERT: E 50 ASN cc_start: 0.8414 (m-40) cc_final: 0.8023 (m110) REVERT: E 51 ARG cc_start: 0.7714 (mmt-90) cc_final: 0.7253 (mpt180) REVERT: E 59 ARG cc_start: 0.7859 (ttt90) cc_final: 0.7605 (ttp-170) REVERT: E 62 MET cc_start: 0.8171 (mtt) cc_final: 0.7786 (mmt) REVERT: E 104 ASP cc_start: 0.7365 (t70) cc_final: 0.6859 (t0) REVERT: E 115 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7244 (mmm160) REVERT: E 116 GLU cc_start: 0.8482 (pt0) cc_final: 0.8091 (mp0) REVERT: E 120 SER cc_start: 0.8092 (m) cc_final: 0.7783 (p) REVERT: E 128 LYS cc_start: 0.7915 (ptmt) cc_final: 0.7584 (ptmt) REVERT: E 155 LYS cc_start: 0.7706 (tttt) cc_final: 0.7155 (mmtt) REVERT: E 165 ASN cc_start: 0.8094 (m110) cc_final: 0.7692 (m-40) REVERT: E 171 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7409 (t0) REVERT: E 174 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7261 (mmmm) REVERT: E 176 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7719 (pm20) REVERT: E 182 MET cc_start: 0.7851 (ttm) cc_final: 0.7546 (tpp) REVERT: E 199 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7111 (mp0) REVERT: E 207 ILE cc_start: 0.7403 (pt) cc_final: 0.7203 (mt) REVERT: E 209 HIS cc_start: 0.7670 (m90) cc_final: 0.6849 (m-70) REVERT: E 233 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6349 (tttp) REVERT: E 242 LYS cc_start: 0.8124 (mttt) cc_final: 0.7534 (mmtm) REVERT: E 254 VAL cc_start: 0.8026 (p) cc_final: 0.7699 (m) REVERT: E 256 LEU cc_start: 0.7481 (pp) cc_final: 0.7242 (pt) REVERT: F 4 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5785 (mp0) REVERT: F 43 ARG cc_start: 0.7597 (mtt180) cc_final: 0.6990 (mmm-85) REVERT: F 47 LYS cc_start: 0.7262 (mttt) cc_final: 0.6775 (mtmt) REVERT: F 51 LYS cc_start: 0.6800 (ttmt) cc_final: 0.6363 (ttmm) REVERT: F 115 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7725 (mmp80) REVERT: F 136 ASN cc_start: 0.8239 (m110) cc_final: 0.7791 (m-40) REVERT: F 180 LYS cc_start: 0.7320 (mmmt) cc_final: 0.7108 (mmmm) REVERT: G 12 MET cc_start: 0.7614 (mmm) cc_final: 0.6953 (tpp) REVERT: G 14 LYS cc_start: 0.8008 (tptm) cc_final: 0.7666 (ptmt) REVERT: G 21 GLU cc_start: 0.7911 (tt0) cc_final: 0.7613 (mm-30) REVERT: G 44 GLU cc_start: 0.8297 (pt0) cc_final: 0.7416 (tt0) REVERT: G 51 ARG cc_start: 0.7101 (ttt-90) cc_final: 0.6835 (ttm110) REVERT: G 78 ARG cc_start: 0.8362 (mmt180) cc_final: 0.8161 (mmm-85) REVERT: G 79 LYS cc_start: 0.8297 (tttt) cc_final: 0.7661 (ttmt) REVERT: G 84 TYR cc_start: 0.7105 (t80) cc_final: 0.6781 (t80) REVERT: G 86 GLN cc_start: 0.7941 (mt0) cc_final: 0.7456 (mt0) REVERT: G 91 GLU cc_start: 0.8097 (tt0) cc_final: 0.7829 (tt0) REVERT: G 114 VAL cc_start: 0.8869 (t) cc_final: 0.8571 (t) REVERT: G 119 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7532 (tp30) REVERT: G 125 THR cc_start: 0.7632 (m) cc_final: 0.7319 (p) REVERT: G 156 TYR cc_start: 0.8048 (m-80) cc_final: 0.7352 (m-80) REVERT: G 161 GLN cc_start: 0.8889 (pt0) cc_final: 0.8443 (tm-30) REVERT: G 162 ILE cc_start: 0.8432 (pt) cc_final: 0.7972 (pt) REVERT: G 179 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7568 (tttt) REVERT: G 186 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7542 (mtp180) REVERT: G 194 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8147 (ptp90) REVERT: G 196 VAL cc_start: 0.8696 (t) cc_final: 0.8282 (m) REVERT: G 202 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7382 (mt-10) REVERT: G 211 SER cc_start: 0.8013 (t) cc_final: 0.7605 (m) REVERT: G 219 LYS cc_start: 0.7698 (mtpp) cc_final: 0.7394 (ptmm) REVERT: H 54 GLU cc_start: 0.7912 (pt0) cc_final: 0.7605 (pp20) REVERT: H 90 LYS cc_start: 0.7806 (tptt) cc_final: 0.7524 (tmtt) REVERT: H 129 MET cc_start: 0.7328 (mmp) cc_final: 0.6916 (mmm) REVERT: H 169 GLU cc_start: 0.7760 (tp30) cc_final: 0.7471 (mp0) REVERT: I 6 ASP cc_start: 0.7829 (p0) cc_final: 0.7604 (p0) REVERT: I 8 ARG cc_start: 0.7275 (mtm110) cc_final: 0.7030 (mtm110) REVERT: I 22 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7991 (pt0) REVERT: I 35 MET cc_start: 0.7960 (mtt) cc_final: 0.7464 (mmp) REVERT: I 47 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7292 (tmt170) REVERT: I 52 ASN cc_start: 0.7841 (m-40) cc_final: 0.7346 (m110) REVERT: I 55 TYR cc_start: 0.7509 (m-80) cc_final: 0.7021 (m-80) REVERT: I 61 ASP cc_start: 0.8352 (t70) cc_final: 0.7791 (t0) REVERT: I 77 ARG cc_start: 0.7900 (ttt180) cc_final: 0.7335 (ttp80) REVERT: I 92 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7355 (ttm-80) REVERT: I 114 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7969 (mmm160) REVERT: I 149 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6425 (mm110) REVERT: I 154 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8448 (mmmt) REVERT: I 190 GLU cc_start: 0.7037 (tp30) cc_final: 0.6599 (tp30) REVERT: I 196 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7847 (mmmm) REVERT: J 8 TYR cc_start: 0.8044 (p90) cc_final: 0.7569 (p90) REVERT: J 13 ARG cc_start: 0.7783 (ptm160) cc_final: 0.7521 (ptm-80) REVERT: J 41 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7310 (mt-10) REVERT: J 46 GLN cc_start: 0.7853 (tp40) cc_final: 0.7064 (mt0) REVERT: J 47 TYR cc_start: 0.8278 (t80) cc_final: 0.7969 (t80) REVERT: J 66 ASP cc_start: 0.7974 (t70) cc_final: 0.7667 (t0) REVERT: J 68 ARG cc_start: 0.7681 (ttt-90) cc_final: 0.7475 (tmt-80) REVERT: J 86 LEU cc_start: 0.7784 (tp) cc_final: 0.7438 (tp) REVERT: J 108 ARG cc_start: 0.6963 (ptm160) cc_final: 0.6595 (ptm-80) REVERT: J 120 LYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6301 (ptmt) REVERT: J 132 ARG cc_start: 0.8016 (tpp80) cc_final: 0.7727 (mtp85) REVERT: J 178 LYS cc_start: 0.7413 (mttt) cc_final: 0.7157 (ptmm) REVERT: K 36 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.7067 (ttmt) REVERT: K 52 MET cc_start: 0.7050 (mmp) cc_final: 0.6546 (ptp) REVERT: K 57 LEU cc_start: 0.6547 (tp) cc_final: 0.6338 (tp) REVERT: K 62 PHE cc_start: 0.5192 (m-80) cc_final: 0.4797 (m-80) REVERT: K 69 TRP cc_start: 0.2552 (m100) cc_final: 0.1216 (m100) REVERT: L 19 SER cc_start: 0.8042 (m) cc_final: 0.7819 (p) REVERT: L 37 TRP cc_start: 0.8347 (p-90) cc_final: 0.7805 (p90) REVERT: L 39 ASP cc_start: 0.7478 (t70) cc_final: 0.6754 (p0) REVERT: L 49 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6829 (tt) REVERT: L 53 SER cc_start: 0.7182 (t) cc_final: 0.6662 (p) REVERT: L 57 ASP cc_start: 0.7992 (t0) cc_final: 0.7628 (t70) REVERT: L 58 LYS cc_start: 0.8626 (ttpt) cc_final: 0.8338 (ttpp) REVERT: L 83 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7777 (ttpp) REVERT: L 87 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.8004 (p) REVERT: L 99 TYR cc_start: 0.7842 (m-80) cc_final: 0.6797 (m-80) REVERT: L 107 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7431 (mmtp) REVERT: L 113 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7394 (tt) REVERT: L 122 GLU cc_start: 0.8014 (tt0) cc_final: 0.7694 (tt0) REVERT: L 125 ILE cc_start: 0.8213 (mt) cc_final: 0.7466 (mt) REVERT: L 141 ASN cc_start: 0.8205 (t0) cc_final: 0.7751 (t0) REVERT: L 145 VAL cc_start: 0.8588 (m) cc_final: 0.8328 (t) REVERT: L 147 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7851 (mmmt) REVERT: L 149 GLN cc_start: 0.7384 (mt0) cc_final: 0.7053 (mt0) REVERT: L 159 ARG cc_start: 0.7473 (ttm170) cc_final: 0.7245 (ttp-170) REVERT: N 29 LYS cc_start: 0.7712 (mttt) cc_final: 0.7376 (mtpp) REVERT: N 34 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7693 (mt-10) REVERT: N 48 SER cc_start: 0.8950 (t) cc_final: 0.8683 (m) REVERT: N 52 VAL cc_start: 0.7999 (t) cc_final: 0.7715 (p) REVERT: N 62 GLN cc_start: 0.6980 (mt0) cc_final: 0.6656 (mm-40) REVERT: N 65 SER cc_start: 0.8342 (m) cc_final: 0.8063 (p) REVERT: N 99 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6682 (mtt-85) REVERT: N 103 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7111 (mm-30) REVERT: N 112 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7833 (tttt) REVERT: N 140 LYS cc_start: 0.8319 (pttt) cc_final: 0.7815 (ttpp) REVERT: O 68 LYS cc_start: 0.7084 (pttm) cc_final: 0.6490 (mmmt) REVERT: O 73 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6932 (mt-10) REVERT: O 80 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6973 (ttm) REVERT: O 81 MET cc_start: 0.7775 (tpp) cc_final: 0.6987 (tpp) REVERT: O 121 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8125 (mt) REVERT: O 148 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7791 (ttpt) REVERT: P 33 MET cc_start: 0.5606 (tpp) cc_final: 0.5381 (ptm) REVERT: P 41 LEU cc_start: 0.7717 (mt) cc_final: 0.7387 (tt) REVERT: P 121 LEU cc_start: 0.8449 (mt) cc_final: 0.8087 (mt) REVERT: Q 13 GLN cc_start: 0.7664 (pt0) cc_final: 0.7281 (pp30) REVERT: Q 31 LYS cc_start: 0.7314 (mmmt) cc_final: 0.6966 (mmtt) REVERT: Q 35 ARG cc_start: 0.5220 (mtp85) cc_final: 0.4642 (mtp85) REVERT: Q 62 LYS cc_start: 0.7588 (mptt) cc_final: 0.7070 (mmmm) REVERT: Q 103 ASP cc_start: 0.7009 (m-30) cc_final: 0.6442 (t70) REVERT: Q 108 LYS cc_start: 0.7620 (tttt) cc_final: 0.7363 (mtmm) REVERT: Q 147 TYR cc_start: 0.7011 (m-80) cc_final: 0.6657 (m-10) REVERT: R 3 ARG cc_start: 0.6253 (mtt-85) cc_final: 0.6033 (mtt-85) REVERT: R 30 ILE cc_start: 0.7580 (tp) cc_final: 0.7379 (pt) REVERT: R 47 ARG cc_start: 0.8010 (ptt90) cc_final: 0.7679 (ttp-170) REVERT: R 69 ILE cc_start: 0.4906 (OUTLIER) cc_final: 0.4624 (mp) REVERT: R 78 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7033 (mtm110) REVERT: R 81 ARG cc_start: 0.6487 (mtt180) cc_final: 0.6242 (mmt180) REVERT: R 82 MET cc_start: 0.5771 (tpt) cc_final: 0.5486 (mtp) REVERT: R 105 MET cc_start: 0.6801 (mmm) cc_final: 0.6339 (mmm) REVERT: S 22 VAL cc_start: 0.6440 (t) cc_final: 0.6205 (p) REVERT: S 44 ASN cc_start: 0.8022 (m-40) cc_final: 0.7562 (m110) REVERT: S 45 LEU cc_start: 0.7917 (mt) cc_final: 0.7650 (tp) REVERT: S 56 LYS cc_start: 0.7152 (mttt) cc_final: 0.6918 (mtmt) REVERT: S 98 LYS cc_start: 0.7219 (tttt) cc_final: 0.6955 (ttmt) REVERT: S 118 LYS cc_start: 0.8751 (mttm) cc_final: 0.8323 (tmtt) REVERT: S 121 LEU cc_start: 0.4889 (mp) cc_final: 0.4292 (mp) REVERT: S 133 VAL cc_start: 0.7953 (t) cc_final: 0.7664 (p) REVERT: S 136 GLN cc_start: 0.7897 (mt0) cc_final: 0.7049 (mt0) REVERT: T 34 HIS cc_start: 0.7556 (t-90) cc_final: 0.6891 (t-90) REVERT: T 37 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7421 (pttp) REVERT: T 45 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7899 (mmmm) REVERT: T 58 LEU cc_start: 0.7399 (tp) cc_final: 0.7148 (mt) REVERT: T 76 HIS cc_start: 0.6558 (t-90) cc_final: 0.6179 (t-90) REVERT: T 107 LYS cc_start: 0.7887 (mttm) cc_final: 0.7327 (mmtt) REVERT: T 125 LEU cc_start: 0.6866 (mt) cc_final: 0.6339 (mp) REVERT: T 136 ARG cc_start: 0.7504 (ttt-90) cc_final: 0.6956 (ttp80) REVERT: T 139 LYS cc_start: 0.6586 (mtpt) cc_final: 0.5566 (mtpp) REVERT: T 143 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.7576 (ptp-170) REVERT: U 155 ASN cc_start: 0.7194 (m-40) cc_final: 0.6759 (t0) REVERT: U 173 LYS cc_start: 0.8026 (mttt) cc_final: 0.7366 (tptt) REVERT: U 195 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7490 (mm-30) REVERT: U 215 ILE cc_start: 0.6547 (mt) cc_final: 0.6180 (tt) REVERT: V 22 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7340 (mtp180) REVERT: V 38 GLN cc_start: 0.7848 (mt0) cc_final: 0.7545 (mt0) REVERT: V 44 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7558 (tpp80) REVERT: V 50 HIS cc_start: 0.6502 (m90) cc_final: 0.6238 (m90) REVERT: V 63 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5394 (tp30) REVERT: V 69 ASN cc_start: 0.7035 (m-40) cc_final: 0.6699 (m110) REVERT: V 70 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7291 (ttp-110) REVERT: V 72 MET cc_start: 0.8830 (mtt) cc_final: 0.8600 (mtt) REVERT: W 23 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7764 (mtp85) REVERT: W 51 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7654 (mt-10) REVERT: W 130 PHE cc_start: 0.7415 (p90) cc_final: 0.7001 (p90) REVERT: X 16 ARG cc_start: 0.7583 (mmm-85) cc_final: 0.7007 (mtt-85) REVERT: X 21 LYS cc_start: 0.7471 (mttt) cc_final: 0.7070 (mtpp) REVERT: X 48 LYS cc_start: 0.7529 (mttt) cc_final: 0.7253 (mtpt) REVERT: X 80 LYS cc_start: 0.7778 (mttt) cc_final: 0.7496 (mtmm) REVERT: Y 15 LYS cc_start: 0.7705 (tptt) cc_final: 0.7366 (tppt) REVERT: Y 37 VAL cc_start: 0.8969 (t) cc_final: 0.8579 (t) REVERT: Y 44 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8267 (tm-30) REVERT: Y 48 LYS cc_start: 0.7947 (pttp) cc_final: 0.7681 (ptmm) REVERT: Y 51 ARG cc_start: 0.8317 (mtt180) cc_final: 0.8046 (mmp80) REVERT: Y 80 ASP cc_start: 0.8569 (p0) cc_final: 0.8238 (p0) REVERT: Y 81 ASN cc_start: 0.8382 (m-40) cc_final: 0.7852 (t0) REVERT: Y 88 PHE cc_start: 0.8416 (m-80) cc_final: 0.7916 (m-10) REVERT: Y 120 LYS cc_start: 0.8304 (mttt) cc_final: 0.7962 (mttt) REVERT: Z 152 GLN cc_start: 0.6401 (mt0) cc_final: 0.6030 (mt0) REVERT: a 22 ARG cc_start: 0.8520 (mmt90) cc_final: 0.8172 (mmm-85) REVERT: a 45 VAL cc_start: 0.8082 (m) cc_final: 0.7731 (p) REVERT: a 54 ARG cc_start: 0.8707 (ttt90) cc_final: 0.8349 (tpp80) REVERT: a 58 VAL cc_start: 0.7831 (t) cc_final: 0.7455 (m) REVERT: a 59 TYR cc_start: 0.7626 (m-80) cc_final: 0.7056 (m-80) REVERT: a 66 LYS cc_start: 0.8194 (mttp) cc_final: 0.7748 (mmtt) REVERT: b 7 HIS cc_start: 0.8274 (m90) cc_final: 0.7731 (m-70) REVERT: b 23 ILE cc_start: 0.8903 (mt) cc_final: 0.8673 (pt) REVERT: b 33 VAL cc_start: 0.7710 (t) cc_final: 0.7508 (t) REVERT: b 38 CYS cc_start: 0.5241 (m) cc_final: 0.4640 (t) REVERT: b 60 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7736 (ttt) REVERT: b 76 SER cc_start: 0.6731 (p) cc_final: 0.6144 (m) REVERT: b 77 PHE cc_start: 0.8470 (p90) cc_final: 0.7893 (p90) REVERT: c 11 LYS cc_start: 0.6734 (tttt) cc_final: 0.6456 (ptmt) REVERT: c 30 MET cc_start: 0.4819 (ttp) cc_final: 0.4383 (ttm) REVERT: c 51 GLU cc_start: 0.8408 (pt0) cc_final: 0.7619 (mt-10) REVERT: c 61 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6345 (tt0) REVERT: d 31 LYS cc_start: 0.7768 (ttmt) cc_final: 0.7427 (tttm) REVERT: d 32 TYR cc_start: 0.8468 (m-80) cc_final: 0.8042 (m-80) REVERT: e 24 LYS cc_start: 0.7022 (ptmt) cc_final: 0.6688 (pttt) REVERT: e 27 LYS cc_start: 0.6865 (pttt) cc_final: 0.6633 (pttt) REVERT: e 35 LYS cc_start: 0.8109 (tttt) cc_final: 0.7603 (ttmt) REVERT: e 39 GLN cc_start: 0.8004 (mt0) cc_final: 0.7344 (mt0) REVERT: m 15 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7399 (tmt) REVERT: m 20 LYS cc_start: 0.7851 (tttp) cc_final: 0.7571 (tttp) REVERT: m 28 GLN cc_start: 0.7877 (mt0) cc_final: 0.7629 (mt0) outliers start: 129 outliers final: 41 residues processed: 1608 average time/residue: 0.8428 time to fit residues: 2156.9940 Evaluate side-chains 1185 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1124 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 132 ASP Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 47 ARG Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 39 ARG Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain L residue 9 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 ASP Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 127 GLU Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 44 ARG Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 57 ILE Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 60 MET Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain m residue 12 ARG Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 16 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 491 optimal weight: 0.3980 chunk 441 optimal weight: 7.9990 chunk 244 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 456 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 339 optimal weight: 0.4980 chunk 528 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS B 180 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS D 127 HIS E 209 HIS E 216 ASN E 251 ASN E 253 GLN F 17 ASN F 39 HIS F 71 ASN F 136 ASN G 13 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 139 HIS ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN J 133 HIS J 155 HIS K 68 ASN K 70 GLN N 105 ASN N 134 GLN N 142 GLN O 48 HIS O 118 GLN P 71 ASN R 31 ASN T 34 HIS V 38 GLN V 69 ASN W 56 HIS X 61 GLN Y 116 ASN Z 116 HIS b 47 HIS b 49 GLN b 63 GLN d 6 ASN m 3 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 73591 Z= 0.191 Angle : 0.699 20.425 107052 Z= 0.361 Chirality : 0.041 0.414 13312 Planarity : 0.005 0.058 7623 Dihedral : 23.333 179.810 29930 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 1.26 % Allowed : 5.51 % Favored : 93.23 % Rotamer: Outliers : 4.60 % Allowed : 14.92 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4283 helix: -0.42 (0.13), residues: 1418 sheet: -1.68 (0.18), residues: 704 loop : -1.99 (0.12), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP m 17 HIS 0.008 0.001 HIS P 133 PHE 0.024 0.002 PHE B 100 TYR 0.026 0.002 TYR P 22 ARG 0.020 0.001 ARG J 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1225 time to evaluate : 3.728 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: A 32 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6879 (mt-10) REVERT: A 36 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7778 (mtp-110) REVERT: A 48 HIS cc_start: 0.7269 (m-70) cc_final: 0.6946 (m90) REVERT: A 51 ASN cc_start: 0.7246 (m-40) cc_final: 0.6532 (t0) REVERT: A 118 MET cc_start: 0.8237 (mtp) cc_final: 0.7794 (mpp) REVERT: A 137 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7191 (mt-10) REVERT: A 200 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7297 (ttm) REVERT: A 203 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7729 (mmm) REVERT: A 206 TRP cc_start: 0.7350 (t60) cc_final: 0.7060 (t60) REVERT: A 208 ASP cc_start: 0.8490 (m-30) cc_final: 0.7894 (t0) REVERT: B 50 LYS cc_start: 0.7323 (mmtm) cc_final: 0.7018 (mmmt) REVERT: B 99 ASP cc_start: 0.8157 (t0) cc_final: 0.7870 (t0) REVERT: B 105 MET cc_start: 0.8829 (ttm) cc_final: 0.8339 (tpp) REVERT: B 111 CYS cc_start: 0.8109 (t) cc_final: 0.7722 (m) REVERT: B 115 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7182 (mmt180) REVERT: B 175 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6723 (mm-30) REVERT: B 177 SER cc_start: 0.6800 (t) cc_final: 0.6496 (p) REVERT: B 179 CYS cc_start: 0.7526 (m) cc_final: 0.6060 (p) REVERT: B 198 GLU cc_start: 0.8445 (tt0) cc_final: 0.8193 (pt0) REVERT: B 224 ASP cc_start: 0.7480 (t0) cc_final: 0.7093 (t0) REVERT: C 52 ILE cc_start: 0.8066 (mt) cc_final: 0.7497 (mm) REVERT: C 53 SER cc_start: 0.7414 (t) cc_final: 0.6912 (p) REVERT: C 67 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7336 (pm20) REVERT: C 76 GLN cc_start: 0.7635 (mm110) cc_final: 0.7313 (mm110) REVERT: C 89 MET cc_start: 0.7442 (mmt) cc_final: 0.6868 (mmm) REVERT: C 91 ILE cc_start: 0.7786 (mt) cc_final: 0.7585 (mm) REVERT: C 95 GLN cc_start: 0.8589 (mt0) cc_final: 0.8243 (mt0) REVERT: C 134 ARG cc_start: 0.6934 (mtt180) cc_final: 0.6577 (mtm-85) REVERT: C 151 TYR cc_start: 0.8001 (m-80) cc_final: 0.7661 (m-80) REVERT: C 169 ARG cc_start: 0.8788 (ptp90) cc_final: 0.8234 (ptt180) REVERT: C 194 LYS cc_start: 0.7282 (mttt) cc_final: 0.6960 (mmtt) REVERT: C 203 ASP cc_start: 0.6990 (m-30) cc_final: 0.6571 (m-30) REVERT: C 209 LYS cc_start: 0.8117 (tttt) cc_final: 0.7735 (ttpt) REVERT: D 7 THR cc_start: 0.7501 (p) cc_final: 0.7298 (p) REVERT: D 15 LYS cc_start: 0.7450 (ttpt) cc_final: 0.7148 (tppt) REVERT: D 20 GLN cc_start: 0.7596 (tp40) cc_final: 0.6728 (mp10) REVERT: D 25 GLU cc_start: 0.7538 (tp30) cc_final: 0.6699 (mp0) REVERT: D 28 SER cc_start: 0.7274 (t) cc_final: 0.6910 (m) REVERT: D 40 GLU cc_start: 0.6152 (tm-30) cc_final: 0.5666 (tm-30) REVERT: D 105 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: D 113 LYS cc_start: 0.7137 (tptt) cc_final: 0.6792 (tptt) REVERT: D 126 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7530 (tpp-160) REVERT: D 137 GLU cc_start: 0.7223 (pt0) cc_final: 0.6528 (pt0) REVERT: D 141 SER cc_start: 0.7044 (m) cc_final: 0.6593 (t) REVERT: D 150 LYS cc_start: 0.7260 (ttpp) cc_final: 0.6839 (ttpp) REVERT: D 153 LYS cc_start: 0.6899 (ttmt) cc_final: 0.6508 (mttp) REVERT: D 180 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7434 (tmm160) REVERT: D 187 ARG cc_start: 0.6943 (mmm-85) cc_final: 0.6525 (mmm-85) REVERT: D 189 LYS cc_start: 0.7468 (ttmt) cc_final: 0.6994 (mtmm) REVERT: E 7 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7036 (mtmt) REVERT: E 50 ASN cc_start: 0.8375 (m-40) cc_final: 0.8109 (m110) REVERT: E 51 ARG cc_start: 0.7836 (mmt-90) cc_final: 0.6994 (mpt180) REVERT: E 62 MET cc_start: 0.8130 (mtt) cc_final: 0.7597 (mmt) REVERT: E 104 ASP cc_start: 0.7239 (t70) cc_final: 0.6994 (t0) REVERT: E 128 LYS cc_start: 0.7767 (ptmt) cc_final: 0.7458 (ptmt) REVERT: E 155 LYS cc_start: 0.7510 (tttt) cc_final: 0.7061 (mmtt) REVERT: E 165 ASN cc_start: 0.8102 (m110) cc_final: 0.7592 (m-40) REVERT: E 171 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7502 (t0) REVERT: E 174 LYS cc_start: 0.7713 (mtpp) cc_final: 0.7278 (mmmm) REVERT: E 176 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7536 (pm20) REVERT: E 180 MET cc_start: 0.8457 (ttm) cc_final: 0.8066 (mtm) REVERT: E 199 GLU cc_start: 0.7661 (mt-10) cc_final: 0.6978 (mp0) REVERT: E 209 HIS cc_start: 0.7116 (m-70) cc_final: 0.6806 (m90) REVERT: E 217 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: E 242 LYS cc_start: 0.8416 (mttt) cc_final: 0.7729 (mmtm) REVERT: E 260 GLN cc_start: 0.8044 (pt0) cc_final: 0.7799 (pt0) REVERT: F 47 LYS cc_start: 0.7160 (mttt) cc_final: 0.6722 (mtmm) REVERT: F 93 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7228 (p0) REVERT: F 115 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.6449 (mmt-90) REVERT: F 124 ARG cc_start: 0.7183 (mtm-85) cc_final: 0.6735 (mtp180) REVERT: F 164 GLU cc_start: 0.7229 (tp30) cc_final: 0.6984 (mm-30) REVERT: F 180 LYS cc_start: 0.6905 (mmmt) cc_final: 0.6419 (mmmt) REVERT: G 7 ASN cc_start: 0.8131 (t0) cc_final: 0.7791 (t0) REVERT: G 15 THR cc_start: 0.7504 (p) cc_final: 0.7259 (p) REVERT: G 22 LYS cc_start: 0.8096 (mptt) cc_final: 0.7791 (mptt) REVERT: G 25 LEU cc_start: 0.7985 (tp) cc_final: 0.7770 (mt) REVERT: G 30 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7307 (mtpt) REVERT: G 44 GLU cc_start: 0.8474 (pt0) cc_final: 0.7926 (tt0) REVERT: G 57 ASP cc_start: 0.8261 (p0) cc_final: 0.7945 (p0) REVERT: G 79 LYS cc_start: 0.7968 (tttt) cc_final: 0.7375 (ttmt) REVERT: G 86 GLN cc_start: 0.7852 (mt0) cc_final: 0.7367 (mt0) REVERT: G 91 GLU cc_start: 0.8119 (tt0) cc_final: 0.7667 (tt0) REVERT: G 161 GLN cc_start: 0.8936 (pt0) cc_final: 0.8445 (tt0) REVERT: G 186 ARG cc_start: 0.7769 (mtp-110) cc_final: 0.7542 (mtp180) REVERT: G 194 ARG cc_start: 0.8483 (ttm110) cc_final: 0.8100 (ptp90) REVERT: G 202 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7462 (mt-10) REVERT: G 211 SER cc_start: 0.7701 (t) cc_final: 0.7339 (m) REVERT: H 57 GLN cc_start: 0.6965 (pt0) cc_final: 0.6353 (tm-30) REVERT: H 86 GLU cc_start: 0.8270 (tt0) cc_final: 0.8052 (tt0) REVERT: H 89 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7880 (pttm) REVERT: H 90 LYS cc_start: 0.7918 (tptt) cc_final: 0.7606 (tmtt) REVERT: H 91 LEU cc_start: 0.7342 (mt) cc_final: 0.6970 (mt) REVERT: H 149 ASP cc_start: 0.4862 (p0) cc_final: 0.4660 (p0) REVERT: H 161 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8432 (ttp80) REVERT: H 169 GLU cc_start: 0.7849 (tp30) cc_final: 0.7638 (mp0) REVERT: H 185 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7813 (mttp) REVERT: I 8 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6587 (mtm110) REVERT: I 22 GLN cc_start: 0.8307 (mt0) cc_final: 0.7859 (pt0) REVERT: I 35 MET cc_start: 0.7897 (mtt) cc_final: 0.7460 (mmp) REVERT: I 47 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6914 (tmt170) REVERT: I 52 ASN cc_start: 0.7844 (m-40) cc_final: 0.7279 (m110) REVERT: I 55 TYR cc_start: 0.7585 (m-80) cc_final: 0.6904 (m-80) REVERT: I 61 ASP cc_start: 0.8501 (t70) cc_final: 0.8051 (t0) REVERT: I 65 TYR cc_start: 0.8782 (m-80) cc_final: 0.7756 (m-80) REVERT: I 77 ARG cc_start: 0.7739 (ttt180) cc_final: 0.7249 (ttp80) REVERT: I 88 ASN cc_start: 0.7741 (m-40) cc_final: 0.7385 (m110) REVERT: I 92 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7116 (mtm110) REVERT: I 114 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7893 (ttm-80) REVERT: I 115 SER cc_start: 0.8778 (t) cc_final: 0.8313 (p) REVERT: I 190 GLU cc_start: 0.6914 (tp30) cc_final: 0.6662 (tp30) REVERT: J 8 TYR cc_start: 0.8074 (p90) cc_final: 0.7596 (p90) REVERT: J 13 ARG cc_start: 0.7898 (ptm160) cc_final: 0.7598 (ptm-80) REVERT: J 41 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7085 (mt-10) REVERT: J 46 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: J 47 TYR cc_start: 0.7868 (t80) cc_final: 0.7663 (t80) REVERT: J 68 ARG cc_start: 0.7792 (ttt-90) cc_final: 0.7559 (tmt-80) REVERT: J 86 LEU cc_start: 0.8010 (tp) cc_final: 0.7568 (tp) REVERT: J 90 GLU cc_start: 0.5290 (pm20) cc_final: 0.5031 (pm20) REVERT: J 120 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6879 (ptmt) REVERT: J 132 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7623 (mtp85) REVERT: J 147 MET cc_start: 0.7792 (mtt) cc_final: 0.7584 (mmm) REVERT: K 33 LYS cc_start: 0.6198 (tptp) cc_final: 0.5799 (tptm) REVERT: K 57 LEU cc_start: 0.6392 (tp) cc_final: 0.6178 (tp) REVERT: K 62 PHE cc_start: 0.5436 (m-80) cc_final: 0.5117 (m-80) REVERT: L 19 SER cc_start: 0.8125 (m) cc_final: 0.7856 (p) REVERT: L 20 SER cc_start: 0.8937 (m) cc_final: 0.8533 (p) REVERT: L 37 TRP cc_start: 0.8425 (p-90) cc_final: 0.7956 (p90) REVERT: L 49 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.5656 (tp) REVERT: L 54 LYS cc_start: 0.8209 (tptt) cc_final: 0.7852 (ttmt) REVERT: L 58 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8600 (ttpp) REVERT: L 83 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7712 (ttpp) REVERT: L 99 TYR cc_start: 0.7810 (m-80) cc_final: 0.6666 (m-80) REVERT: L 125 ILE cc_start: 0.8019 (mt) cc_final: 0.7751 (mt) REVERT: L 141 ASN cc_start: 0.7640 (t0) cc_final: 0.7438 (t0) REVERT: L 147 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8011 (mmmt) REVERT: N 11 MET cc_start: 0.7418 (ttp) cc_final: 0.6571 (ptm) REVERT: N 19 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7710 (ptm-80) REVERT: N 29 LYS cc_start: 0.7647 (mttt) cc_final: 0.7198 (mtpp) REVERT: N 34 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7579 (mt-10) REVERT: N 103 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6861 (mm-30) REVERT: N 112 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7689 (tttt) REVERT: N 140 LYS cc_start: 0.8387 (pttt) cc_final: 0.7823 (ttpp) REVERT: O 41 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8478 (p) REVERT: O 52 LEU cc_start: 0.8768 (tt) cc_final: 0.8564 (tt) REVERT: O 73 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6919 (mt-10) REVERT: O 80 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7013 (ttm) REVERT: O 81 MET cc_start: 0.7096 (tpp) cc_final: 0.6390 (tpp) REVERT: O 85 ASP cc_start: 0.7706 (m-30) cc_final: 0.7104 (m-30) REVERT: O 98 VAL cc_start: 0.8651 (t) cc_final: 0.8442 (p) REVERT: O 149 SER cc_start: 0.8136 (p) cc_final: 0.7783 (p) REVERT: P 25 VAL cc_start: 0.6416 (m) cc_final: 0.5402 (m) REVERT: P 27 LEU cc_start: 0.6647 (mt) cc_final: 0.6289 (mm) REVERT: P 29 LYS cc_start: 0.7189 (tptp) cc_final: 0.6781 (ptpp) REVERT: P 35 MET cc_start: 0.5636 (mmp) cc_final: 0.5411 (mmp) REVERT: P 41 LEU cc_start: 0.7752 (mt) cc_final: 0.7489 (tt) REVERT: P 51 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6796 (mt0) REVERT: Q 9 LYS cc_start: 0.7366 (mtpp) cc_final: 0.7050 (mmtm) REVERT: Q 103 ASP cc_start: 0.7199 (m-30) cc_final: 0.6390 (t70) REVERT: R 81 ARG cc_start: 0.6984 (mtt180) cc_final: 0.6505 (mmt180) REVERT: S 44 ASN cc_start: 0.8078 (m-40) cc_final: 0.7654 (m110) REVERT: S 114 GLU cc_start: 0.7710 (mp0) cc_final: 0.7465 (mp0) REVERT: S 121 LEU cc_start: 0.4874 (mp) cc_final: 0.4529 (mp) REVERT: S 136 GLN cc_start: 0.7706 (mt0) cc_final: 0.6977 (mt0) REVERT: T 34 HIS cc_start: 0.6935 (t70) cc_final: 0.6629 (t-90) REVERT: T 37 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7387 (pttp) REVERT: T 41 PHE cc_start: 0.7321 (t80) cc_final: 0.7091 (t80) REVERT: T 45 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8130 (mmmm) REVERT: T 47 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7270 (mm) REVERT: T 51 LYS cc_start: 0.3344 (OUTLIER) cc_final: 0.2443 (ttpt) REVERT: T 107 LYS cc_start: 0.7704 (mttm) cc_final: 0.7390 (mtpp) REVERT: T 118 GLN cc_start: 0.7874 (mt0) cc_final: 0.7531 (mm-40) REVERT: T 123 MET cc_start: 0.7500 (ptp) cc_final: 0.7257 (pmm) REVERT: T 136 ARG cc_start: 0.7380 (ttt-90) cc_final: 0.6752 (ttp80) REVERT: T 139 LYS cc_start: 0.6451 (mtpt) cc_final: 0.6013 (ptpp) REVERT: T 143 ARG cc_start: 0.7776 (ptm-80) cc_final: 0.7451 (ptp-110) REVERT: T 144 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7863 (tm-30) REVERT: U 155 ASN cc_start: 0.7087 (m-40) cc_final: 0.6471 (p0) REVERT: U 176 ARG cc_start: 0.7202 (mtt180) cc_final: 0.5891 (mtm-85) REVERT: U 195 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7541 (mm-30) REVERT: U 215 ILE cc_start: 0.6512 (mt) cc_final: 0.6260 (tt) REVERT: V 22 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7315 (ptp-110) REVERT: V 44 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7578 (ttm170) REVERT: V 50 HIS cc_start: 0.6321 (m90) cc_final: 0.5802 (m90) REVERT: V 63 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5102 (tp30) REVERT: V 70 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7559 (ttp-110) REVERT: V 72 MET cc_start: 0.8787 (mtt) cc_final: 0.8406 (mtt) REVERT: W 82 GLN cc_start: 0.7315 (mt0) cc_final: 0.6828 (mt0) REVERT: W 117 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7967 (tpp80) REVERT: X 16 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.6900 (mtt-85) REVERT: X 21 LYS cc_start: 0.7611 (mttt) cc_final: 0.7149 (mtpm) REVERT: X 48 LYS cc_start: 0.7614 (mttt) cc_final: 0.7312 (mtpt) REVERT: X 58 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7274 (mt-10) REVERT: X 80 LYS cc_start: 0.7849 (mttt) cc_final: 0.7574 (mtmm) REVERT: X 95 ASP cc_start: 0.7308 (m-30) cc_final: 0.6919 (m-30) REVERT: X 114 ASP cc_start: 0.3551 (OUTLIER) cc_final: 0.3221 (t0) REVERT: Y 15 LYS cc_start: 0.7674 (tptt) cc_final: 0.7302 (tppt) REVERT: Y 37 VAL cc_start: 0.8908 (t) cc_final: 0.8683 (t) REVERT: Y 51 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7870 (mmp80) REVERT: Y 54 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6627 (p0) REVERT: Y 80 ASP cc_start: 0.8377 (p0) cc_final: 0.8062 (p0) REVERT: Y 81 ASN cc_start: 0.8258 (m-40) cc_final: 0.7917 (t0) REVERT: Y 91 ARG cc_start: 0.7595 (mtp85) cc_final: 0.7263 (ttt-90) REVERT: Z 102 LYS cc_start: 0.8042 (mptt) cc_final: 0.7715 (pttt) REVERT: Z 152 GLN cc_start: 0.6102 (mt0) cc_final: 0.5766 (mt0) REVERT: a 45 VAL cc_start: 0.7908 (m) cc_final: 0.7671 (p) REVERT: a 55 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8030 (tm-30) REVERT: a 62 TYR cc_start: 0.7731 (t80) cc_final: 0.7378 (t80) REVERT: a 71 GLN cc_start: 0.7781 (mm110) cc_final: 0.7413 (mm-40) REVERT: b 7 HIS cc_start: 0.8185 (m90) cc_final: 0.7935 (m-70) REVERT: b 16 LYS cc_start: 0.7068 (mttt) cc_final: 0.6807 (mtmt) REVERT: b 23 ILE cc_start: 0.8930 (mt) cc_final: 0.8607 (pt) REVERT: b 38 CYS cc_start: 0.4757 (m) cc_final: 0.4457 (t) REVERT: b 71 LEU cc_start: 0.8067 (mp) cc_final: 0.7843 (mm) REVERT: c 11 LYS cc_start: 0.6831 (tttt) cc_final: 0.6485 (ptmt) REVERT: c 51 GLU cc_start: 0.8506 (pt0) cc_final: 0.7760 (tt0) REVERT: c 61 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5651 (tt0) REVERT: d 18 GLN cc_start: 0.7999 (pt0) cc_final: 0.7366 (pt0) REVERT: d 23 PHE cc_start: 0.6694 (m-10) cc_final: 0.6425 (m-10) REVERT: d 25 ARG cc_start: 0.6010 (mtt-85) cc_final: 0.5602 (mpp80) REVERT: d 32 TYR cc_start: 0.8384 (m-80) cc_final: 0.8073 (m-80) REVERT: d 35 MET cc_start: 0.6777 (mmm) cc_final: 0.6572 (tpp) REVERT: e 27 LYS cc_start: 0.7039 (pttt) cc_final: 0.6263 (mmmt) REVERT: e 39 GLN cc_start: 0.7835 (mt0) cc_final: 0.7173 (tp40) REVERT: m 20 LYS cc_start: 0.7787 (tttp) cc_final: 0.7470 (ttmm) REVERT: m 29 ARG cc_start: 0.8440 (ttp-170) cc_final: 0.8002 (mtm180) outliers start: 166 outliers final: 90 residues processed: 1318 average time/residue: 0.7500 time to fit residues: 1591.7719 Evaluate side-chains 1177 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1069 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 47 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 120 LYS Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 9 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 80 MET Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 22 TYR Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 8 TYR Chi-restraints excluded: chain T residue 47 ILE Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 142 GLN Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain U residue 146 ILE Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 52 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 60 LYS Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain Y residue 29 ILE Chi-restraints excluded: chain Y residue 54 ASP Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain e residue 31 THR Chi-restraints excluded: chain m residue 12 ARG Chi-restraints excluded: chain m residue 27 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 293 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 chunk 439 optimal weight: 9.9990 chunk 359 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 529 optimal weight: 0.9980 chunk 571 optimal weight: 0.4980 chunk 471 optimal weight: 4.9990 chunk 525 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 424 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS E 151 HIS ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 45 GLN F 67 HIS F 71 ASN G 59 GLN G 146 ASN G 215 HIS H 100 GLN I 64 ASN J 110 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN X 61 GLN X 63 ASN ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 ASN b 63 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 73591 Z= 0.169 Angle : 0.602 13.419 107052 Z= 0.312 Chirality : 0.037 0.287 13312 Planarity : 0.004 0.057 7623 Dihedral : 23.166 179.944 29851 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 1.10 % Allowed : 5.98 % Favored : 92.93 % Rotamer: Outliers : 4.91 % Allowed : 17.41 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4283 helix: 0.16 (0.13), residues: 1436 sheet: -1.31 (0.18), residues: 684 loop : -1.83 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 69 HIS 0.008 0.001 HIS G 215 PHE 0.033 0.002 PHE b 77 TYR 0.023 0.002 TYR V 12 ARG 0.007 0.001 ARG H 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1167 time to evaluate : 3.810 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: A 19 MET cc_start: 0.8850 (mtm) cc_final: 0.8644 (mtm) REVERT: A 118 MET cc_start: 0.8303 (mtp) cc_final: 0.7966 (mpp) REVERT: A 137 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7046 (mt-10) REVERT: A 170 GLU cc_start: 0.7408 (tt0) cc_final: 0.7112 (pm20) REVERT: A 175 MET cc_start: 0.8200 (mmp) cc_final: 0.7976 (tpp) REVERT: A 182 GLU cc_start: 0.8095 (tp30) cc_final: 0.7872 (tp30) REVERT: A 203 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7631 (tpt) REVERT: A 206 TRP cc_start: 0.7291 (t60) cc_final: 0.6990 (t60) REVERT: B 46 THR cc_start: 0.7761 (p) cc_final: 0.7437 (p) REVERT: B 66 TYR cc_start: 0.7875 (m-80) cc_final: 0.7637 (m-80) REVERT: B 99 ASP cc_start: 0.8051 (t0) cc_final: 0.7732 (t0) REVERT: B 105 MET cc_start: 0.8535 (ttm) cc_final: 0.8186 (tpp) REVERT: B 111 CYS cc_start: 0.8163 (t) cc_final: 0.7508 (m) REVERT: B 115 ARG cc_start: 0.8003 (mtt90) cc_final: 0.6906 (mmt180) REVERT: B 139 CYS cc_start: 0.8429 (t) cc_final: 0.8138 (p) REVERT: B 177 SER cc_start: 0.6869 (t) cc_final: 0.6592 (p) REVERT: B 198 GLU cc_start: 0.8424 (tt0) cc_final: 0.8180 (pt0) REVERT: B 224 ASP cc_start: 0.7649 (t0) cc_final: 0.7201 (t0) REVERT: B 227 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8229 (tmtt) REVERT: B 229 MET cc_start: 0.8866 (mmp) cc_final: 0.8455 (mmm) REVERT: C 52 ILE cc_start: 0.8129 (mt) cc_final: 0.7706 (mm) REVERT: C 53 SER cc_start: 0.7459 (t) cc_final: 0.7000 (p) REVERT: C 67 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7055 (pm20) REVERT: C 76 GLN cc_start: 0.7799 (mm110) cc_final: 0.7393 (mm110) REVERT: C 95 GLN cc_start: 0.8550 (mt0) cc_final: 0.8266 (mt0) REVERT: C 134 ARG cc_start: 0.6768 (mtt180) cc_final: 0.6454 (mtm-85) REVERT: C 158 GLU cc_start: 0.7190 (pm20) cc_final: 0.6934 (pm20) REVERT: C 209 LYS cc_start: 0.8127 (tttt) cc_final: 0.7474 (ttpt) REVERT: D 7 THR cc_start: 0.7605 (p) cc_final: 0.7054 (p) REVERT: D 15 LYS cc_start: 0.7397 (ttpt) cc_final: 0.7086 (tppt) REVERT: D 20 GLN cc_start: 0.7645 (tp40) cc_final: 0.6775 (mp10) REVERT: D 25 GLU cc_start: 0.7661 (tp30) cc_final: 0.7216 (tp30) REVERT: D 28 SER cc_start: 0.7485 (t) cc_final: 0.7126 (m) REVERT: D 58 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7706 (mmm160) REVERT: D 96 ARG cc_start: 0.7304 (ptp90) cc_final: 0.6874 (ptm160) REVERT: D 105 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7279 (mt-10) REVERT: D 121 CYS cc_start: 0.8134 (m) cc_final: 0.7607 (p) REVERT: D 126 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7476 (tpp-160) REVERT: D 141 SER cc_start: 0.7214 (m) cc_final: 0.6691 (t) REVERT: D 150 LYS cc_start: 0.7235 (ttpp) cc_final: 0.6807 (ttpp) REVERT: D 153 LYS cc_start: 0.6907 (ttmt) cc_final: 0.6640 (mtmt) REVERT: D 187 ARG cc_start: 0.7014 (mmm-85) cc_final: 0.6378 (mmm-85) REVERT: D 189 LYS cc_start: 0.7452 (ttmt) cc_final: 0.6916 (mtmm) REVERT: E 7 LYS cc_start: 0.7973 (mmtt) cc_final: 0.6979 (mttt) REVERT: E 51 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.7197 (mpt180) REVERT: E 62 MET cc_start: 0.8235 (mtt) cc_final: 0.7525 (mmt) REVERT: E 104 ASP cc_start: 0.7212 (t70) cc_final: 0.6914 (t70) REVERT: E 151 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7524 (t-90) REVERT: E 155 LYS cc_start: 0.7420 (tttt) cc_final: 0.6972 (mmtt) REVERT: E 159 CYS cc_start: 0.8904 (p) cc_final: 0.8286 (p) REVERT: E 165 ASN cc_start: 0.7978 (m110) cc_final: 0.7439 (m-40) REVERT: E 171 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7460 (t0) REVERT: E 174 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7360 (mmmm) REVERT: E 176 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7714 (pm20) REVERT: E 180 MET cc_start: 0.8588 (ttm) cc_final: 0.8165 (mtm) REVERT: E 199 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7115 (mp0) REVERT: E 209 HIS cc_start: 0.7114 (m-70) cc_final: 0.6707 (m170) REVERT: E 217 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: E 242 LYS cc_start: 0.8454 (mttt) cc_final: 0.7883 (mmtm) REVERT: E 247 SER cc_start: 0.7310 (t) cc_final: 0.6851 (m) REVERT: E 250 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7577 (mm-30) REVERT: E 260 GLN cc_start: 0.7994 (pt0) cc_final: 0.7764 (pt0) REVERT: F 43 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.7153 (mmm-85) REVERT: F 47 LYS cc_start: 0.7298 (mttt) cc_final: 0.6816 (mtmm) REVERT: F 115 ARG cc_start: 0.7811 (mmt-90) cc_final: 0.7418 (mmt-90) REVERT: F 180 LYS cc_start: 0.6938 (mmmt) cc_final: 0.6653 (mmmm) REVERT: G 7 ASN cc_start: 0.8049 (t0) cc_final: 0.7714 (t0) REVERT: G 12 MET cc_start: 0.7586 (mmt) cc_final: 0.7152 (mmt) REVERT: G 23 LYS cc_start: 0.6879 (mttt) cc_final: 0.6592 (mppt) REVERT: G 30 LYS cc_start: 0.7495 (mmmt) cc_final: 0.7142 (mtpt) REVERT: G 44 GLU cc_start: 0.8503 (pt0) cc_final: 0.7672 (tt0) REVERT: G 57 ASP cc_start: 0.8502 (p0) cc_final: 0.8284 (p0) REVERT: G 79 LYS cc_start: 0.8097 (tttt) cc_final: 0.7513 (ttmt) REVERT: G 86 GLN cc_start: 0.7818 (mt0) cc_final: 0.7407 (mt0) REVERT: G 91 GLU cc_start: 0.8157 (tt0) cc_final: 0.7770 (tt0) REVERT: G 97 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7361 (p) REVERT: G 119 GLU cc_start: 0.7977 (mm-30) cc_final: 0.6720 (tp30) REVERT: G 125 THR cc_start: 0.8049 (m) cc_final: 0.7834 (p) REVERT: G 161 GLN cc_start: 0.8901 (pt0) cc_final: 0.8466 (tt0) REVERT: G 186 ARG cc_start: 0.7858 (mtp-110) cc_final: 0.7535 (mtp180) REVERT: G 191 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7652 (ttmm) REVERT: G 194 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8074 (ptp90) REVERT: G 202 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7545 (mt-10) REVERT: G 211 SER cc_start: 0.7449 (t) cc_final: 0.7046 (m) REVERT: H 89 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7908 (pttm) REVERT: H 90 LYS cc_start: 0.7985 (tptt) cc_final: 0.7600 (tmtt) REVERT: H 91 LEU cc_start: 0.7341 (mt) cc_final: 0.6963 (mt) REVERT: H 161 ARG cc_start: 0.8845 (mtp-110) cc_final: 0.8325 (ttp80) REVERT: I 22 GLN cc_start: 0.8342 (mt0) cc_final: 0.7691 (pt0) REVERT: I 35 MET cc_start: 0.7909 (mtt) cc_final: 0.7467 (mmp) REVERT: I 52 ASN cc_start: 0.8006 (m-40) cc_final: 0.7698 (m110) REVERT: I 53 MET cc_start: 0.8760 (mmm) cc_final: 0.8369 (mmm) REVERT: I 61 ASP cc_start: 0.8347 (t70) cc_final: 0.8007 (t0) REVERT: I 64 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7305 (t0) REVERT: I 65 TYR cc_start: 0.8822 (m-80) cc_final: 0.7722 (m-80) REVERT: I 77 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7114 (ttp80) REVERT: I 88 ASN cc_start: 0.7810 (m-40) cc_final: 0.7570 (m110) REVERT: I 92 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7201 (mtm110) REVERT: I 115 SER cc_start: 0.8831 (t) cc_final: 0.8346 (p) REVERT: I 154 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8385 (tttp) REVERT: I 162 GLN cc_start: 0.8190 (tt0) cc_final: 0.7934 (tt0) REVERT: I 190 GLU cc_start: 0.6975 (tp30) cc_final: 0.6726 (tp30) REVERT: J 8 TYR cc_start: 0.8434 (p90) cc_final: 0.8205 (p90) REVERT: J 13 ARG cc_start: 0.7911 (ptm160) cc_final: 0.7622 (ptm-80) REVERT: J 26 GLN cc_start: 0.7002 (mp10) cc_final: 0.6559 (mp10) REVERT: J 41 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6965 (mt-10) REVERT: J 46 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7000 (mt0) REVERT: J 47 TYR cc_start: 0.7926 (t80) cc_final: 0.7701 (t80) REVERT: J 88 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7799 (tp30) REVERT: J 116 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6597 (mm) REVERT: J 132 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7500 (mtp85) REVERT: J 147 MET cc_start: 0.7804 (mtt) cc_final: 0.7570 (mmm) REVERT: K 62 PHE cc_start: 0.5441 (m-80) cc_final: 0.5117 (m-80) REVERT: L 9 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: L 19 SER cc_start: 0.7952 (m) cc_final: 0.7746 (p) REVERT: L 20 SER cc_start: 0.8964 (m) cc_final: 0.8598 (p) REVERT: L 37 TRP cc_start: 0.8300 (p-90) cc_final: 0.7802 (p90) REVERT: L 49 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6163 (tp) REVERT: L 54 LYS cc_start: 0.7949 (tptt) cc_final: 0.7683 (ttmt) REVERT: L 57 ASP cc_start: 0.7449 (t0) cc_final: 0.6972 (t70) REVERT: L 58 LYS cc_start: 0.8900 (ttpt) cc_final: 0.8611 (ttpp) REVERT: L 83 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7713 (ttpp) REVERT: L 154 VAL cc_start: 0.7901 (m) cc_final: 0.7627 (p) REVERT: N 11 MET cc_start: 0.7380 (ttp) cc_final: 0.6901 (ptm) REVERT: N 29 LYS cc_start: 0.7516 (mttt) cc_final: 0.7128 (mtpp) REVERT: N 34 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7619 (mt-10) REVERT: N 103 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6990 (mm-30) REVERT: N 106 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7657 (ttp80) REVERT: N 112 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7524 (tttt) REVERT: N 140 LYS cc_start: 0.8348 (pttt) cc_final: 0.7836 (ttpp) REVERT: O 68 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.4895 (mmmt) REVERT: O 73 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6838 (mt-10) REVERT: O 81 MET cc_start: 0.7041 (tpp) cc_final: 0.6410 (tpp) REVERT: O 85 ASP cc_start: 0.7686 (m-30) cc_final: 0.7101 (m-30) REVERT: O 98 VAL cc_start: 0.8736 (t) cc_final: 0.8535 (p) REVERT: O 111 LYS cc_start: 0.6592 (mtmt) cc_final: 0.6065 (mtmm) REVERT: P 25 VAL cc_start: 0.6325 (m) cc_final: 0.6037 (m) REVERT: P 41 LEU cc_start: 0.7808 (mt) cc_final: 0.7524 (tt) REVERT: P 51 GLN cc_start: 0.7232 (tm-30) cc_final: 0.6997 (mt0) REVERT: P 62 MET cc_start: 0.7390 (tmm) cc_final: 0.7085 (tmm) REVERT: P 63 LYS cc_start: 0.7795 (mttt) cc_final: 0.7513 (mttm) REVERT: P 120 TYR cc_start: 0.7579 (m-80) cc_final: 0.6821 (m-10) REVERT: P 128 TYR cc_start: 0.6270 (p90) cc_final: 0.6044 (p90) REVERT: Q 9 LYS cc_start: 0.7459 (mtpp) cc_final: 0.7245 (mmtm) REVERT: Q 103 ASP cc_start: 0.7266 (m-30) cc_final: 0.6466 (t70) REVERT: R 81 ARG cc_start: 0.6965 (mtt180) cc_final: 0.6503 (tpt170) REVERT: R 82 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5534 (mtp) REVERT: S 44 ASN cc_start: 0.7871 (m-40) cc_final: 0.7515 (m110) REVERT: S 115 ARG cc_start: 0.7073 (tmm-80) cc_final: 0.6782 (tmm-80) REVERT: S 121 LEU cc_start: 0.4806 (mp) cc_final: 0.4461 (mp) REVERT: S 136 GLN cc_start: 0.7586 (mt0) cc_final: 0.6856 (mt0) REVERT: T 31 TYR cc_start: 0.7998 (t80) cc_final: 0.7773 (t80) REVERT: T 41 PHE cc_start: 0.7322 (t80) cc_final: 0.6979 (t80) REVERT: T 45 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8209 (mmmm) REVERT: T 47 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7298 (mm) REVERT: T 51 LYS cc_start: 0.3605 (OUTLIER) cc_final: 0.2815 (ttpt) REVERT: T 58 LEU cc_start: 0.7297 (tp) cc_final: 0.6949 (mt) REVERT: T 107 LYS cc_start: 0.7656 (mttm) cc_final: 0.7397 (mtpp) REVERT: T 136 ARG cc_start: 0.7322 (ttt-90) cc_final: 0.6763 (ttp80) REVERT: U 155 ASN cc_start: 0.6919 (m-40) cc_final: 0.6236 (p0) REVERT: U 176 ARG cc_start: 0.7391 (mtt180) cc_final: 0.6974 (mtm-85) REVERT: U 215 ILE cc_start: 0.6525 (mt) cc_final: 0.6244 (tt) REVERT: V 22 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7263 (ptp-110) REVERT: V 44 ARG cc_start: 0.7887 (ttt-90) cc_final: 0.7637 (tpp80) REVERT: V 50 HIS cc_start: 0.6057 (m90) cc_final: 0.5743 (m90) REVERT: V 70 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7336 (ttp-110) REVERT: W 82 GLN cc_start: 0.7402 (mt0) cc_final: 0.6900 (mt0) REVERT: W 117 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7900 (tpp80) REVERT: X 16 ARG cc_start: 0.7420 (mmm-85) cc_final: 0.6993 (mtt-85) REVERT: X 21 LYS cc_start: 0.7544 (mttt) cc_final: 0.7313 (mtpt) REVERT: X 48 LYS cc_start: 0.7633 (mttt) cc_final: 0.7309 (mtpt) REVERT: X 55 LEU cc_start: 0.6860 (tt) cc_final: 0.6611 (tt) REVERT: X 58 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7288 (mt-10) REVERT: X 71 ARG cc_start: 0.6926 (ttm-80) cc_final: 0.6547 (ttt90) REVERT: X 80 LYS cc_start: 0.7914 (mttt) cc_final: 0.7364 (mtmm) REVERT: X 105 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.8020 (t80) REVERT: X 108 SER cc_start: 0.8270 (m) cc_final: 0.8038 (p) REVERT: Y 15 LYS cc_start: 0.7654 (tptt) cc_final: 0.7327 (tppt) REVERT: Y 37 VAL cc_start: 0.8848 (t) cc_final: 0.8628 (t) REVERT: Y 51 ARG cc_start: 0.8431 (mtt180) cc_final: 0.7735 (mmp80) REVERT: Y 80 ASP cc_start: 0.8351 (p0) cc_final: 0.8089 (p0) REVERT: Y 81 ASN cc_start: 0.8276 (m-40) cc_final: 0.7953 (t0) REVERT: Y 122 ARG cc_start: 0.8145 (ttt180) cc_final: 0.7934 (ttt180) REVERT: Z 102 LYS cc_start: 0.8111 (mptt) cc_final: 0.7716 (pttt) REVERT: Z 137 LYS cc_start: 0.8044 (tppt) cc_final: 0.7498 (tppt) REVERT: Z 152 GLN cc_start: 0.6263 (mt0) cc_final: 0.5878 (mt0) REVERT: a 42 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7118 (ttp80) REVERT: a 45 VAL cc_start: 0.7998 (m) cc_final: 0.7673 (p) REVERT: a 52 ASP cc_start: 0.7341 (t0) cc_final: 0.6907 (t70) REVERT: a 55 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8066 (tm-30) REVERT: a 71 GLN cc_start: 0.7795 (mm110) cc_final: 0.7409 (mm-40) REVERT: a 77 CYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7649 (m) REVERT: a 89 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7627 (t) REVERT: b 7 HIS cc_start: 0.8146 (m90) cc_final: 0.7866 (m-70) REVERT: b 23 ILE cc_start: 0.8921 (mt) cc_final: 0.8619 (pt) REVERT: b 71 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7771 (mm) REVERT: c 11 LYS cc_start: 0.7359 (tttt) cc_final: 0.6834 (ptmt) REVERT: c 50 ARG cc_start: 0.7927 (ptt180) cc_final: 0.7170 (ptt180) REVERT: c 51 GLU cc_start: 0.8552 (pt0) cc_final: 0.7931 (tt0) REVERT: d 18 GLN cc_start: 0.7950 (pt0) cc_final: 0.7721 (pt0) REVERT: d 32 TYR cc_start: 0.8410 (m-80) cc_final: 0.8095 (m-80) REVERT: e 27 LYS cc_start: 0.7019 (pttt) cc_final: 0.6297 (mmmt) REVERT: e 39 GLN cc_start: 0.7789 (mt0) cc_final: 0.7199 (mt0) REVERT: m 12 ARG cc_start: 0.8575 (tmm160) cc_final: 0.8348 (ttp-110) REVERT: m 20 LYS cc_start: 0.7771 (tttp) cc_final: 0.7496 (ttmm) REVERT: m 29 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.7895 (mtm110) outliers start: 177 outliers final: 101 residues processed: 1258 average time/residue: 0.7751 time to fit residues: 1600.1072 Evaluate side-chains 1212 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1091 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 151 HIS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain L residue 9 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 56 GLU Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 47 ILE Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain U residue 146 ILE Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 52 ILE Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 60 LYS Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain Y residue 29 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 93 LYS Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 31 MET Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 54 CYS Chi-restraints excluded: chain b residue 71 LEU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 30 MET Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain e residue 31 THR Chi-restraints excluded: chain m residue 27 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 523 optimal weight: 5.9990 chunk 398 optimal weight: 0.9990 chunk 274 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 355 optimal weight: 0.8980 chunk 531 optimal weight: 5.9990 chunk 562 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 chunk 503 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 HIS E 151 HIS ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN G 13 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 ASN H 80 GLN H 85 GLN H 100 GLN I 64 ASN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS T 103 ASN V 38 GLN W 92 ASN X 5 ASN ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 63 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 73591 Z= 0.184 Angle : 0.592 11.601 107052 Z= 0.303 Chirality : 0.036 0.251 13312 Planarity : 0.004 0.059 7623 Dihedral : 23.109 179.964 29828 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 1.05 % Allowed : 5.77 % Favored : 93.18 % Rotamer: Outliers : 5.32 % Allowed : 19.24 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.30 (0.12), residues: 4283 helix: 0.41 (0.14), residues: 1444 sheet: -0.96 (0.18), residues: 700 loop : -1.75 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 67 HIS 0.035 0.001 HIS E 151 PHE 0.024 0.002 PHE Y 92 TYR 0.033 0.002 TYR a 59 ARG 0.006 0.000 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1138 time to evaluate : 3.788 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: A 12 GLN cc_start: 0.5769 (OUTLIER) cc_final: 0.5142 (pp30) REVERT: A 32 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6762 (mt-10) REVERT: A 104 TRP cc_start: 0.7941 (t60) cc_final: 0.7711 (t-100) REVERT: A 137 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7339 (mt-10) REVERT: A 170 GLU cc_start: 0.7389 (tt0) cc_final: 0.7111 (pm20) REVERT: A 206 TRP cc_start: 0.7241 (t60) cc_final: 0.6991 (t60) REVERT: B 92 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6881 (pp30) REVERT: B 99 ASP cc_start: 0.7971 (t0) cc_final: 0.7716 (t0) REVERT: B 105 MET cc_start: 0.8505 (ttm) cc_final: 0.8133 (tpp) REVERT: B 111 CYS cc_start: 0.8221 (t) cc_final: 0.7592 (m) REVERT: B 115 ARG cc_start: 0.7903 (mtt90) cc_final: 0.6960 (mmt180) REVERT: B 177 SER cc_start: 0.6853 (t) cc_final: 0.6576 (p) REVERT: B 198 GLU cc_start: 0.8385 (tt0) cc_final: 0.8170 (pt0) REVERT: B 224 ASP cc_start: 0.7623 (t0) cc_final: 0.7209 (t0) REVERT: B 227 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8253 (tmtt) REVERT: B 229 MET cc_start: 0.8888 (mmp) cc_final: 0.8494 (mmm) REVERT: C 52 ILE cc_start: 0.8371 (mt) cc_final: 0.8018 (mm) REVERT: C 53 SER cc_start: 0.7459 (t) cc_final: 0.7015 (p) REVERT: C 55 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6398 (tp) REVERT: C 67 GLU cc_start: 0.7761 (mt-10) cc_final: 0.6976 (mp0) REVERT: C 76 GLN cc_start: 0.7965 (mm110) cc_final: 0.7628 (mm110) REVERT: C 95 GLN cc_start: 0.8544 (mt0) cc_final: 0.8272 (mt0) REVERT: C 97 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6529 (tt0) REVERT: C 134 ARG cc_start: 0.6786 (mtt180) cc_final: 0.6435 (mtm-85) REVERT: C 143 SER cc_start: 0.7857 (t) cc_final: 0.7420 (p) REVERT: C 151 TYR cc_start: 0.8760 (m-80) cc_final: 0.8243 (m-80) REVERT: C 209 LYS cc_start: 0.8129 (tttt) cc_final: 0.7407 (ttpt) REVERT: D 7 THR cc_start: 0.7311 (p) cc_final: 0.7064 (p) REVERT: D 20 GLN cc_start: 0.7712 (tp40) cc_final: 0.7025 (mt0) REVERT: D 25 GLU cc_start: 0.7643 (tp30) cc_final: 0.7184 (tp30) REVERT: D 28 SER cc_start: 0.7527 (t) cc_final: 0.7106 (m) REVERT: D 58 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7164 (tpm170) REVERT: D 87 GLU cc_start: 0.6526 (pt0) cc_final: 0.6248 (pm20) REVERT: D 96 ARG cc_start: 0.7361 (ptp90) cc_final: 0.6886 (ptm160) REVERT: D 105 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: D 118 ARG cc_start: 0.7028 (tpp-160) cc_final: 0.6791 (tpp80) REVERT: D 121 CYS cc_start: 0.8111 (m) cc_final: 0.7390 (p) REVERT: D 126 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7249 (tpp-160) REVERT: D 134 LYS cc_start: 0.7141 (tptt) cc_final: 0.6729 (mtpp) REVERT: D 141 SER cc_start: 0.7263 (m) cc_final: 0.6608 (t) REVERT: D 150 LYS cc_start: 0.7266 (ttpp) cc_final: 0.6873 (ttpp) REVERT: D 153 LYS cc_start: 0.6934 (ttmt) cc_final: 0.6466 (mtmt) REVERT: D 154 PHE cc_start: 0.6701 (m-80) cc_final: 0.6062 (m-80) REVERT: D 172 GLN cc_start: 0.8006 (pt0) cc_final: 0.7650 (mp10) REVERT: D 189 LYS cc_start: 0.7557 (ttmt) cc_final: 0.6895 (mtmm) REVERT: E 7 LYS cc_start: 0.8001 (mmtt) cc_final: 0.6991 (mttt) REVERT: E 51 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7148 (mpt180) REVERT: E 62 MET cc_start: 0.8240 (mtt) cc_final: 0.7535 (mmt) REVERT: E 104 ASP cc_start: 0.7406 (t70) cc_final: 0.7106 (t70) REVERT: E 155 LYS cc_start: 0.7399 (tttt) cc_final: 0.6960 (mmtt) REVERT: E 165 ASN cc_start: 0.8102 (m110) cc_final: 0.7490 (m-40) REVERT: E 171 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7490 (t0) REVERT: E 174 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7623 (mmmm) REVERT: E 176 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7707 (pm20) REVERT: E 180 MET cc_start: 0.8798 (ttm) cc_final: 0.8450 (mtm) REVERT: E 199 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7018 (mp0) REVERT: E 209 HIS cc_start: 0.7043 (m-70) cc_final: 0.6679 (m170) REVERT: E 217 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: E 242 LYS cc_start: 0.8426 (mttt) cc_final: 0.7904 (mmtm) REVERT: E 247 SER cc_start: 0.7128 (t) cc_final: 0.6671 (m) REVERT: E 250 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7550 (mm-30) REVERT: F 8 PHE cc_start: 0.8530 (m-80) cc_final: 0.8149 (m-80) REVERT: F 43 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.7072 (mmm-85) REVERT: F 47 LYS cc_start: 0.7331 (mttt) cc_final: 0.6837 (mtmm) REVERT: F 64 MET cc_start: 0.7737 (mmm) cc_final: 0.7536 (mmp) REVERT: F 115 ARG cc_start: 0.7792 (mmt-90) cc_final: 0.6883 (mmt-90) REVERT: F 124 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6781 (mtp180) REVERT: F 180 LYS cc_start: 0.6937 (mmmt) cc_final: 0.6660 (mmmm) REVERT: G 7 ASN cc_start: 0.8038 (t0) cc_final: 0.7715 (t0) REVERT: G 12 MET cc_start: 0.7584 (mmt) cc_final: 0.7167 (mmt) REVERT: G 23 LYS cc_start: 0.7021 (mttt) cc_final: 0.6781 (mppt) REVERT: G 30 LYS cc_start: 0.7555 (mmmt) cc_final: 0.7127 (mtpt) REVERT: G 44 GLU cc_start: 0.8519 (pt0) cc_final: 0.7967 (tt0) REVERT: G 57 ASP cc_start: 0.8325 (p0) cc_final: 0.8101 (p0) REVERT: G 79 LYS cc_start: 0.8134 (tttt) cc_final: 0.7578 (ttmt) REVERT: G 86 GLN cc_start: 0.7600 (mt0) cc_final: 0.7131 (mt0) REVERT: G 91 GLU cc_start: 0.8198 (tt0) cc_final: 0.7906 (tt0) REVERT: G 97 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7408 (p) REVERT: G 119 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7218 (mp0) REVERT: G 120 THR cc_start: 0.7087 (p) cc_final: 0.6221 (p) REVERT: G 161 GLN cc_start: 0.8910 (pt0) cc_final: 0.8437 (tt0) REVERT: G 194 ARG cc_start: 0.8534 (ttm110) cc_final: 0.8096 (ptp90) REVERT: G 202 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7260 (mt-10) REVERT: G 211 SER cc_start: 0.7419 (t) cc_final: 0.7031 (m) REVERT: H 89 LYS cc_start: 0.8097 (ptpt) cc_final: 0.7864 (pttm) REVERT: H 90 LYS cc_start: 0.8055 (tptt) cc_final: 0.7585 (tmtt) REVERT: H 91 LEU cc_start: 0.7636 (mt) cc_final: 0.7280 (mt) REVERT: I 8 ARG cc_start: 0.7081 (mtm110) cc_final: 0.6654 (mtm110) REVERT: I 22 GLN cc_start: 0.8272 (mt0) cc_final: 0.7863 (pt0) REVERT: I 35 MET cc_start: 0.7923 (mtt) cc_final: 0.7473 (mmp) REVERT: I 52 ASN cc_start: 0.7864 (m-40) cc_final: 0.7537 (m110) REVERT: I 53 MET cc_start: 0.8651 (mmm) cc_final: 0.8434 (mmm) REVERT: I 61 ASP cc_start: 0.8149 (t70) cc_final: 0.7914 (t0) REVERT: I 64 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7278 (t0) REVERT: I 65 TYR cc_start: 0.8704 (m-80) cc_final: 0.7972 (m-80) REVERT: I 77 ARG cc_start: 0.7493 (ttt180) cc_final: 0.6940 (ttp80) REVERT: I 88 ASN cc_start: 0.7833 (m-40) cc_final: 0.7562 (m110) REVERT: I 92 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7198 (mtm110) REVERT: I 114 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8045 (ttm170) REVERT: I 115 SER cc_start: 0.8916 (t) cc_final: 0.8444 (p) REVERT: I 155 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.6726 (mp) REVERT: I 162 GLN cc_start: 0.8361 (tt0) cc_final: 0.8015 (tt0) REVERT: I 190 GLU cc_start: 0.7002 (tp30) cc_final: 0.6579 (tp30) REVERT: J 13 ARG cc_start: 0.7983 (ptm160) cc_final: 0.7625 (ptm-80) REVERT: J 26 GLN cc_start: 0.7104 (mp10) cc_final: 0.6564 (mp10) REVERT: J 41 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6996 (mt-10) REVERT: J 46 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7062 (mt0) REVERT: J 116 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6648 (mm) REVERT: J 147 MET cc_start: 0.7809 (mtt) cc_final: 0.7543 (mmm) REVERT: L 9 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: L 20 SER cc_start: 0.8947 (m) cc_final: 0.8702 (p) REVERT: L 37 TRP cc_start: 0.8416 (p-90) cc_final: 0.7764 (p90) REVERT: L 49 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6162 (tt) REVERT: L 53 SER cc_start: 0.6635 (t) cc_final: 0.6257 (p) REVERT: L 54 LYS cc_start: 0.7910 (tptt) cc_final: 0.7610 (ttmt) REVERT: L 58 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8579 (ttpp) REVERT: L 83 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7709 (ttpp) REVERT: L 141 ASN cc_start: 0.7594 (t0) cc_final: 0.7311 (t0) REVERT: L 154 VAL cc_start: 0.7856 (m) cc_final: 0.7633 (p) REVERT: L 159 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6700 (ttp-170) REVERT: N 11 MET cc_start: 0.7331 (ttp) cc_final: 0.6883 (ptm) REVERT: N 29 LYS cc_start: 0.7512 (mttt) cc_final: 0.7153 (mtpp) REVERT: N 34 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7629 (mt-10) REVERT: N 103 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6849 (mm-30) REVERT: N 106 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7757 (ttp-170) REVERT: N 112 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7587 (tttm) REVERT: N 140 LYS cc_start: 0.8372 (pttt) cc_final: 0.7915 (ttpp) REVERT: N 147 SER cc_start: 0.8514 (m) cc_final: 0.8205 (m) REVERT: O 68 LYS cc_start: 0.6469 (pptt) cc_final: 0.4801 (mmmt) REVERT: O 73 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6708 (mt-10) REVERT: O 81 MET cc_start: 0.7053 (tpp) cc_final: 0.6383 (tpp) REVERT: O 85 ASP cc_start: 0.7794 (m-30) cc_final: 0.7223 (m-30) REVERT: O 111 LYS cc_start: 0.6956 (mtmt) cc_final: 0.6407 (mtmm) REVERT: P 41 LEU cc_start: 0.7829 (mt) cc_final: 0.7524 (tt) REVERT: P 51 GLN cc_start: 0.7280 (tm-30) cc_final: 0.7021 (mt0) REVERT: P 93 GLU cc_start: 0.7980 (tt0) cc_final: 0.7512 (mm-30) REVERT: Q 103 ASP cc_start: 0.7351 (m-30) cc_final: 0.6409 (t70) REVERT: Q 108 LYS cc_start: 0.7291 (tppt) cc_final: 0.6645 (mtmm) REVERT: Q 111 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7480 (tpm170) REVERT: R 29 GLN cc_start: 0.7505 (mt0) cc_final: 0.7222 (mm110) REVERT: R 81 ARG cc_start: 0.7056 (mtt180) cc_final: 0.6510 (tpt170) REVERT: S 117 LYS cc_start: 0.8810 (mttt) cc_final: 0.8590 (mtmm) REVERT: S 136 GLN cc_start: 0.7601 (mt0) cc_final: 0.6837 (mt0) REVERT: T 23 LYS cc_start: 0.5455 (tppt) cc_final: 0.5125 (mttm) REVERT: T 47 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7303 (mm) REVERT: T 58 LEU cc_start: 0.7344 (tp) cc_final: 0.7124 (mt) REVERT: T 107 LYS cc_start: 0.7635 (mttm) cc_final: 0.7373 (mtpp) REVERT: U 155 ASN cc_start: 0.6954 (m-40) cc_final: 0.6254 (p0) REVERT: U 176 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6985 (mtm-85) REVERT: U 186 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6935 (tm-30) REVERT: U 195 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8100 (mt-10) REVERT: U 215 ILE cc_start: 0.6534 (mt) cc_final: 0.6252 (tt) REVERT: V 22 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7206 (ptp-110) REVERT: V 50 HIS cc_start: 0.5979 (m90) cc_final: 0.5769 (m90) REVERT: V 63 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.4497 (tm-30) REVERT: V 70 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7126 (ttp-110) REVERT: V 71 LEU cc_start: 0.7947 (mt) cc_final: 0.7738 (mp) REVERT: W 82 GLN cc_start: 0.7476 (mt0) cc_final: 0.6905 (mt0) REVERT: W 117 ARG cc_start: 0.8227 (tpp80) cc_final: 0.7925 (tpp80) REVERT: X 21 LYS cc_start: 0.7663 (mttt) cc_final: 0.7387 (mtmt) REVERT: X 48 LYS cc_start: 0.7623 (mttt) cc_final: 0.7360 (mtpt) REVERT: X 55 LEU cc_start: 0.6739 (tt) cc_final: 0.6367 (tt) REVERT: X 58 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7488 (mt-10) REVERT: X 71 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6546 (ttt90) REVERT: X 80 LYS cc_start: 0.7829 (mttt) cc_final: 0.7216 (mtmm) REVERT: X 105 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8245 (t80) REVERT: Y 15 LYS cc_start: 0.7697 (tptt) cc_final: 0.7376 (tppt) REVERT: Y 37 VAL cc_start: 0.8825 (t) cc_final: 0.8597 (t) REVERT: Y 51 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7715 (mmp80) REVERT: Y 81 ASN cc_start: 0.8273 (m-40) cc_final: 0.7984 (t0) REVERT: Z 102 LYS cc_start: 0.8339 (mptt) cc_final: 0.7945 (pttt) REVERT: Z 152 GLN cc_start: 0.6435 (mt0) cc_final: 0.6149 (mt0) REVERT: a 45 VAL cc_start: 0.8014 (m) cc_final: 0.7608 (p) REVERT: a 55 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8274 (tm-30) REVERT: a 66 LYS cc_start: 0.8616 (mttp) cc_final: 0.7962 (mmtt) REVERT: a 71 GLN cc_start: 0.7821 (mm110) cc_final: 0.7440 (mm-40) REVERT: a 77 CYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7546 (m) REVERT: b 23 ILE cc_start: 0.8930 (mt) cc_final: 0.8625 (pt) REVERT: b 40 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6514 (pp30) REVERT: b 77 PHE cc_start: 0.8424 (p90) cc_final: 0.8176 (p90) REVERT: c 11 LYS cc_start: 0.7316 (tttt) cc_final: 0.6582 (tttm) REVERT: c 24 GLN cc_start: 0.7148 (mt0) cc_final: 0.6713 (mm-40) REVERT: c 50 ARG cc_start: 0.7917 (ptt180) cc_final: 0.7197 (ptt180) REVERT: c 51 GLU cc_start: 0.8611 (pt0) cc_final: 0.7982 (tt0) REVERT: d 17 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5881 (ptp90) REVERT: d 31 LYS cc_start: 0.7766 (tttt) cc_final: 0.7345 (tttp) REVERT: d 32 TYR cc_start: 0.8439 (m-80) cc_final: 0.8092 (m-80) REVERT: e 27 LYS cc_start: 0.6952 (pttt) cc_final: 0.6143 (mmmt) REVERT: e 43 ARG cc_start: 0.7032 (mtt90) cc_final: 0.6714 (mtt-85) REVERT: m 20 LYS cc_start: 0.7846 (tttp) cc_final: 0.7581 (ttmm) REVERT: m 29 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.7702 (mtm110) outliers start: 192 outliers final: 120 residues processed: 1235 average time/residue: 0.7305 time to fit residues: 1465.7001 Evaluate side-chains 1215 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1075 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 9 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 111 CYS Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 159 ARG Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 43 HIS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 47 ILE Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain U residue 146 ILE Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain Y residue 29 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain a residue 77 CYS Chi-restraints excluded: chain a residue 93 LYS Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 54 CYS Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 63 GLU Chi-restraints excluded: chain d residue 17 ARG Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain e residue 31 THR Chi-restraints excluded: chain m residue 3 HIS Chi-restraints excluded: chain m residue 27 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 468 optimal weight: 6.9990 chunk 319 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 418 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 504 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS E 188 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 146 ASN G 151 GLN H 80 GLN H 184 ASN J 133 HIS R 15 GLN S 13 HIS ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 HIS W 24 GLN X 73 GLN Z 148 HIS ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 ASN a 40 ASN b 47 HIS c 24 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 73591 Z= 0.522 Angle : 0.825 10.213 107052 Z= 0.415 Chirality : 0.047 0.338 13312 Planarity : 0.006 0.083 7623 Dihedral : 23.401 179.745 29824 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 1.07 % Allowed : 7.19 % Favored : 91.73 % Rotamer: Outliers : 6.85 % Allowed : 20.43 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.24 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4283 helix: -0.06 (0.13), residues: 1413 sheet: -1.04 (0.19), residues: 695 loop : -1.99 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 67 HIS 0.010 0.002 HIS E 17 PHE 0.036 0.003 PHE X 41 TYR 0.038 0.003 TYR a 59 ARG 0.013 0.001 ARG m 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1114 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.5608 (OUTLIER) cc_final: 0.5097 (pp30) REVERT: A 13 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6724 (mm-30) REVERT: A 51 ASN cc_start: 0.6819 (m-40) cc_final: 0.6332 (t0) REVERT: A 110 THR cc_start: 0.7368 (p) cc_final: 0.7124 (p) REVERT: A 156 GLU cc_start: 0.8602 (mp0) cc_final: 0.7626 (pm20) REVERT: A 170 GLU cc_start: 0.7427 (tt0) cc_final: 0.7146 (pm20) REVERT: A 200 MET cc_start: 0.8017 (mtp) cc_final: 0.6922 (ttm) REVERT: A 206 TRP cc_start: 0.7443 (t60) cc_final: 0.7045 (t60) REVERT: A 208 ASP cc_start: 0.8513 (m-30) cc_final: 0.8274 (m-30) REVERT: B 79 GLN cc_start: 0.7396 (mp10) cc_final: 0.7177 (mp10) REVERT: B 85 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7538 (mtpt) REVERT: B 89 GLU cc_start: 0.7880 (mm-30) cc_final: 0.6626 (mp0) REVERT: B 92 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6993 (pp30) REVERT: B 111 CYS cc_start: 0.8273 (t) cc_final: 0.7606 (m) REVERT: B 115 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7089 (mmt180) REVERT: B 177 SER cc_start: 0.6856 (t) cc_final: 0.6524 (p) REVERT: B 179 CYS cc_start: 0.7219 (m) cc_final: 0.5826 (p) REVERT: B 198 GLU cc_start: 0.8495 (tt0) cc_final: 0.8233 (pt0) REVERT: C 36 ASP cc_start: 0.7979 (m-30) cc_final: 0.7057 (p0) REVERT: C 52 ILE cc_start: 0.8376 (mt) cc_final: 0.8108 (mm) REVERT: C 53 SER cc_start: 0.7342 (t) cc_final: 0.6896 (p) REVERT: C 67 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6905 (mp0) REVERT: C 73 HIS cc_start: 0.7159 (t-90) cc_final: 0.6887 (t-90) REVERT: C 76 GLN cc_start: 0.7658 (mm110) cc_final: 0.7354 (mm110) REVERT: C 102 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6627 (tt0) REVERT: C 124 LYS cc_start: 0.7456 (tttt) cc_final: 0.7089 (tttm) REVERT: C 134 ARG cc_start: 0.6975 (mtt180) cc_final: 0.6640 (mtm-85) REVERT: C 143 SER cc_start: 0.8152 (t) cc_final: 0.7820 (p) REVERT: C 151 TYR cc_start: 0.8601 (m-80) cc_final: 0.8184 (m-80) REVERT: C 164 MET cc_start: 0.8099 (pmm) cc_final: 0.7847 (pmm) REVERT: C 209 LYS cc_start: 0.8318 (tttt) cc_final: 0.7899 (ttpp) REVERT: C 227 SER cc_start: 0.7861 (t) cc_final: 0.7642 (m) REVERT: D 20 GLN cc_start: 0.7754 (tp40) cc_final: 0.7337 (mp10) REVERT: D 28 SER cc_start: 0.7548 (t) cc_final: 0.6897 (m) REVERT: D 33 GLU cc_start: 0.8239 (tt0) cc_final: 0.7814 (mm-30) REVERT: D 58 ARG cc_start: 0.7335 (mmt90) cc_final: 0.7024 (mmm160) REVERT: D 87 GLU cc_start: 0.6297 (pt0) cc_final: 0.5994 (pm20) REVERT: D 96 ARG cc_start: 0.7230 (ptp90) cc_final: 0.6874 (ptm160) REVERT: D 105 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: D 118 ARG cc_start: 0.7034 (tpp-160) cc_final: 0.6694 (tpp80) REVERT: D 119 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.7815 (ttt-90) REVERT: D 121 CYS cc_start: 0.7952 (m) cc_final: 0.7491 (p) REVERT: D 126 ARG cc_start: 0.7653 (mmm160) cc_final: 0.7305 (tpp-160) REVERT: D 129 MET cc_start: 0.7739 (mmt) cc_final: 0.7472 (mmt) REVERT: D 134 LYS cc_start: 0.7370 (tptt) cc_final: 0.6933 (mtpt) REVERT: D 150 LYS cc_start: 0.7324 (ttpp) cc_final: 0.6958 (ttpp) REVERT: D 153 LYS cc_start: 0.6777 (ttmt) cc_final: 0.6335 (mttp) REVERT: D 175 ARG cc_start: 0.7347 (mmt-90) cc_final: 0.6473 (mmm-85) REVERT: D 187 ARG cc_start: 0.6894 (mmm-85) cc_final: 0.6337 (mmm-85) REVERT: D 189 LYS cc_start: 0.7618 (ttmt) cc_final: 0.6983 (mtmm) REVERT: E 26 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.7671 (t-170) REVERT: E 51 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.7346 (mpt180) REVERT: E 62 MET cc_start: 0.8109 (mtt) cc_final: 0.7698 (mmt) REVERT: E 79 ASP cc_start: 0.8402 (t70) cc_final: 0.7859 (t70) REVERT: E 104 ASP cc_start: 0.7701 (t70) cc_final: 0.7428 (t70) REVERT: E 155 LYS cc_start: 0.7505 (tttt) cc_final: 0.7039 (mmtm) REVERT: E 165 ASN cc_start: 0.8033 (m110) cc_final: 0.7486 (m-40) REVERT: E 171 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6946 (t0) REVERT: E 174 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7866 (mtpp) REVERT: E 176 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7460 (pm20) REVERT: E 180 MET cc_start: 0.8492 (ttm) cc_final: 0.8161 (mtm) REVERT: E 199 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6907 (mp0) REVERT: E 209 HIS cc_start: 0.7173 (m-70) cc_final: 0.6673 (m90) REVERT: E 217 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: E 242 LYS cc_start: 0.8465 (mttt) cc_final: 0.7947 (mmtm) REVERT: E 247 SER cc_start: 0.7030 (t) cc_final: 0.6782 (p) REVERT: F 43 ARG cc_start: 0.7157 (mmm-85) cc_final: 0.6625 (mmm-85) REVERT: F 47 LYS cc_start: 0.7587 (mttt) cc_final: 0.7305 (mmmt) REVERT: F 115 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.7547 (mmt-90) REVERT: F 180 LYS cc_start: 0.6909 (mmmt) cc_final: 0.6629 (mmmm) REVERT: G 7 ASN cc_start: 0.7989 (t0) cc_final: 0.7510 (t0) REVERT: G 30 LYS cc_start: 0.7414 (mmmt) cc_final: 0.6904 (mtpt) REVERT: G 44 GLU cc_start: 0.8690 (pt0) cc_final: 0.8423 (pm20) REVERT: G 79 LYS cc_start: 0.8398 (tttt) cc_final: 0.7985 (tppt) REVERT: G 91 GLU cc_start: 0.8247 (tt0) cc_final: 0.7967 (tt0) REVERT: G 119 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7212 (mp0) REVERT: G 161 GLN cc_start: 0.8738 (pt0) cc_final: 0.8385 (tt0) REVERT: G 191 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7680 (tppt) REVERT: G 194 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8111 (ptp90) REVERT: G 202 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6920 (mt-10) REVERT: H 90 LYS cc_start: 0.8091 (tptt) cc_final: 0.7651 (tmtt) REVERT: I 35 MET cc_start: 0.8042 (mtt) cc_final: 0.7657 (mmp) REVERT: I 55 TYR cc_start: 0.7845 (m-80) cc_final: 0.7560 (m-80) REVERT: I 77 ARG cc_start: 0.7428 (ttt180) cc_final: 0.6957 (ttp80) REVERT: I 88 ASN cc_start: 0.7887 (m-40) cc_final: 0.7580 (m110) REVERT: I 92 ARG cc_start: 0.7878 (ttt180) cc_final: 0.6980 (mtp85) REVERT: I 114 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8062 (ttm170) REVERT: I 115 SER cc_start: 0.9008 (t) cc_final: 0.8519 (p) REVERT: I 162 GLN cc_start: 0.8427 (tt0) cc_final: 0.7935 (tt0) REVERT: I 190 GLU cc_start: 0.7403 (tp30) cc_final: 0.7158 (tp30) REVERT: J 26 GLN cc_start: 0.7566 (mp10) cc_final: 0.7109 (mp10) REVERT: J 41 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6886 (mt-10) REVERT: J 46 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7262 (mt0) REVERT: J 65 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7939 (mtpp) REVERT: J 116 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6457 (mm) REVERT: J 147 MET cc_start: 0.7903 (mtt) cc_final: 0.7634 (mmm) REVERT: K 32 GLN cc_start: 0.6557 (tt0) cc_final: 0.6027 (tp40) REVERT: L 9 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: L 20 SER cc_start: 0.8976 (m) cc_final: 0.8754 (p) REVERT: L 21 LEU cc_start: 0.8363 (mm) cc_final: 0.8026 (mt) REVERT: L 37 TRP cc_start: 0.8569 (p-90) cc_final: 0.8020 (p90) REVERT: L 39 ASP cc_start: 0.7146 (t70) cc_final: 0.6274 (p0) REVERT: L 53 SER cc_start: 0.7175 (t) cc_final: 0.6593 (p) REVERT: L 54 LYS cc_start: 0.8182 (tptt) cc_final: 0.7861 (ttmm) REVERT: L 57 ASP cc_start: 0.7622 (t0) cc_final: 0.7072 (t70) REVERT: L 58 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8474 (ttpp) REVERT: L 111 CYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8260 (m) REVERT: L 125 ILE cc_start: 0.8088 (mt) cc_final: 0.7831 (mm) REVERT: L 159 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6744 (ttp-170) REVERT: N 11 MET cc_start: 0.7603 (ttp) cc_final: 0.7131 (ptm) REVERT: N 29 LYS cc_start: 0.7539 (mttt) cc_final: 0.7263 (mtpp) REVERT: N 34 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7607 (mt-10) REVERT: N 103 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6647 (mm-30) REVERT: N 106 ARG cc_start: 0.8501 (mtm110) cc_final: 0.7985 (ttp-170) REVERT: N 112 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7626 (tttm) REVERT: N 140 LYS cc_start: 0.8588 (pttt) cc_final: 0.8163 (tptm) REVERT: N 147 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7657 (m) REVERT: O 81 MET cc_start: 0.7270 (tpp) cc_final: 0.6637 (tpp) REVERT: O 85 ASP cc_start: 0.7726 (m-30) cc_final: 0.7108 (m-30) REVERT: O 92 GLU cc_start: 0.8822 (mp0) cc_final: 0.8544 (mp0) REVERT: O 111 LYS cc_start: 0.7297 (mtmt) cc_final: 0.7065 (mtpp) REVERT: P 29 LYS cc_start: 0.6791 (mtmm) cc_final: 0.6417 (pttm) REVERT: P 41 LEU cc_start: 0.7448 (mt) cc_final: 0.7035 (tt) REVERT: P 42 PHE cc_start: 0.7069 (m-80) cc_final: 0.6704 (m-80) REVERT: P 51 GLN cc_start: 0.7473 (tm-30) cc_final: 0.6937 (mt0) REVERT: P 93 GLU cc_start: 0.8038 (tt0) cc_final: 0.7586 (mp0) REVERT: Q 103 ASP cc_start: 0.7358 (m-30) cc_final: 0.6107 (t70) REVERT: R 29 GLN cc_start: 0.7490 (mt0) cc_final: 0.7201 (mm-40) REVERT: R 78 ARG cc_start: 0.7353 (mmt180) cc_final: 0.6809 (mmp-170) REVERT: R 81 ARG cc_start: 0.7097 (mtt180) cc_final: 0.5868 (mmm160) REVERT: S 117 LYS cc_start: 0.8794 (mttt) cc_final: 0.8556 (mtmm) REVERT: T 8 TYR cc_start: 0.5920 (OUTLIER) cc_final: 0.5323 (p90) REVERT: T 41 PHE cc_start: 0.7166 (t80) cc_final: 0.6787 (t80) REVERT: T 52 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6514 (p) REVERT: T 61 TYR cc_start: 0.8003 (m-80) cc_final: 0.7803 (m-10) REVERT: T 96 GLN cc_start: 0.6921 (tt0) cc_final: 0.6155 (tm-30) REVERT: T 107 LYS cc_start: 0.7682 (mttm) cc_final: 0.7440 (mtpp) REVERT: T 115 TYR cc_start: 0.7897 (t80) cc_final: 0.6938 (t80) REVERT: U 176 ARG cc_start: 0.7147 (mtt180) cc_final: 0.5992 (mtm-85) REVERT: U 186 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7000 (tm-30) REVERT: U 195 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7700 (mm-30) REVERT: U 215 ILE cc_start: 0.6567 (mt) cc_final: 0.6256 (tt) REVERT: V 22 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7579 (ptp-110) REVERT: V 50 HIS cc_start: 0.5835 (m90) cc_final: 0.5621 (m90) REVERT: V 63 GLU cc_start: 0.5623 (OUTLIER) cc_final: 0.4245 (tm-30) REVERT: W 82 GLN cc_start: 0.7869 (mt0) cc_final: 0.7597 (mt0) REVERT: X 21 LYS cc_start: 0.7777 (mttt) cc_final: 0.7436 (mtmt) REVERT: X 35 ARG cc_start: 0.7295 (ttp-170) cc_final: 0.6778 (ptt-90) REVERT: X 48 LYS cc_start: 0.7404 (mttt) cc_final: 0.6988 (mtpt) REVERT: X 71 ARG cc_start: 0.7014 (ttm-80) cc_final: 0.6477 (ttt90) REVERT: X 80 LYS cc_start: 0.7823 (mttt) cc_final: 0.7494 (mtmm) REVERT: Y 15 LYS cc_start: 0.7752 (tptt) cc_final: 0.7476 (tppt) REVERT: Y 51 ARG cc_start: 0.8525 (mtt180) cc_final: 0.7833 (mmp80) REVERT: Y 81 ASN cc_start: 0.8276 (m-40) cc_final: 0.7817 (t0) REVERT: Y 89 GLU cc_start: 0.7419 (tp30) cc_final: 0.7176 (tp30) REVERT: a 33 ASP cc_start: 0.8020 (p0) cc_final: 0.7782 (p0) REVERT: a 42 ARG cc_start: 0.7290 (ttp80) cc_final: 0.7008 (ttp80) REVERT: a 45 VAL cc_start: 0.8468 (m) cc_final: 0.8133 (p) REVERT: a 52 ASP cc_start: 0.7580 (t0) cc_final: 0.7303 (t70) REVERT: a 66 LYS cc_start: 0.8659 (mttp) cc_final: 0.8042 (mmpt) REVERT: a 96 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: b 23 ILE cc_start: 0.8793 (mt) cc_final: 0.8582 (pt) REVERT: c 11 LYS cc_start: 0.7079 (tttt) cc_final: 0.6671 (tttm) REVERT: c 51 GLU cc_start: 0.8623 (pt0) cc_final: 0.7966 (tt0) REVERT: d 10 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6594 (mmtp) REVERT: d 17 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.5880 (ptp90) REVERT: d 26 HIS cc_start: 0.7776 (m90) cc_final: 0.7307 (m90) REVERT: d 39 GLN cc_start: 0.8552 (mp10) cc_final: 0.7846 (mp10) REVERT: d 53 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6128 (p90) REVERT: e 25 GLU cc_start: 0.7782 (pm20) cc_final: 0.7465 (pm20) REVERT: e 39 GLN cc_start: 0.7963 (mt0) cc_final: 0.7745 (mt0) REVERT: e 43 ARG cc_start: 0.7084 (mtt90) cc_final: 0.6576 (mtt-85) REVERT: m 20 LYS cc_start: 0.7941 (tttp) cc_final: 0.7723 (ttmm) outliers start: 247 outliers final: 172 residues processed: 1253 average time/residue: 0.7332 time to fit residues: 1494.0608 Evaluate side-chains 1259 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1067 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 9 GLU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 111 CYS Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 159 ARG Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain N residue 147 SER Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 131 ILE Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 35 MET Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain S residue 98 LYS Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 8 TYR Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 19 VAL Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain U residue 146 ILE Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 52 ILE Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 60 LYS Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain Y residue 9 LEU Chi-restraints excluded: chain Y residue 29 ILE Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 96 GLU Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 54 CYS Chi-restraints excluded: chain b residue 62 CYS Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 17 ARG Chi-restraints excluded: chain d residue 34 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain e residue 31 THR Chi-restraints excluded: chain m residue 14 LYS Chi-restraints excluded: chain m residue 27 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 189 optimal weight: 4.9990 chunk 506 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 330 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 563 optimal weight: 2.9990 chunk 467 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 186 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 ASN G 151 GLN Q 82 GLN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 HIS ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 ASN m 3 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 : 0.005 0.055 73591 Z= 0.315 Angle : 0.675 13.080 107052 Z= 0.343 Chirality : 0.040 0.284 13312 Planarity : 0.005 0.055 7623 Dihedral : 23.259 179.118 29822 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.98 % Allowed : 6.98 % Favored : 92.04 % Rotamer: Outliers : 6.46 % Allowed : 22.01 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.60 (0.12), residues: 4283 helix: 0.10 (0.14), residues: 1415 sheet: -0.94 (0.19), residues: 690 loop : -1.92 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 67 HIS 0.008 0.001 HIS S 122 PHE 0.034 0.002 PHE b 77 TYR 0.034 0.002 TYR a 59 ARG 0.008 0.001 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1114 time to evaluate : 3.863 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: A 12 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5408 (pp30) REVERT: A 13 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6663 (mm-30) REVERT: A 22 CYS cc_start: 0.7172 (m) cc_final: 0.6474 (m) REVERT: A 32 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 156 GLU cc_start: 0.8600 (mp0) cc_final: 0.7716 (pm20) REVERT: A 200 MET cc_start: 0.7925 (mtp) cc_final: 0.6713 (ttm) REVERT: A 206 TRP cc_start: 0.7152 (t60) cc_final: 0.6795 (t60) REVERT: A 208 ASP cc_start: 0.8470 (m-30) cc_final: 0.8202 (m-30) REVERT: B 79 GLN cc_start: 0.7487 (mp10) cc_final: 0.7265 (mp10) REVERT: B 85 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7617 (mtpt) REVERT: B 89 GLU cc_start: 0.7847 (mm-30) cc_final: 0.6608 (mp0) REVERT: B 92 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7028 (pp30) REVERT: B 99 ASP cc_start: 0.7675 (t0) cc_final: 0.7176 (t0) REVERT: B 111 CYS cc_start: 0.8262 (t) cc_final: 0.7596 (m) REVERT: B 177 SER cc_start: 0.6803 (t) cc_final: 0.6490 (p) REVERT: B 198 GLU cc_start: 0.8440 (tt0) cc_final: 0.8149 (pt0) REVERT: B 224 ASP cc_start: 0.8058 (t0) cc_final: 0.7595 (t0) REVERT: C 36 ASP cc_start: 0.7964 (m-30) cc_final: 0.7086 (p0) REVERT: C 40 ILE cc_start: 0.6693 (tp) cc_final: 0.6161 (tp) REVERT: C 52 ILE cc_start: 0.8372 (mt) cc_final: 0.8100 (mm) REVERT: C 53 SER cc_start: 0.7315 (t) cc_final: 0.6868 (p) REVERT: C 55 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6539 (tp) REVERT: C 67 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6918 (mp0) REVERT: C 73 HIS cc_start: 0.7172 (t-90) cc_final: 0.6846 (t-90) REVERT: C 76 GLN cc_start: 0.7768 (mm110) cc_final: 0.7433 (mm110) REVERT: C 102 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6094 (tt0) REVERT: C 124 LYS cc_start: 0.7475 (tttt) cc_final: 0.7122 (tttm) REVERT: C 134 ARG cc_start: 0.6902 (mtt180) cc_final: 0.6589 (mtm-85) REVERT: C 143 SER cc_start: 0.7965 (t) cc_final: 0.7620 (p) REVERT: C 151 TYR cc_start: 0.8520 (m-80) cc_final: 0.8234 (m-80) REVERT: C 164 MET cc_start: 0.8106 (pmm) cc_final: 0.7865 (pmm) REVERT: C 209 LYS cc_start: 0.8267 (tttt) cc_final: 0.7845 (ttpp) REVERT: C 227 SER cc_start: 0.7970 (t) cc_final: 0.7738 (m) REVERT: D 20 GLN cc_start: 0.7679 (tp40) cc_final: 0.7283 (mp10) REVERT: D 28 SER cc_start: 0.7565 (t) cc_final: 0.6893 (m) REVERT: D 33 GLU cc_start: 0.8231 (tt0) cc_final: 0.7692 (mm-30) REVERT: D 58 ARG cc_start: 0.7239 (mmt90) cc_final: 0.6983 (mmm160) REVERT: D 59 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7099 (mp0) REVERT: D 87 GLU cc_start: 0.6436 (pt0) cc_final: 0.6157 (pm20) REVERT: D 96 ARG cc_start: 0.7167 (ptp90) cc_final: 0.6572 (ptm-80) REVERT: D 105 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: D 119 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.7895 (ttt-90) REVERT: D 121 CYS cc_start: 0.7947 (m) cc_final: 0.7442 (p) REVERT: D 126 ARG cc_start: 0.7653 (mmm160) cc_final: 0.6969 (mtm-85) REVERT: D 129 MET cc_start: 0.7727 (mmt) cc_final: 0.7484 (mmt) REVERT: D 134 LYS cc_start: 0.7370 (tptt) cc_final: 0.6944 (mtpt) REVERT: D 150 LYS cc_start: 0.7223 (ttpp) cc_final: 0.6912 (ttpp) REVERT: D 153 LYS cc_start: 0.6743 (ttmt) cc_final: 0.6267 (mtmt) REVERT: D 164 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7431 (tm-30) REVERT: D 172 GLN cc_start: 0.7844 (pt0) cc_final: 0.7641 (mt0) REVERT: D 175 ARG cc_start: 0.7263 (mmt-90) cc_final: 0.6296 (mmm-85) REVERT: D 187 ARG cc_start: 0.6999 (mmm-85) cc_final: 0.6425 (mmm-85) REVERT: D 189 LYS cc_start: 0.7622 (ttmt) cc_final: 0.6982 (mtmm) REVERT: E 7 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7479 (mmtt) REVERT: E 26 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7684 (t-170) REVERT: E 51 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7403 (mpt180) REVERT: E 62 MET cc_start: 0.8077 (mtt) cc_final: 0.7681 (mmt) REVERT: E 79 ASP cc_start: 0.8444 (t70) cc_final: 0.8153 (t70) REVERT: E 104 ASP cc_start: 0.7610 (t70) cc_final: 0.7337 (t70) REVERT: E 154 ILE cc_start: 0.8491 (mt) cc_final: 0.8172 (mt) REVERT: E 155 LYS cc_start: 0.7481 (tttt) cc_final: 0.7009 (mmtt) REVERT: E 165 ASN cc_start: 0.7876 (m110) cc_final: 0.7351 (m-40) REVERT: E 171 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7066 (t0) REVERT: E 174 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7625 (mtpp) REVERT: E 176 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7352 (pm20) REVERT: E 180 MET cc_start: 0.8417 (ttm) cc_final: 0.8183 (mtm) REVERT: E 199 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6900 (mp0) REVERT: E 209 HIS cc_start: 0.7105 (m-70) cc_final: 0.6511 (m-70) REVERT: E 217 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: E 242 LYS cc_start: 0.8424 (mttt) cc_final: 0.7872 (mmtm) REVERT: E 246 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7592 (pp) REVERT: E 247 SER cc_start: 0.7094 (t) cc_final: 0.6672 (p) REVERT: F 43 ARG cc_start: 0.7304 (mmm-85) cc_final: 0.6872 (mmm160) REVERT: F 93 ASP cc_start: 0.7645 (p0) cc_final: 0.7341 (m-30) REVERT: F 115 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.5982 (mmp80) REVERT: F 124 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6876 (mtp85) REVERT: F 180 LYS cc_start: 0.6875 (mmmt) cc_final: 0.6588 (mmmm) REVERT: G 7 ASN cc_start: 0.7970 (t0) cc_final: 0.7563 (t0) REVERT: G 23 LYS cc_start: 0.7158 (mttt) cc_final: 0.6621 (mttm) REVERT: G 30 LYS cc_start: 0.7451 (mmmt) cc_final: 0.7044 (mtpt) REVERT: G 44 GLU cc_start: 0.8658 (pt0) cc_final: 0.8329 (pm20) REVERT: G 79 LYS cc_start: 0.8345 (tttt) cc_final: 0.7964 (tppt) REVERT: G 119 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7293 (mp0) REVERT: G 161 GLN cc_start: 0.8698 (pt0) cc_final: 0.8342 (tt0) REVERT: G 165 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7415 (ttmt) REVERT: G 194 ARG cc_start: 0.8676 (ttm110) cc_final: 0.8124 (ptp90) REVERT: G 202 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6984 (mt-10) REVERT: H 90 LYS cc_start: 0.8177 (tptt) cc_final: 0.7792 (tptp) REVERT: I 7 ARG cc_start: 0.6993 (ttm-80) cc_final: 0.6782 (ttm-80) REVERT: I 35 MET cc_start: 0.7935 (mtt) cc_final: 0.7504 (mmp) REVERT: I 65 TYR cc_start: 0.8852 (m-80) cc_final: 0.8029 (m-80) REVERT: I 77 ARG cc_start: 0.7306 (ttt180) cc_final: 0.6837 (ttp80) REVERT: I 88 ASN cc_start: 0.7739 (m-40) cc_final: 0.7433 (m-40) REVERT: I 92 ARG cc_start: 0.7912 (ttt180) cc_final: 0.7380 (mtp85) REVERT: I 114 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8087 (ttm170) REVERT: I 115 SER cc_start: 0.8988 (t) cc_final: 0.8480 (p) REVERT: I 162 GLN cc_start: 0.8369 (tt0) cc_final: 0.7820 (tt0) REVERT: I 190 GLU cc_start: 0.7322 (tp30) cc_final: 0.7065 (tp30) REVERT: J 17 ARG cc_start: 0.7703 (mtt90) cc_final: 0.7501 (mtt90) REVERT: J 26 GLN cc_start: 0.7503 (mp10) cc_final: 0.6989 (mp10) REVERT: J 41 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6964 (mt-10) REVERT: J 46 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7105 (mt0) REVERT: J 65 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7945 (mtpp) REVERT: J 68 ARG cc_start: 0.7513 (ttt-90) cc_final: 0.7082 (tpt170) REVERT: J 116 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6800 (mm) REVERT: J 147 MET cc_start: 0.7919 (mtt) cc_final: 0.7623 (mmm) REVERT: K 32 GLN cc_start: 0.6901 (tt0) cc_final: 0.6493 (tp40) REVERT: L 21 LEU cc_start: 0.8329 (mm) cc_final: 0.7982 (mt) REVERT: L 37 TRP cc_start: 0.8482 (p-90) cc_final: 0.7919 (p90) REVERT: L 39 ASP cc_start: 0.7147 (t70) cc_final: 0.6443 (p0) REVERT: L 53 SER cc_start: 0.7168 (t) cc_final: 0.6532 (p) REVERT: L 54 LYS cc_start: 0.8064 (tptt) cc_final: 0.7725 (ttmm) REVERT: L 57 ASP cc_start: 0.7691 (t0) cc_final: 0.7134 (t70) REVERT: L 58 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8515 (ttpp) REVERT: L 141 ASN cc_start: 0.7964 (t0) cc_final: 0.7662 (t0) REVERT: N 34 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7632 (mt-10) REVERT: N 106 ARG cc_start: 0.8491 (mtm110) cc_final: 0.8171 (ttp-110) REVERT: N 112 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7762 (tttm) REVERT: N 140 LYS cc_start: 0.8572 (pttt) cc_final: 0.8120 (tptt) REVERT: N 147 SER cc_start: 0.8405 (m) cc_final: 0.8051 (m) REVERT: O 81 MET cc_start: 0.7222 (tpp) cc_final: 0.6536 (tpp) REVERT: O 92 GLU cc_start: 0.8801 (mp0) cc_final: 0.8474 (mp0) REVERT: O 111 LYS cc_start: 0.7396 (mtmt) cc_final: 0.6873 (mtmm) REVERT: P 29 LYS cc_start: 0.6849 (mtmm) cc_final: 0.6458 (pttm) REVERT: P 41 LEU cc_start: 0.7446 (mt) cc_final: 0.7004 (tt) REVERT: P 42 PHE cc_start: 0.7051 (m-80) cc_final: 0.6703 (m-80) REVERT: P 51 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6980 (mt0) REVERT: P 93 GLU cc_start: 0.8135 (tt0) cc_final: 0.7661 (mp0) REVERT: P 129 LYS cc_start: 0.7086 (mtmt) cc_final: 0.6882 (ptmt) REVERT: Q 103 ASP cc_start: 0.7396 (m-30) cc_final: 0.6140 (t70) REVERT: Q 111 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7383 (ttp80) REVERT: Q 140 ARG cc_start: 0.7565 (mtt90) cc_final: 0.7248 (mtt90) REVERT: R 46 MET cc_start: 0.8165 (mmm) cc_final: 0.7742 (mmm) REVERT: R 73 LEU cc_start: 0.5287 (mt) cc_final: 0.4702 (tp) REVERT: R 78 ARG cc_start: 0.7346 (mmt180) cc_final: 0.6808 (mmp-170) REVERT: R 81 ARG cc_start: 0.7171 (mtt180) cc_final: 0.5872 (mmm160) REVERT: S 117 LYS cc_start: 0.8816 (mttt) cc_final: 0.8615 (mtmm) REVERT: S 136 GLN cc_start: 0.7823 (mt0) cc_final: 0.6965 (mt0) REVERT: T 8 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5238 (p90) REVERT: T 36 LYS cc_start: 0.7306 (mmtm) cc_final: 0.7089 (mmtm) REVERT: T 41 PHE cc_start: 0.7126 (t80) cc_final: 0.6871 (t80) REVERT: T 89 ARG cc_start: 0.6811 (mtp180) cc_final: 0.6497 (mtp180) REVERT: T 107 LYS cc_start: 0.7669 (mttm) cc_final: 0.7353 (mtpp) REVERT: T 115 TYR cc_start: 0.7894 (t80) cc_final: 0.6879 (t80) REVERT: T 151 GLN cc_start: 0.7990 (mt0) cc_final: 0.7766 (mt0) REVERT: U 176 ARG cc_start: 0.7189 (mtt180) cc_final: 0.6185 (mtm-85) REVERT: U 195 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7680 (mm-30) REVERT: U 215 ILE cc_start: 0.6589 (mt) cc_final: 0.6273 (tt) REVERT: V 22 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7303 (ptp-110) REVERT: V 50 HIS cc_start: 0.5861 (m90) cc_final: 0.5645 (m90) REVERT: V 63 GLU cc_start: 0.5546 (OUTLIER) cc_final: 0.4123 (tm-30) REVERT: W 82 GLN cc_start: 0.7808 (mt0) cc_final: 0.7380 (mt0) REVERT: X 21 LYS cc_start: 0.7810 (mttt) cc_final: 0.7533 (mtmt) REVERT: X 35 ARG cc_start: 0.7337 (ttp-170) cc_final: 0.6860 (ptt-90) REVERT: X 48 LYS cc_start: 0.7408 (mttt) cc_final: 0.7002 (mtpt) REVERT: X 71 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6649 (ttt90) REVERT: X 80 LYS cc_start: 0.7862 (mttt) cc_final: 0.7539 (mtmm) REVERT: X 114 ASP cc_start: 0.6065 (OUTLIER) cc_final: 0.5624 (m-30) REVERT: Y 15 LYS cc_start: 0.7754 (tptt) cc_final: 0.7413 (tppt) REVERT: Y 51 ARG cc_start: 0.8491 (mtt180) cc_final: 0.7701 (mmp80) REVERT: Y 81 ASN cc_start: 0.8249 (m-40) cc_final: 0.7697 (t0) REVERT: Y 89 GLU cc_start: 0.7326 (tp30) cc_final: 0.6756 (tp30) REVERT: a 33 ASP cc_start: 0.8002 (p0) cc_final: 0.7764 (p0) REVERT: a 45 VAL cc_start: 0.8452 (m) cc_final: 0.8178 (p) REVERT: a 52 ASP cc_start: 0.7495 (t0) cc_final: 0.7006 (t70) REVERT: a 66 LYS cc_start: 0.8664 (mttp) cc_final: 0.8050 (mmpt) REVERT: b 4 ASP cc_start: 0.7479 (t0) cc_final: 0.7120 (t0) REVERT: c 11 LYS cc_start: 0.7386 (tttt) cc_final: 0.6843 (tttm) REVERT: c 24 GLN cc_start: 0.7392 (mt0) cc_final: 0.6871 (mm-40) REVERT: c 50 ARG cc_start: 0.8030 (ptt180) cc_final: 0.7610 (ptt180) REVERT: c 51 GLU cc_start: 0.8584 (pt0) cc_final: 0.7810 (tt0) REVERT: c 63 GLU cc_start: 0.6648 (pm20) cc_final: 0.6402 (pm20) REVERT: d 10 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6588 (mmtp) REVERT: d 17 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.5968 (ptp90) REVERT: d 26 HIS cc_start: 0.7664 (m90) cc_final: 0.7193 (m90) REVERT: d 39 GLN cc_start: 0.8228 (mp10) cc_final: 0.8010 (mp10) REVERT: d 53 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6337 (p90) REVERT: e 27 LYS cc_start: 0.6968 (pttt) cc_final: 0.6423 (tptp) REVERT: e 39 GLN cc_start: 0.7934 (mt0) cc_final: 0.7699 (mt0) REVERT: e 43 ARG cc_start: 0.7116 (mtt90) cc_final: 0.6611 (mtt-85) REVERT: m 20 LYS cc_start: 0.7989 (tttp) cc_final: 0.7668 (ttmm) REVERT: m 29 ARG cc_start: 0.8470 (ttp-170) cc_final: 0.7983 (mtm180) outliers start: 233 outliers final: 177 residues processed: 1229 average time/residue: 0.7329 time to fit residues: 1470.9578 Evaluate side-chains 1271 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1077 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 80 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 96 VAL Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 145 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 131 ILE Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 40 GLU Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 144 HIS Chi-restraints excluded: chain T residue 8 TYR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 64 ASP Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain U residue 146 ILE Chi-restraints excluded: chain U residue 211 VAL Chi-restraints excluded: chain V residue 8 ILE Chi-restraints excluded: chain V residue 11 LEU Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 52 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 50 ILE Chi-restraints excluded: chain X residue 60 LYS Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain Y residue 29 ILE Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 73 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 54 CYS Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain b residue 62 CYS Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain d residue 10 LYS Chi-restraints excluded: chain d residue 17 ARG Chi-restraints excluded: chain d residue 34 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain e residue 31 THR Chi-restraints excluded: chain m residue 27 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 542 optimal weight: 0.0570 chunk 63 optimal weight: 6.9990 chunk 320 optimal weight: 1.9990 chunk 411 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 474 optimal weight: 4.9990 chunk 314 optimal weight: 0.6980 chunk 560 optimal weight: 8.9990 chunk 351 optimal weight: 0.4980 chunk 341 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN C 102 GLN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 HIS S 87 ASN S 99 HIS V 60 GLN Z 139 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 73591 Z= 0.149 Angle : 0.587 11.648 107052 Z= 0.298 Chirality : 0.035 0.247 13312 Planarity : 0.004 0.053 7623 Dihedral : 23.100 179.409 29818 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.96 % Allowed : 6.44 % Favored : 92.60 % Rotamer: Outliers : 4.41 % Allowed : 24.56 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.21 (0.13), residues: 4283 helix: 0.47 (0.14), residues: 1428 sheet: -0.62 (0.19), residues: 685 loop : -1.78 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 69 HIS 0.006 0.001 HIS S 122 PHE 0.035 0.002 PHE b 77 TYR 0.034 0.002 TYR a 59 ARG 0.016 0.001 ARG I 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1121 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.5944 (OUTLIER) cc_final: 0.5427 (pp30) REVERT: A 22 CYS cc_start: 0.7377 (m) cc_final: 0.7144 (m) REVERT: A 32 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7027 (mt-10) REVERT: A 33 HIS cc_start: 0.7261 (t70) cc_final: 0.6948 (t-90) REVERT: A 137 GLU cc_start: 0.7988 (mm-30) cc_final: 0.6920 (mt-10) REVERT: A 156 GLU cc_start: 0.8589 (mp0) cc_final: 0.8095 (mp0) REVERT: A 200 MET cc_start: 0.7334 (mtp) cc_final: 0.6595 (tpt) REVERT: A 202 ASP cc_start: 0.7801 (m-30) cc_final: 0.7363 (m-30) REVERT: A 206 TRP cc_start: 0.7074 (t60) cc_final: 0.6694 (t60) REVERT: A 208 ASP cc_start: 0.8394 (m-30) cc_final: 0.8107 (m-30) REVERT: B 29 TRP cc_start: 0.8048 (m100) cc_final: 0.7436 (m-10) REVERT: B 111 CYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7578 (m) REVERT: B 224 ASP cc_start: 0.7704 (t0) cc_final: 0.7387 (t0) REVERT: B 229 MET cc_start: 0.8820 (mmp) cc_final: 0.8394 (mmm) REVERT: C 52 ILE cc_start: 0.8344 (mt) cc_final: 0.8097 (mm) REVERT: C 53 SER cc_start: 0.7256 (t) cc_final: 0.6933 (p) REVERT: C 55 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6454 (tp) REVERT: C 67 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7048 (mp0) REVERT: C 76 GLN cc_start: 0.7978 (mm110) cc_final: 0.7616 (mm110) REVERT: C 97 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.6238 (tt0) REVERT: C 103 ARG cc_start: 0.7416 (ptm160) cc_final: 0.7100 (ptm-80) REVERT: C 124 LYS cc_start: 0.7482 (tttt) cc_final: 0.7234 (tttm) REVERT: C 134 ARG cc_start: 0.6883 (mtt180) cc_final: 0.6530 (mtm-85) REVERT: C 143 SER cc_start: 0.7896 (t) cc_final: 0.7521 (p) REVERT: C 151 TYR cc_start: 0.8480 (m-80) cc_final: 0.8251 (m-80) REVERT: C 164 MET cc_start: 0.8164 (pmm) cc_final: 0.7923 (pmm) REVERT: C 209 LYS cc_start: 0.8212 (tttt) cc_final: 0.7723 (ttpt) REVERT: C 249 GLN cc_start: 0.7986 (tp40) cc_final: 0.7746 (tp40) REVERT: D 20 GLN cc_start: 0.7649 (tp40) cc_final: 0.7213 (mp10) REVERT: D 28 SER cc_start: 0.7513 (t) cc_final: 0.6949 (m) REVERT: D 33 GLU cc_start: 0.8281 (tt0) cc_final: 0.7920 (mm-30) REVERT: D 58 ARG cc_start: 0.7192 (mmt90) cc_final: 0.6828 (mmm160) REVERT: D 59 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7005 (mp0) REVERT: D 87 GLU cc_start: 0.6566 (pt0) cc_final: 0.6213 (pm20) REVERT: D 96 ARG cc_start: 0.7206 (ptp90) cc_final: 0.6578 (ptm-80) REVERT: D 105 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: D 119 ARG cc_start: 0.8101 (ttt-90) cc_final: 0.7745 (ttt-90) REVERT: D 121 CYS cc_start: 0.7989 (m) cc_final: 0.7413 (p) REVERT: D 126 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7023 (mtm-85) REVERT: D 134 LYS cc_start: 0.7337 (tptt) cc_final: 0.6916 (mtpt) REVERT: D 150 LYS cc_start: 0.7210 (ttpp) cc_final: 0.6959 (ttpp) REVERT: D 153 LYS cc_start: 0.6841 (ttmt) cc_final: 0.6287 (mtmt) REVERT: D 154 PHE cc_start: 0.6687 (m-80) cc_final: 0.6054 (m-80) REVERT: D 164 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7184 (tm-30) REVERT: D 175 ARG cc_start: 0.7176 (mmt-90) cc_final: 0.6639 (mmm-85) REVERT: D 187 ARG cc_start: 0.7027 (mmm-85) cc_final: 0.6366 (mmm-85) REVERT: D 189 LYS cc_start: 0.7531 (ttmt) cc_final: 0.6755 (mtmm) REVERT: E 7 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7609 (mmmt) REVERT: E 51 ARG cc_start: 0.7994 (mmt-90) cc_final: 0.7513 (mpt180) REVERT: E 62 MET cc_start: 0.7851 (mtt) cc_final: 0.7436 (mmt) REVERT: E 79 ASP cc_start: 0.8342 (t70) cc_final: 0.8031 (t70) REVERT: E 155 LYS cc_start: 0.7492 (tttt) cc_final: 0.7034 (mmtt) REVERT: E 165 ASN cc_start: 0.7751 (m110) cc_final: 0.7167 (m-40) REVERT: E 174 LYS cc_start: 0.8082 (mtpp) cc_final: 0.7499 (mmmm) REVERT: E 176 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7459 (pm20) REVERT: E 180 MET cc_start: 0.8533 (ttm) cc_final: 0.8323 (mtm) REVERT: E 199 GLU cc_start: 0.7686 (mt-10) cc_final: 0.6982 (mp0) REVERT: E 209 HIS cc_start: 0.7128 (m-70) cc_final: 0.6539 (m-70) REVERT: E 217 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: E 242 LYS cc_start: 0.8478 (mttt) cc_final: 0.7960 (mmtm) REVERT: E 246 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7278 (pp) REVERT: E 247 SER cc_start: 0.7226 (t) cc_final: 0.6728 (m) REVERT: F 43 ARG cc_start: 0.7116 (mmm-85) cc_final: 0.6637 (mmm-85) REVERT: F 63 SER cc_start: 0.7291 (t) cc_final: 0.7059 (m) REVERT: F 93 ASP cc_start: 0.7600 (p0) cc_final: 0.7318 (m-30) REVERT: F 115 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.6886 (mmt-90) REVERT: F 124 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.6975 (mtp180) REVERT: F 180 LYS cc_start: 0.6867 (mmmt) cc_final: 0.6575 (mmmm) REVERT: G 7 ASN cc_start: 0.7979 (t0) cc_final: 0.7554 (t0) REVERT: G 12 MET cc_start: 0.7747 (mmt) cc_final: 0.6540 (mmt) REVERT: G 23 LYS cc_start: 0.6991 (mttt) cc_final: 0.6583 (mppt) REVERT: G 30 LYS cc_start: 0.7426 (mmmt) cc_final: 0.6965 (mtpt) REVERT: G 44 GLU cc_start: 0.8540 (pt0) cc_final: 0.8243 (pm20) REVERT: G 79 LYS cc_start: 0.8311 (tttt) cc_final: 0.7931 (tppt) REVERT: G 119 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7096 (mp0) REVERT: G 156 TYR cc_start: 0.8070 (m-80) cc_final: 0.7716 (m-80) REVERT: G 161 GLN cc_start: 0.8695 (pt0) cc_final: 0.8332 (tt0) REVERT: G 194 ARG cc_start: 0.8625 (ttm110) cc_final: 0.8062 (ptp90) REVERT: G 202 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6996 (mt-10) REVERT: H 43 ARG cc_start: 0.8375 (mmm160) cc_final: 0.7937 (tpt90) REVERT: H 89 LYS cc_start: 0.8349 (ptmm) cc_final: 0.7876 (pttm) REVERT: H 90 LYS cc_start: 0.8130 (tptt) cc_final: 0.7738 (tptp) REVERT: I 8 ARG cc_start: 0.6978 (mtm110) cc_final: 0.5790 (mtp180) REVERT: I 22 GLN cc_start: 0.8328 (mt0) cc_final: 0.8077 (pt0) REVERT: I 35 MET cc_start: 0.7934 (mtt) cc_final: 0.7491 (mmp) REVERT: I 65 TYR cc_start: 0.8902 (m-80) cc_final: 0.8147 (m-80) REVERT: I 77 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7042 (ttp80) REVERT: I 88 ASN cc_start: 0.7688 (m-40) cc_final: 0.7334 (m110) REVERT: I 92 ARG cc_start: 0.7945 (ttt180) cc_final: 0.7417 (mtp85) REVERT: I 114 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7991 (ttm170) REVERT: I 115 SER cc_start: 0.8911 (t) cc_final: 0.8414 (p) REVERT: I 154 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7627 (tttp) REVERT: I 162 GLN cc_start: 0.8333 (tt0) cc_final: 0.7750 (tt0) REVERT: I 190 GLU cc_start: 0.6955 (tp30) cc_final: 0.6630 (tp30) REVERT: J 13 ARG cc_start: 0.8337 (ptm160) cc_final: 0.8080 (ptm160) REVERT: J 26 GLN cc_start: 0.7427 (mp10) cc_final: 0.6863 (mp10) REVERT: J 41 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7149 (mt-10) REVERT: J 46 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7017 (mt0) REVERT: J 65 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7909 (mtpp) REVERT: J 66 ASP cc_start: 0.6711 (t0) cc_final: 0.6159 (t0) REVERT: J 86 LEU cc_start: 0.8279 (tp) cc_final: 0.7551 (mt) REVERT: J 115 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8022 (mmtp) REVERT: J 116 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6693 (mm) REVERT: J 147 MET cc_start: 0.7868 (mtt) cc_final: 0.7544 (mmm) REVERT: L 53 SER cc_start: 0.6841 (t) cc_final: 0.6289 (p) REVERT: L 54 LYS cc_start: 0.7935 (tptt) cc_final: 0.7635 (ttmm) REVERT: L 141 ASN cc_start: 0.7729 (t0) cc_final: 0.7428 (t0) REVERT: N 34 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7632 (mt-10) REVERT: N 112 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7550 (tttm) REVERT: N 140 LYS cc_start: 0.8460 (pttt) cc_final: 0.8067 (tptt) REVERT: N 141 TYR cc_start: 0.8461 (t80) cc_final: 0.8130 (t80) REVERT: N 147 SER cc_start: 0.8435 (m) cc_final: 0.8067 (m) REVERT: O 81 MET cc_start: 0.6912 (tpp) cc_final: 0.6286 (tpp) REVERT: O 95 ILE cc_start: 0.7875 (mm) cc_final: 0.7413 (mm) REVERT: O 111 LYS cc_start: 0.7393 (mtmt) cc_final: 0.6882 (mtmm) REVERT: P 29 LYS cc_start: 0.7032 (mtmm) cc_final: 0.6668 (ptpp) REVERT: P 41 LEU cc_start: 0.7268 (mt) cc_final: 0.7019 (tt) REVERT: P 42 PHE cc_start: 0.6897 (m-80) cc_final: 0.6497 (m-80) REVERT: P 43 ARG cc_start: 0.6895 (mtt90) cc_final: 0.6592 (ttm110) REVERT: P 51 GLN cc_start: 0.7484 (tm-30) cc_final: 0.6997 (mt0) REVERT: P 61 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4652 (mm) REVERT: P 93 GLU cc_start: 0.8114 (tt0) cc_final: 0.7597 (mp0) REVERT: Q 88 GLN cc_start: 0.8055 (tt0) cc_final: 0.7551 (tp40) REVERT: Q 103 ASP cc_start: 0.7414 (m-30) cc_final: 0.6190 (t70) REVERT: R 73 LEU cc_start: 0.5285 (mt) cc_final: 0.4793 (tp) REVERT: R 78 ARG cc_start: 0.7442 (mmt180) cc_final: 0.6896 (mmp-170) REVERT: R 81 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6579 (mmt90) REVERT: R 118 VAL cc_start: 0.5537 (t) cc_final: 0.5296 (m) REVERT: S 12 GLN cc_start: 0.8221 (tt0) cc_final: 0.7419 (tp40) REVERT: S 44 ASN cc_start: 0.7790 (m-40) cc_final: 0.7483 (m110) REVERT: S 110 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7795 (ttp80) REVERT: S 136 GLN cc_start: 0.7839 (mt0) cc_final: 0.6750 (mt0) REVERT: T 8 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.4791 (p90) REVERT: T 23 LYS cc_start: 0.5181 (tppt) cc_final: 0.4759 (mttm) REVERT: T 89 ARG cc_start: 0.6807 (mtp180) cc_final: 0.6510 (mtp180) REVERT: T 107 LYS cc_start: 0.7626 (mttm) cc_final: 0.7328 (mtpp) REVERT: T 151 GLN cc_start: 0.8020 (mt0) cc_final: 0.7773 (mt0) REVERT: U 176 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6359 (mtt90) REVERT: U 195 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7629 (mm-30) REVERT: U 215 ILE cc_start: 0.6241 (mt) cc_final: 0.5920 (tt) REVERT: V 22 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7386 (ptp-110) REVERT: V 63 GLU cc_start: 0.5123 (OUTLIER) cc_final: 0.3917 (tm-30) REVERT: W 82 GLN cc_start: 0.7368 (mt0) cc_final: 0.6954 (mt0) REVERT: X 21 LYS cc_start: 0.7800 (mttt) cc_final: 0.7500 (mtmt) REVERT: X 35 ARG cc_start: 0.7258 (ttp-170) cc_final: 0.6811 (ptt-90) REVERT: X 48 LYS cc_start: 0.7556 (mttt) cc_final: 0.7196 (mtpt) REVERT: X 71 ARG cc_start: 0.6944 (ttm-80) cc_final: 0.6454 (ttt90) REVERT: X 80 LYS cc_start: 0.7915 (mttt) cc_final: 0.7549 (mtmm) REVERT: X 105 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8302 (t80) REVERT: X 114 ASP cc_start: 0.6264 (m-30) cc_final: 0.5842 (m-30) REVERT: Y 15 LYS cc_start: 0.7798 (tptt) cc_final: 0.7466 (tppt) REVERT: Y 51 ARG cc_start: 0.8481 (mtt180) cc_final: 0.7691 (mmp80) REVERT: Y 81 ASN cc_start: 0.8230 (m-40) cc_final: 0.7927 (t0) REVERT: Y 89 GLU cc_start: 0.7193 (tp30) cc_final: 0.6613 (tp30) REVERT: Y 90 ASN cc_start: 0.5282 (p0) cc_final: 0.4908 (p0) REVERT: Z 139 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7828 (pp30) REVERT: a 33 ASP cc_start: 0.7884 (p0) cc_final: 0.7660 (p0) REVERT: a 45 VAL cc_start: 0.8340 (m) cc_final: 0.8077 (p) REVERT: a 66 LYS cc_start: 0.8499 (mttp) cc_final: 0.7844 (mmpt) REVERT: a 74 CYS cc_start: 0.6865 (t) cc_final: 0.6631 (p) REVERT: b 4 ASP cc_start: 0.7641 (t0) cc_final: 0.7392 (t0) REVERT: c 11 LYS cc_start: 0.7352 (tttt) cc_final: 0.6802 (tttm) REVERT: c 24 GLN cc_start: 0.7424 (mt0) cc_final: 0.7212 (mm-40) REVERT: c 30 MET cc_start: 0.5079 (ttt) cc_final: 0.4789 (ppp) REVERT: c 50 ARG cc_start: 0.7929 (ptt180) cc_final: 0.7389 (ptt180) REVERT: c 51 GLU cc_start: 0.8611 (pt0) cc_final: 0.7857 (mt-10) REVERT: d 17 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6097 (ptp90) REVERT: d 25 ARG cc_start: 0.6440 (mtt-85) cc_final: 0.5457 (mmt180) REVERT: d 32 TYR cc_start: 0.8352 (m-80) cc_final: 0.7804 (m-80) REVERT: d 53 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.6398 (p90) REVERT: e 39 GLN cc_start: 0.7880 (mt0) cc_final: 0.7640 (mt0) REVERT: e 43 ARG cc_start: 0.7131 (mtt90) cc_final: 0.6769 (mtt-85) REVERT: m 20 LYS cc_start: 0.7936 (tttp) cc_final: 0.7702 (ttmm) REVERT: m 29 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.7780 (mtm110) outliers start: 159 outliers final: 100 residues processed: 1205 average time/residue: 0.7420 time to fit residues: 1455.6461 Evaluate side-chains 1183 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1067 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 8 TYR Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 138 THR Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 139 GLN Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 17 ARG Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 53 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 347 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 356 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 440 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 GLN C 102 GLN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN J 91 GLN L 119 GLN N 105 ASN R 74 GLN S 99 HIS ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 206 HIS ** Z 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 36 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 73591 Z= 0.291 Angle : 0.647 11.275 107052 Z= 0.327 Chirality : 0.038 0.267 13312 Planarity : 0.005 0.053 7623 Dihedral : 23.108 179.869 29813 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.19 % Favored : 91.87 % Rotamer: Outliers : 5.05 % Allowed : 24.51 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.28 (0.13), residues: 4283 helix: 0.41 (0.14), residues: 1420 sheet: -0.60 (0.19), residues: 681 loop : -1.83 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 251 HIS 0.007 0.001 HIS E 17 PHE 0.021 0.002 PHE K 75 TYR 0.039 0.002 TYR a 59 ARG 0.008 0.001 ARG I 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1071 time to evaluate : 3.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.5194 (OUTLIER) cc_final: 0.4410 (pp30) REVERT: A 22 CYS cc_start: 0.7313 (m) cc_final: 0.7033 (m) REVERT: A 32 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 156 GLU cc_start: 0.8533 (mp0) cc_final: 0.7724 (pm20) REVERT: A 200 MET cc_start: 0.7666 (mtp) cc_final: 0.6542 (ttm) REVERT: A 206 TRP cc_start: 0.7227 (t60) cc_final: 0.6794 (t60) REVERT: A 208 ASP cc_start: 0.8452 (m-30) cc_final: 0.8221 (m-30) REVERT: B 29 TRP cc_start: 0.7935 (m100) cc_final: 0.7437 (m-10) REVERT: B 79 GLN cc_start: 0.7500 (mp10) cc_final: 0.6866 (mp10) REVERT: B 89 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7225 (tp30) REVERT: B 92 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7021 (pp30) REVERT: B 111 CYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7591 (m) REVERT: B 177 SER cc_start: 0.6964 (t) cc_final: 0.6714 (p) REVERT: B 198 GLU cc_start: 0.8588 (tt0) cc_final: 0.8051 (pt0) REVERT: B 224 ASP cc_start: 0.7725 (t0) cc_final: 0.7420 (t0) REVERT: B 229 MET cc_start: 0.8854 (mmp) cc_final: 0.8414 (mmm) REVERT: C 52 ILE cc_start: 0.8305 (mt) cc_final: 0.8079 (mm) REVERT: C 53 SER cc_start: 0.7321 (t) cc_final: 0.6940 (p) REVERT: C 55 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6529 (tp) REVERT: C 67 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6922 (mp0) REVERT: C 73 HIS cc_start: 0.7233 (t-90) cc_final: 0.6901 (t-90) REVERT: C 76 GLN cc_start: 0.7874 (mm110) cc_final: 0.7503 (mm110) REVERT: C 124 LYS cc_start: 0.7481 (tttt) cc_final: 0.7126 (tttm) REVERT: C 134 ARG cc_start: 0.7031 (mtt180) cc_final: 0.6691 (mtm-85) REVERT: C 143 SER cc_start: 0.8099 (t) cc_final: 0.7797 (p) REVERT: C 164 MET cc_start: 0.8148 (pmm) cc_final: 0.7925 (pmm) REVERT: C 209 LYS cc_start: 0.8283 (tttt) cc_final: 0.7940 (ttpt) REVERT: D 12 LYS cc_start: 0.7860 (mttm) cc_final: 0.7297 (mtmm) REVERT: D 20 GLN cc_start: 0.7532 (tp40) cc_final: 0.7171 (mp10) REVERT: D 28 SER cc_start: 0.7509 (t) cc_final: 0.7141 (m) REVERT: D 33 GLU cc_start: 0.8333 (tt0) cc_final: 0.7858 (mm-30) REVERT: D 58 ARG cc_start: 0.7480 (mmt90) cc_final: 0.7253 (mmm160) REVERT: D 59 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6946 (mp0) REVERT: D 87 GLU cc_start: 0.6542 (pt0) cc_final: 0.6017 (pm20) REVERT: D 96 ARG cc_start: 0.7186 (ptp90) cc_final: 0.6593 (ptm-80) REVERT: D 105 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: D 121 CYS cc_start: 0.7994 (m) cc_final: 0.7407 (p) REVERT: D 126 ARG cc_start: 0.7647 (mmm160) cc_final: 0.7038 (mtm-85) REVERT: D 134 LYS cc_start: 0.7374 (tptt) cc_final: 0.6939 (mtpt) REVERT: D 150 LYS cc_start: 0.7171 (ttpp) cc_final: 0.6931 (ttpp) REVERT: D 153 LYS cc_start: 0.6799 (ttmt) cc_final: 0.6283 (mtmt) REVERT: D 164 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7462 (tm-30) REVERT: D 187 ARG cc_start: 0.6986 (mmm-85) cc_final: 0.6394 (mmm-85) REVERT: D 189 LYS cc_start: 0.7449 (ttmt) cc_final: 0.6791 (mtmm) REVERT: E 7 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7469 (mmtt) REVERT: E 26 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.7606 (t-170) REVERT: E 51 ARG cc_start: 0.7970 (mmt-90) cc_final: 0.7601 (mpt180) REVERT: E 62 MET cc_start: 0.7939 (mtt) cc_final: 0.7489 (mmt) REVERT: E 79 ASP cc_start: 0.8445 (t70) cc_final: 0.8149 (t70) REVERT: E 153 SER cc_start: 0.8998 (m) cc_final: 0.8370 (t) REVERT: E 155 LYS cc_start: 0.7468 (tttt) cc_final: 0.7022 (mmtm) REVERT: E 165 ASN cc_start: 0.7804 (m110) cc_final: 0.7264 (m-40) REVERT: E 174 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7569 (mtpp) REVERT: E 176 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7393 (pm20) REVERT: E 180 MET cc_start: 0.8457 (ttm) cc_final: 0.8216 (mtm) REVERT: E 199 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6993 (mp0) REVERT: E 209 HIS cc_start: 0.7079 (m-70) cc_final: 0.6566 (m-70) REVERT: E 217 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: E 242 LYS cc_start: 0.8433 (mttt) cc_final: 0.7954 (mmtm) REVERT: E 246 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7267 (pp) REVERT: E 247 SER cc_start: 0.7147 (t) cc_final: 0.6594 (m) REVERT: F 93 ASP cc_start: 0.7593 (p0) cc_final: 0.7316 (m-30) REVERT: F 115 ARG cc_start: 0.7784 (mmt-90) cc_final: 0.6749 (mmt-90) REVERT: F 124 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.7002 (mtp180) REVERT: F 180 LYS cc_start: 0.6904 (mmmt) cc_final: 0.6617 (mmmm) REVERT: G 7 ASN cc_start: 0.7948 (t0) cc_final: 0.7588 (t0) REVERT: G 12 MET cc_start: 0.7736 (mmt) cc_final: 0.6271 (mmt) REVERT: G 30 LYS cc_start: 0.7318 (mmmt) cc_final: 0.6881 (mtpt) REVERT: G 44 GLU cc_start: 0.8636 (pt0) cc_final: 0.8284 (pm20) REVERT: G 79 LYS cc_start: 0.8351 (tttt) cc_final: 0.7953 (tppt) REVERT: G 161 GLN cc_start: 0.8687 (pt0) cc_final: 0.8312 (tt0) REVERT: G 194 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8046 (ptp90) REVERT: G 202 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6987 (mt-10) REVERT: H 90 LYS cc_start: 0.8241 (tptt) cc_final: 0.7794 (tmtt) REVERT: I 8 ARG cc_start: 0.7153 (mtm110) cc_final: 0.5941 (mtp180) REVERT: I 22 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: I 35 MET cc_start: 0.7936 (mtt) cc_final: 0.7482 (mmp) REVERT: I 65 TYR cc_start: 0.8900 (m-80) cc_final: 0.7949 (m-80) REVERT: I 77 ARG cc_start: 0.7377 (ttt180) cc_final: 0.6923 (ttp80) REVERT: I 88 ASN cc_start: 0.7769 (m-40) cc_final: 0.7285 (m110) REVERT: I 92 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7052 (mtp85) REVERT: I 114 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8053 (mmm160) REVERT: I 115 SER cc_start: 0.8990 (t) cc_final: 0.8489 (p) REVERT: I 154 LYS cc_start: 0.8585 (mmmt) cc_final: 0.7917 (tttp) REVERT: I 162 GLN cc_start: 0.8303 (tt0) cc_final: 0.7790 (tt0) REVERT: I 190 GLU cc_start: 0.7184 (tp30) cc_final: 0.6929 (tp30) REVERT: J 41 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7015 (mt-10) REVERT: J 46 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: J 47 TYR cc_start: 0.7641 (t80) cc_final: 0.7414 (t80) REVERT: J 65 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7927 (mtpp) REVERT: J 66 ASP cc_start: 0.6670 (t0) cc_final: 0.6011 (t0) REVERT: J 86 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8021 (tp) REVERT: J 116 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6736 (mm) REVERT: J 147 MET cc_start: 0.7902 (mtt) cc_final: 0.7623 (mmm) REVERT: K 32 GLN cc_start: 0.6969 (tt0) cc_final: 0.6521 (tp40) REVERT: K 75 PHE cc_start: 0.6301 (m-10) cc_final: 0.5565 (m-80) REVERT: L 53 SER cc_start: 0.7285 (t) cc_final: 0.6680 (p) REVERT: L 54 LYS cc_start: 0.8070 (tptt) cc_final: 0.7747 (ttmm) REVERT: L 141 ASN cc_start: 0.7897 (t0) cc_final: 0.7539 (t0) REVERT: N 34 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7635 (mt-10) REVERT: N 112 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7569 (tttm) REVERT: N 140 LYS cc_start: 0.8473 (pttt) cc_final: 0.8062 (tptt) REVERT: N 147 SER cc_start: 0.8425 (m) cc_final: 0.8075 (m) REVERT: O 81 MET cc_start: 0.6925 (tpp) cc_final: 0.6326 (tpp) REVERT: O 111 LYS cc_start: 0.7349 (mtmt) cc_final: 0.6907 (mtmm) REVERT: P 33 MET cc_start: 0.3568 (OUTLIER) cc_final: 0.3029 (ttt) REVERT: P 41 LEU cc_start: 0.7262 (mt) cc_final: 0.7010 (tt) REVERT: P 42 PHE cc_start: 0.6897 (m-80) cc_final: 0.6517 (m-80) REVERT: P 51 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7009 (mt0) REVERT: P 93 GLU cc_start: 0.8309 (tt0) cc_final: 0.7693 (mp0) REVERT: Q 103 ASP cc_start: 0.7407 (m-30) cc_final: 0.6188 (t70) REVERT: Q 111 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7130 (tpm170) REVERT: R 78 ARG cc_start: 0.7476 (mmt180) cc_final: 0.6819 (mmm160) REVERT: R 81 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6360 (tpt90) REVERT: S 12 GLN cc_start: 0.8236 (tt0) cc_final: 0.7424 (tp40) REVERT: S 136 GLN cc_start: 0.7804 (mt0) cc_final: 0.6954 (mt0) REVERT: T 8 TYR cc_start: 0.5933 (OUTLIER) cc_final: 0.5087 (p90) REVERT: T 89 ARG cc_start: 0.6959 (mtp180) cc_final: 0.6585 (mtp180) REVERT: T 107 LYS cc_start: 0.7651 (mttm) cc_final: 0.7170 (mtpp) REVERT: T 151 GLN cc_start: 0.7987 (mt0) cc_final: 0.7757 (mt0) REVERT: U 155 ASN cc_start: 0.6813 (m-40) cc_final: 0.6301 (t0) REVERT: U 176 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6399 (mtt90) REVERT: U 195 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7698 (mm-30) REVERT: U 215 ILE cc_start: 0.6577 (mt) cc_final: 0.6266 (tt) REVERT: V 22 ARG cc_start: 0.7829 (mtp180) cc_final: 0.7325 (ptp-110) REVERT: V 63 GLU cc_start: 0.5266 (OUTLIER) cc_final: 0.3948 (tm-30) REVERT: X 21 LYS cc_start: 0.7849 (mttt) cc_final: 0.7562 (mtmt) REVERT: X 35 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.6809 (ptt-90) REVERT: X 48 LYS cc_start: 0.7530 (mttt) cc_final: 0.7130 (mtpt) REVERT: X 71 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6708 (ttt90) REVERT: X 80 LYS cc_start: 0.7861 (mttt) cc_final: 0.7525 (mtmm) REVERT: X 114 ASP cc_start: 0.6290 (m-30) cc_final: 0.5957 (m-30) REVERT: Y 15 LYS cc_start: 0.7747 (tptt) cc_final: 0.7390 (tppt) REVERT: Y 51 ARG cc_start: 0.8485 (mtt180) cc_final: 0.7666 (mmp80) REVERT: Y 72 SER cc_start: 0.8168 (t) cc_final: 0.7930 (p) REVERT: Y 89 GLU cc_start: 0.7261 (tp30) cc_final: 0.6613 (tp30) REVERT: a 33 ASP cc_start: 0.7929 (p0) cc_final: 0.7699 (p0) REVERT: a 45 VAL cc_start: 0.8221 (m) cc_final: 0.7959 (p) REVERT: a 52 ASP cc_start: 0.7912 (t70) cc_final: 0.7505 (t70) REVERT: a 66 LYS cc_start: 0.8504 (mttp) cc_final: 0.7837 (mmpt) REVERT: b 4 ASP cc_start: 0.7583 (t0) cc_final: 0.7344 (t0) REVERT: c 11 LYS cc_start: 0.7611 (tttt) cc_final: 0.7075 (tttm) REVERT: c 24 GLN cc_start: 0.7655 (mt0) cc_final: 0.7381 (mm-40) REVERT: c 50 ARG cc_start: 0.7728 (ptt180) cc_final: 0.7298 (ptp-170) REVERT: c 51 GLU cc_start: 0.8564 (pt0) cc_final: 0.7929 (mt-10) REVERT: d 17 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6049 (ptp90) REVERT: d 25 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.5509 (mmt180) REVERT: d 26 HIS cc_start: 0.7718 (m90) cc_final: 0.7222 (m90) REVERT: d 32 TYR cc_start: 0.8315 (m-80) cc_final: 0.7910 (m-80) REVERT: d 39 GLN cc_start: 0.8190 (mp10) cc_final: 0.7963 (mp10) REVERT: d 53 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6327 (p90) REVERT: e 39 GLN cc_start: 0.7937 (mt0) cc_final: 0.7710 (mt0) REVERT: e 43 ARG cc_start: 0.7050 (mtt90) cc_final: 0.6676 (mtt-85) REVERT: m 20 LYS cc_start: 0.7986 (tttp) cc_final: 0.7669 (ttmm) REVERT: m 29 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.8053 (mtm180) outliers start: 182 outliers final: 138 residues processed: 1162 average time/residue: 0.7423 time to fit residues: 1412.3587 Evaluate side-chains 1207 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1052 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 8 TYR Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain U residue 211 VAL Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 17 ARG Chi-restraints excluded: chain d residue 20 ARG Chi-restraints excluded: chain d residue 34 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain e residue 31 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 510 optimal weight: 2.9990 chunk 537 optimal weight: 7.9990 chunk 490 optimal weight: 8.9990 chunk 522 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 410 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 472 optimal weight: 1.9990 chunk 494 optimal weight: 0.1980 chunk 520 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN I 87 ASN S 99 HIS ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 73591 Z= 0.243 Angle : 0.630 11.608 107052 Z= 0.319 Chirality : 0.037 0.279 13312 Planarity : 0.005 0.054 7623 Dihedral : 23.086 179.954 29810 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.26 % Favored : 91.87 % Rotamer: Outliers : 4.55 % Allowed : 25.03 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.24 (0.13), residues: 4283 helix: 0.41 (0.14), residues: 1428 sheet: -0.43 (0.20), residues: 668 loop : -1.84 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 84 HIS 0.010 0.001 HIS J 124 PHE 0.021 0.002 PHE K 62 TYR 0.038 0.002 TYR a 59 ARG 0.010 0.001 ARG H 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1071 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.4441 (pp30) REVERT: A 22 CYS cc_start: 0.7448 (m) cc_final: 0.7217 (m) REVERT: A 104 TRP cc_start: 0.8111 (t60) cc_final: 0.7899 (t-100) REVERT: A 137 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7202 (mt-10) REVERT: A 156 GLU cc_start: 0.8524 (mp0) cc_final: 0.7723 (pm20) REVERT: A 200 MET cc_start: 0.7749 (mtp) cc_final: 0.6231 (ttp) REVERT: A 206 TRP cc_start: 0.7270 (t60) cc_final: 0.6853 (t60) REVERT: A 208 ASP cc_start: 0.8442 (m-30) cc_final: 0.8199 (m-30) REVERT: B 29 TRP cc_start: 0.7995 (m100) cc_final: 0.7483 (m-10) REVERT: B 79 GLN cc_start: 0.7598 (mp10) cc_final: 0.7237 (mp10) REVERT: B 89 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7198 (tp30) REVERT: B 111 CYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7438 (m) REVERT: B 177 SER cc_start: 0.6972 (t) cc_final: 0.6726 (p) REVERT: B 224 ASP cc_start: 0.7907 (t0) cc_final: 0.7569 (t0) REVERT: B 229 MET cc_start: 0.8856 (mmp) cc_final: 0.8438 (mmm) REVERT: C 52 ILE cc_start: 0.8289 (mt) cc_final: 0.8073 (mm) REVERT: C 53 SER cc_start: 0.7331 (t) cc_final: 0.6960 (p) REVERT: C 55 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6497 (tp) REVERT: C 67 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7024 (mp0) REVERT: C 73 HIS cc_start: 0.7239 (t-90) cc_final: 0.6883 (t-90) REVERT: C 76 GLN cc_start: 0.7884 (mm110) cc_final: 0.7482 (mm110) REVERT: C 124 LYS cc_start: 0.7477 (tttt) cc_final: 0.7123 (tttm) REVERT: C 134 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6666 (mtm-85) REVERT: C 143 SER cc_start: 0.7972 (t) cc_final: 0.7666 (p) REVERT: C 164 MET cc_start: 0.8150 (pmm) cc_final: 0.7932 (pmm) REVERT: C 209 LYS cc_start: 0.8305 (tttt) cc_final: 0.7614 (ttpt) REVERT: D 12 LYS cc_start: 0.7845 (mttm) cc_final: 0.7309 (mtmm) REVERT: D 20 GLN cc_start: 0.7536 (tp40) cc_final: 0.7164 (mp10) REVERT: D 28 SER cc_start: 0.7507 (t) cc_final: 0.7117 (m) REVERT: D 50 ILE cc_start: 0.4631 (mm) cc_final: 0.4249 (mt) REVERT: D 58 ARG cc_start: 0.7396 (mmt90) cc_final: 0.7191 (mmm160) REVERT: D 59 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7068 (mp0) REVERT: D 87 GLU cc_start: 0.6497 (pt0) cc_final: 0.6059 (pm20) REVERT: D 96 ARG cc_start: 0.7167 (ptp90) cc_final: 0.6545 (ptm-80) REVERT: D 105 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7287 (tt0) REVERT: D 121 CYS cc_start: 0.8015 (m) cc_final: 0.7425 (p) REVERT: D 126 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7091 (mtm-85) REVERT: D 134 LYS cc_start: 0.7324 (tptt) cc_final: 0.6870 (mtpt) REVERT: D 150 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6909 (ttpp) REVERT: D 153 LYS cc_start: 0.6850 (ttmt) cc_final: 0.6275 (mtmt) REVERT: D 164 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7455 (tm-30) REVERT: D 187 ARG cc_start: 0.7019 (mmm-85) cc_final: 0.6522 (mmm-85) REVERT: D 189 LYS cc_start: 0.7485 (ttmt) cc_final: 0.6854 (mtmm) REVERT: D 213 MET cc_start: 0.5376 (ppp) cc_final: 0.4151 (tpp) REVERT: E 7 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7545 (mmmt) REVERT: E 26 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.7597 (t-170) REVERT: E 51 ARG cc_start: 0.7998 (mmt-90) cc_final: 0.7552 (mpt180) REVERT: E 62 MET cc_start: 0.7934 (mtt) cc_final: 0.7520 (mmt) REVERT: E 79 ASP cc_start: 0.8441 (t70) cc_final: 0.8146 (t70) REVERT: E 87 MET cc_start: 0.8225 (mmm) cc_final: 0.7161 (tpp) REVERT: E 153 SER cc_start: 0.9023 (m) cc_final: 0.8341 (t) REVERT: E 155 LYS cc_start: 0.7455 (tttt) cc_final: 0.7009 (mmtm) REVERT: E 165 ASN cc_start: 0.7932 (m110) cc_final: 0.7448 (m-40) REVERT: E 174 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7601 (mtpp) REVERT: E 176 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7433 (pm20) REVERT: E 180 MET cc_start: 0.8441 (ttm) cc_final: 0.8219 (mtm) REVERT: E 199 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6984 (mp0) REVERT: E 209 HIS cc_start: 0.7057 (m-70) cc_final: 0.6538 (m-70) REVERT: E 217 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: E 242 LYS cc_start: 0.8452 (mttt) cc_final: 0.7956 (mmtm) REVERT: E 246 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7346 (pp) REVERT: E 247 SER cc_start: 0.7137 (t) cc_final: 0.6609 (m) REVERT: F 63 SER cc_start: 0.7390 (t) cc_final: 0.7169 (m) REVERT: F 93 ASP cc_start: 0.7575 (p0) cc_final: 0.7313 (m-30) REVERT: F 115 ARG cc_start: 0.7855 (mmt-90) cc_final: 0.6636 (mmt-90) REVERT: F 124 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.6985 (mtp180) REVERT: F 180 LYS cc_start: 0.6902 (mmmt) cc_final: 0.6614 (mmmm) REVERT: G 7 ASN cc_start: 0.7952 (t0) cc_final: 0.7599 (t0) REVERT: G 12 MET cc_start: 0.7583 (mmt) cc_final: 0.6208 (mmt) REVERT: G 30 LYS cc_start: 0.7252 (mmmt) cc_final: 0.6787 (mtpt) REVERT: G 44 GLU cc_start: 0.8719 (pt0) cc_final: 0.8353 (pm20) REVERT: G 79 LYS cc_start: 0.8324 (tttt) cc_final: 0.7937 (tppt) REVERT: G 161 GLN cc_start: 0.8678 (pt0) cc_final: 0.8281 (tt0) REVERT: G 194 ARG cc_start: 0.8593 (ttm110) cc_final: 0.8026 (ptp90) REVERT: G 202 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6984 (mt-10) REVERT: H 90 LYS cc_start: 0.8103 (tptt) cc_final: 0.7545 (tmtt) REVERT: I 8 ARG cc_start: 0.7112 (mtm110) cc_final: 0.5946 (mtp180) REVERT: I 22 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: I 35 MET cc_start: 0.7879 (mtt) cc_final: 0.7388 (mmp) REVERT: I 65 TYR cc_start: 0.8903 (m-80) cc_final: 0.8036 (m-80) REVERT: I 77 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7006 (ttp80) REVERT: I 92 ARG cc_start: 0.7898 (ttt180) cc_final: 0.7476 (ttm-80) REVERT: I 114 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8056 (mmm160) REVERT: I 115 SER cc_start: 0.8990 (t) cc_final: 0.8485 (p) REVERT: I 154 LYS cc_start: 0.8531 (mmmt) cc_final: 0.7918 (tttp) REVERT: I 162 GLN cc_start: 0.8351 (tt0) cc_final: 0.7818 (tt0) REVERT: I 190 GLU cc_start: 0.7014 (tp30) cc_final: 0.6735 (tp30) REVERT: J 13 ARG cc_start: 0.8335 (ptm160) cc_final: 0.8077 (ptm160) REVERT: J 41 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7118 (mt-10) REVERT: J 46 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: J 47 TYR cc_start: 0.7673 (t80) cc_final: 0.7458 (t80) REVERT: J 65 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7975 (mtpp) REVERT: J 68 ARG cc_start: 0.7504 (tmt-80) cc_final: 0.6495 (tpt170) REVERT: J 116 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6577 (mm) REVERT: J 147 MET cc_start: 0.7966 (mtt) cc_final: 0.7697 (mmm) REVERT: K 32 GLN cc_start: 0.6879 (tt0) cc_final: 0.6474 (tp40) REVERT: L 53 SER cc_start: 0.7176 (t) cc_final: 0.6535 (p) REVERT: L 54 LYS cc_start: 0.8030 (tptt) cc_final: 0.7703 (ttmm) REVERT: L 141 ASN cc_start: 0.7850 (t0) cc_final: 0.7479 (t0) REVERT: N 34 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7626 (mt-10) REVERT: N 112 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7562 (tttm) REVERT: N 140 LYS cc_start: 0.8496 (pttt) cc_final: 0.8057 (tptt) REVERT: N 147 SER cc_start: 0.8456 (m) cc_final: 0.8106 (m) REVERT: O 80 MET cc_start: 0.7529 (ttm) cc_final: 0.6736 (mtt) REVERT: O 81 MET cc_start: 0.6928 (tpp) cc_final: 0.6228 (tpp) REVERT: O 111 LYS cc_start: 0.7348 (mtmt) cc_final: 0.6915 (mtmm) REVERT: P 41 LEU cc_start: 0.7248 (mt) cc_final: 0.6975 (tt) REVERT: P 42 PHE cc_start: 0.6993 (m-80) cc_final: 0.6566 (m-80) REVERT: P 51 GLN cc_start: 0.7238 (tm-30) cc_final: 0.7005 (mt0) REVERT: P 93 GLU cc_start: 0.8271 (tt0) cc_final: 0.7814 (mp0) REVERT: Q 103 ASP cc_start: 0.7412 (m-30) cc_final: 0.6201 (t70) REVERT: R 81 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6498 (tpt170) REVERT: R 82 MET cc_start: 0.5813 (mtm) cc_final: 0.5599 (mtm) REVERT: S 12 GLN cc_start: 0.8197 (tt0) cc_final: 0.7346 (tp40) REVERT: S 136 GLN cc_start: 0.7762 (mt0) cc_final: 0.6907 (mt0) REVERT: T 8 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.5072 (p90) REVERT: T 23 LYS cc_start: 0.4990 (tppt) cc_final: 0.4512 (mttm) REVERT: T 89 ARG cc_start: 0.6938 (mtp180) cc_final: 0.6564 (mtp180) REVERT: T 107 LYS cc_start: 0.7647 (mttm) cc_final: 0.7163 (mtpp) REVERT: T 115 TYR cc_start: 0.7640 (t80) cc_final: 0.7031 (t80) REVERT: T 151 GLN cc_start: 0.7979 (mt0) cc_final: 0.7737 (mt0) REVERT: U 155 ASN cc_start: 0.6837 (m-40) cc_final: 0.6308 (t0) REVERT: U 176 ARG cc_start: 0.7172 (mtt180) cc_final: 0.6412 (mtt90) REVERT: U 195 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7685 (mm-30) REVERT: U 215 ILE cc_start: 0.6524 (mt) cc_final: 0.6221 (tt) REVERT: V 22 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7378 (ptp-110) REVERT: V 63 GLU cc_start: 0.5109 (OUTLIER) cc_final: 0.3828 (tm-30) REVERT: X 21 LYS cc_start: 0.7843 (mttt) cc_final: 0.7564 (mtmt) REVERT: X 35 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6797 (ptt-90) REVERT: X 48 LYS cc_start: 0.7509 (mttt) cc_final: 0.7111 (mtpt) REVERT: X 80 LYS cc_start: 0.7862 (mttt) cc_final: 0.7619 (mtmm) REVERT: X 114 ASP cc_start: 0.6241 (m-30) cc_final: 0.5944 (m-30) REVERT: Y 15 LYS cc_start: 0.7743 (tptt) cc_final: 0.7382 (tppt) REVERT: Y 51 ARG cc_start: 0.8486 (mtt180) cc_final: 0.7757 (mmp80) REVERT: Y 72 SER cc_start: 0.8231 (t) cc_final: 0.7979 (p) REVERT: Y 81 ASN cc_start: 0.8260 (m110) cc_final: 0.7873 (t0) REVERT: Y 89 GLU cc_start: 0.7220 (tp30) cc_final: 0.6527 (tp30) REVERT: Y 90 ASN cc_start: 0.5608 (p0) cc_final: 0.5100 (p0) REVERT: a 33 ASP cc_start: 0.7931 (p0) cc_final: 0.7681 (p0) REVERT: a 45 VAL cc_start: 0.8255 (m) cc_final: 0.8045 (p) REVERT: a 66 LYS cc_start: 0.8506 (mttp) cc_final: 0.7838 (mmpt) REVERT: b 4 ASP cc_start: 0.7479 (t0) cc_final: 0.7243 (t0) REVERT: c 11 LYS cc_start: 0.7587 (tttt) cc_final: 0.7030 (tttm) REVERT: c 24 GLN cc_start: 0.7555 (mt0) cc_final: 0.7305 (mm-40) REVERT: c 50 ARG cc_start: 0.7763 (ptt180) cc_final: 0.7220 (ptp-170) REVERT: c 51 GLU cc_start: 0.8536 (pt0) cc_final: 0.7903 (mt-10) REVERT: d 17 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6045 (ptp90) REVERT: d 25 ARG cc_start: 0.6447 (mtt-85) cc_final: 0.5512 (mmt180) REVERT: d 26 HIS cc_start: 0.7725 (m90) cc_final: 0.7270 (m90) REVERT: d 39 GLN cc_start: 0.8204 (mp10) cc_final: 0.7832 (mp10) REVERT: d 53 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6360 (p90) REVERT: e 39 GLN cc_start: 0.7924 (mt0) cc_final: 0.7698 (mt0) REVERT: e 43 ARG cc_start: 0.7023 (mtt90) cc_final: 0.6645 (mtt-85) REVERT: m 20 LYS cc_start: 0.7983 (tttp) cc_final: 0.7677 (ttmm) REVERT: m 29 ARG cc_start: 0.8443 (ttp-170) cc_final: 0.7790 (mtm110) outliers start: 164 outliers final: 143 residues processed: 1150 average time/residue: 0.7439 time to fit residues: 1394.8390 Evaluate side-chains 1213 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1056 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 164 CYS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 98 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 8 TYR Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 112 ILE Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 95 PHE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain d residue 17 ARG Chi-restraints excluded: chain d residue 20 ARG Chi-restraints excluded: chain d residue 34 LEU Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain e residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 343 optimal weight: 6.9990 chunk 552 optimal weight: 4.9990 chunk 337 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 579 optimal weight: 3.9990 chunk 533 optimal weight: 1.9990 chunk 461 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 356 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN S 99 HIS V 60 GLN ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 73591 Z= 0.196 Angle : 0.609 12.862 107052 Z= 0.308 Chirality : 0.036 0.315 13312 Planarity : 0.004 0.052 7623 Dihedral : 23.041 179.768 29810 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.26 % Favored : 91.97 % Rotamer: Outliers : 4.30 % Allowed : 25.59 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % Twisted Proline : 0.57 % 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: -1.14 (0.13), residues: 4283 helix: 0.54 (0.14), residues: 1420 sheet: -0.38 (0.20), residues: 679 loop : -1.81 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP S 84 HIS 0.009 0.001 HIS P 133 PHE 0.023 0.002 PHE K 75 TYR 0.040 0.002 TYR a 59 ARG 0.009 0.001 ARG H 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1073 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.5543 (OUTLIER) cc_final: 0.4827 (pp30) REVERT: A 19 MET cc_start: 0.8730 (mtp) cc_final: 0.8440 (mtt) REVERT: A 22 CYS cc_start: 0.7414 (m) cc_final: 0.7127 (m) REVERT: A 32 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 104 TRP cc_start: 0.8186 (t60) cc_final: 0.7907 (t-100) REVERT: A 137 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7189 (mt-10) REVERT: A 156 GLU cc_start: 0.8513 (mp0) cc_final: 0.7697 (pm20) REVERT: A 200 MET cc_start: 0.7732 (mtp) cc_final: 0.6228 (ttp) REVERT: A 206 TRP cc_start: 0.7098 (t60) cc_final: 0.6691 (t60) REVERT: A 208 ASP cc_start: 0.8429 (m-30) cc_final: 0.8183 (m-30) REVERT: B 29 TRP cc_start: 0.8018 (m100) cc_final: 0.7455 (m-10) REVERT: B 79 GLN cc_start: 0.7595 (mp10) cc_final: 0.7230 (mp10) REVERT: B 89 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7179 (tp30) REVERT: B 92 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7003 (pp30) REVERT: B 111 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7430 (m) REVERT: B 177 SER cc_start: 0.6958 (t) cc_final: 0.6722 (p) REVERT: B 198 GLU cc_start: 0.8541 (tt0) cc_final: 0.8153 (pt0) REVERT: B 199 ASN cc_start: 0.7433 (m-40) cc_final: 0.7228 (m110) REVERT: B 224 ASP cc_start: 0.7909 (t0) cc_final: 0.7545 (t0) REVERT: B 229 MET cc_start: 0.8844 (mmp) cc_final: 0.8438 (mmm) REVERT: C 52 ILE cc_start: 0.8322 (mt) cc_final: 0.8117 (mm) REVERT: C 53 SER cc_start: 0.7326 (t) cc_final: 0.6994 (p) REVERT: C 55 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6484 (tp) REVERT: C 67 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7075 (mp0) REVERT: C 73 HIS cc_start: 0.7314 (t-90) cc_final: 0.6921 (t-90) REVERT: C 76 GLN cc_start: 0.7943 (mm110) cc_final: 0.7510 (mm110) REVERT: C 124 LYS cc_start: 0.7515 (tttt) cc_final: 0.7156 (tttm) REVERT: C 134 ARG cc_start: 0.6969 (mtt180) cc_final: 0.6637 (mtm-85) REVERT: C 143 SER cc_start: 0.7967 (t) cc_final: 0.7666 (p) REVERT: C 164 MET cc_start: 0.8276 (pmm) cc_final: 0.8027 (pmm) REVERT: C 209 LYS cc_start: 0.8383 (tttt) cc_final: 0.7661 (ttpt) REVERT: D 12 LYS cc_start: 0.7899 (mttm) cc_final: 0.7375 (mtmm) REVERT: D 20 GLN cc_start: 0.7546 (tp40) cc_final: 0.7155 (mp10) REVERT: D 33 GLU cc_start: 0.8242 (tt0) cc_final: 0.7716 (mm-30) REVERT: D 50 ILE cc_start: 0.4625 (mm) cc_final: 0.4260 (mt) REVERT: D 59 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7093 (mp0) REVERT: D 87 GLU cc_start: 0.6609 (pt0) cc_final: 0.6271 (pm20) REVERT: D 96 ARG cc_start: 0.7204 (ptp90) cc_final: 0.6570 (ptm-80) REVERT: D 105 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: D 121 CYS cc_start: 0.8022 (m) cc_final: 0.7406 (p) REVERT: D 126 ARG cc_start: 0.7700 (mmm160) cc_final: 0.7108 (mtm-85) REVERT: D 134 LYS cc_start: 0.7299 (tptt) cc_final: 0.6908 (mtpt) REVERT: D 150 LYS cc_start: 0.7218 (ttpp) cc_final: 0.6998 (ttpp) REVERT: D 153 LYS cc_start: 0.7167 (ttmt) cc_final: 0.6582 (mtmt) REVERT: D 164 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 187 ARG cc_start: 0.7023 (mmm-85) cc_final: 0.6531 (mmm-85) REVERT: D 189 LYS cc_start: 0.7469 (ttmt) cc_final: 0.6845 (mtmm) REVERT: D 213 MET cc_start: 0.5441 (ppp) cc_final: 0.4183 (tpp) REVERT: E 7 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7022 (mttt) REVERT: E 26 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.7585 (t-170) REVERT: E 51 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.7592 (mpt180) REVERT: E 62 MET cc_start: 0.7902 (mtt) cc_final: 0.7466 (mmt) REVERT: E 79 ASP cc_start: 0.8433 (t70) cc_final: 0.8137 (t70) REVERT: E 87 MET cc_start: 0.8196 (mmm) cc_final: 0.7149 (tpp) REVERT: E 153 SER cc_start: 0.9008 (m) cc_final: 0.8524 (t) REVERT: E 155 LYS cc_start: 0.7478 (tttt) cc_final: 0.7012 (mmtt) REVERT: E 165 ASN cc_start: 0.7995 (m110) cc_final: 0.7494 (m-40) REVERT: E 174 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7581 (mtpp) REVERT: E 176 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7430 (pm20) REVERT: E 180 MET cc_start: 0.8603 (ttm) cc_final: 0.8383 (mtm) REVERT: E 199 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6993 (mp0) REVERT: E 209 HIS cc_start: 0.7209 (m-70) cc_final: 0.6617 (m-70) REVERT: E 217 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: E 242 LYS cc_start: 0.8394 (mttt) cc_final: 0.7923 (mmtm) REVERT: E 247 SER cc_start: 0.7181 (t) cc_final: 0.6701 (m) REVERT: F 93 ASP cc_start: 0.7562 (p0) cc_final: 0.7315 (m-30) REVERT: F 115 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.6581 (mmt-90) REVERT: F 124 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6983 (mtp180) REVERT: F 180 LYS cc_start: 0.6897 (mmmt) cc_final: 0.6651 (mmmm) REVERT: F 184 ILE cc_start: 0.7975 (mt) cc_final: 0.7654 (tt) REVERT: G 7 ASN cc_start: 0.7897 (t0) cc_final: 0.7584 (t0) REVERT: G 12 MET cc_start: 0.7545 (mmt) cc_final: 0.6326 (mmt) REVERT: G 30 LYS cc_start: 0.7092 (mmmt) cc_final: 0.6650 (mtpt) REVERT: G 44 GLU cc_start: 0.8695 (pt0) cc_final: 0.8307 (pm20) REVERT: G 79 LYS cc_start: 0.8309 (tttt) cc_final: 0.7922 (tppt) REVERT: G 161 GLN cc_start: 0.8661 (pt0) cc_final: 0.8287 (tt0) REVERT: G 194 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8038 (ptp90) REVERT: G 202 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6986 (mt-10) REVERT: H 41 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7260 (p0) REVERT: H 90 LYS cc_start: 0.8125 (tptt) cc_final: 0.7556 (tmtt) REVERT: I 8 ARG cc_start: 0.7014 (mtm110) cc_final: 0.6004 (mtp180) REVERT: I 22 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: I 35 MET cc_start: 0.7960 (mtt) cc_final: 0.7484 (mmp) REVERT: I 65 TYR cc_start: 0.8919 (m-80) cc_final: 0.8125 (m-80) REVERT: I 77 ARG cc_start: 0.7531 (ttt180) cc_final: 0.7062 (ttp80) REVERT: I 92 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7475 (ttm-80) REVERT: I 114 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8061 (mmm160) REVERT: I 115 SER cc_start: 0.8918 (t) cc_final: 0.8428 (p) REVERT: I 154 LYS cc_start: 0.8532 (mmmt) cc_final: 0.7954 (tttp) REVERT: I 162 GLN cc_start: 0.8363 (tt0) cc_final: 0.7831 (tt0) REVERT: I 190 GLU cc_start: 0.7006 (tp30) cc_final: 0.6722 (tp30) REVERT: J 13 ARG cc_start: 0.8339 (ptm160) cc_final: 0.8082 (ptm160) REVERT: J 41 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7115 (mt-10) REVERT: J 46 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: J 47 TYR cc_start: 0.7712 (t80) cc_final: 0.7488 (t80) REVERT: J 65 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7958 (mtpp) REVERT: J 66 ASP cc_start: 0.6465 (t0) cc_final: 0.5856 (t0) REVERT: J 116 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6494 (mm) REVERT: J 147 MET cc_start: 0.7912 (mtt) cc_final: 0.7646 (mmm) REVERT: L 53 SER cc_start: 0.7208 (t) cc_final: 0.6585 (p) REVERT: L 54 LYS cc_start: 0.8024 (tptt) cc_final: 0.7692 (ttmm) REVERT: L 141 ASN cc_start: 0.7841 (t0) cc_final: 0.7452 (t0) REVERT: N 34 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7629 (mt-10) REVERT: N 112 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7506 (tttt) REVERT: N 140 LYS cc_start: 0.8498 (pttt) cc_final: 0.8067 (tptt) REVERT: N 147 SER cc_start: 0.8507 (m) cc_final: 0.8145 (m) REVERT: O 57 THR cc_start: 0.8786 (m) cc_final: 0.8564 (m) REVERT: O 80 MET cc_start: 0.7513 (ttm) cc_final: 0.6682 (mtt) REVERT: O 81 MET cc_start: 0.6908 (tpp) cc_final: 0.6265 (tpp) REVERT: O 111 LYS cc_start: 0.7334 (mtmt) cc_final: 0.7117 (mtpp) REVERT: P 33 MET cc_start: 0.4215 (ptp) cc_final: 0.3726 (ttt) REVERT: P 41 LEU cc_start: 0.7217 (mt) cc_final: 0.6942 (tt) REVERT: P 42 PHE cc_start: 0.6998 (m-80) cc_final: 0.6569 (m-80) REVERT: P 51 GLN cc_start: 0.7229 (tm-30) cc_final: 0.7004 (mt0) REVERT: P 61 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4818 (mm) REVERT: P 93 GLU cc_start: 0.8407 (tt0) cc_final: 0.7850 (mp0) REVERT: Q 13 GLN cc_start: 0.7557 (pm20) cc_final: 0.7017 (pm20) REVERT: Q 103 ASP cc_start: 0.7440 (m-30) cc_final: 0.6245 (t70) REVERT: Q 111 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7147 (tpm170) REVERT: R 78 ARG cc_start: 0.7271 (mmt180) cc_final: 0.6682 (mmm160) REVERT: R 81 ARG cc_start: 0.7129 (mtt180) cc_final: 0.6377 (tpt90) REVERT: S 12 GLN cc_start: 0.8204 (tt0) cc_final: 0.7345 (tp40) REVERT: S 17 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7401 (mt) REVERT: S 110 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7644 (ttp80) REVERT: S 136 GLN cc_start: 0.7752 (mt0) cc_final: 0.6900 (mt0) REVERT: T 8 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.5123 (p90) REVERT: T 23 LYS cc_start: 0.5275 (tppt) cc_final: 0.4764 (mttm) REVERT: T 89 ARG cc_start: 0.6937 (mtp180) cc_final: 0.6550 (mtp180) REVERT: T 107 LYS cc_start: 0.7635 (mttm) cc_final: 0.7151 (mtpp) REVERT: T 151 GLN cc_start: 0.7982 (mt0) cc_final: 0.7737 (mt0) REVERT: U 155 ASN cc_start: 0.6817 (m-40) cc_final: 0.6305 (t0) REVERT: U 176 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6437 (mtt90) REVERT: U 195 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7708 (mm-30) REVERT: U 215 ILE cc_start: 0.6574 (mt) cc_final: 0.6258 (tt) REVERT: V 22 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7438 (ptp-110) REVERT: X 21 LYS cc_start: 0.7820 (mttt) cc_final: 0.7552 (mtmt) REVERT: X 35 ARG cc_start: 0.7284 (ttp-170) cc_final: 0.6813 (ptt-90) REVERT: X 48 LYS cc_start: 0.7534 (mttt) cc_final: 0.7158 (mtpt) REVERT: X 71 ARG cc_start: 0.6991 (ttm-80) cc_final: 0.6523 (ttt90) REVERT: X 80 LYS cc_start: 0.7873 (mttt) cc_final: 0.7499 (mtmm) REVERT: X 114 ASP cc_start: 0.6243 (m-30) cc_final: 0.5963 (m-30) REVERT: Y 15 LYS cc_start: 0.7773 (tptt) cc_final: 0.7413 (tppt) REVERT: Y 51 ARG cc_start: 0.8469 (mtt180) cc_final: 0.7735 (mmp80) REVERT: Y 72 SER cc_start: 0.8251 (t) cc_final: 0.7989 (p) REVERT: Y 81 ASN cc_start: 0.8252 (m110) cc_final: 0.7934 (t0) REVERT: Y 89 GLU cc_start: 0.7162 (tp30) cc_final: 0.6547 (tp30) REVERT: Y 90 ASN cc_start: 0.5575 (p0) cc_final: 0.5108 (p0) REVERT: Z 158 ASN cc_start: 0.6236 (t0) cc_final: 0.5882 (m-40) REVERT: a 33 ASP cc_start: 0.7925 (p0) cc_final: 0.7664 (p0) REVERT: a 52 ASP cc_start: 0.7670 (t70) cc_final: 0.6772 (t70) REVERT: a 66 LYS cc_start: 0.8502 (mttp) cc_final: 0.7836 (mmpt) REVERT: a 74 CYS cc_start: 0.7038 (t) cc_final: 0.6728 (p) REVERT: b 4 ASP cc_start: 0.7483 (t0) cc_final: 0.7244 (t0) REVERT: c 11 LYS cc_start: 0.7605 (tttt) cc_final: 0.7109 (ptmt) REVERT: c 50 ARG cc_start: 0.7749 (ptt180) cc_final: 0.7271 (ptp-170) REVERT: c 51 GLU cc_start: 0.8478 (pt0) cc_final: 0.7800 (mt-10) REVERT: d 17 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6032 (ptp90) REVERT: d 25 ARG cc_start: 0.6447 (mtt-85) cc_final: 0.5502 (mmt180) REVERT: d 26 HIS cc_start: 0.7745 (m90) cc_final: 0.7242 (m90) REVERT: d 39 GLN cc_start: 0.8137 (mp10) cc_final: 0.7767 (mp10) REVERT: d 53 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6411 (p90) REVERT: e 39 GLN cc_start: 0.7908 (mt0) cc_final: 0.7679 (mt0) REVERT: e 43 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6624 (mtt-85) REVERT: m 20 LYS cc_start: 0.7945 (tttp) cc_final: 0.7680 (ttmm) REVERT: m 29 ARG cc_start: 0.8416 (ttp-170) cc_final: 0.7773 (mtm110) outliers start: 155 outliers final: 130 residues processed: 1149 average time/residue: 0.7267 time to fit residues: 1359.1974 Evaluate side-chains 1201 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1055 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 154 CYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 160 CYS Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 153 MET Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 155 LEU Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 46 GLN Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 134 ILE Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 36 HIS Chi-restraints excluded: chain N residue 48 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 86 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 55 LYS Chi-restraints excluded: chain P residue 61 LEU Chi-restraints excluded: chain Q residue 27 CYS Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 8 TYR Chi-restraints excluded: chain T residue 49 TYR Chi-restraints excluded: chain T residue 54 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 148 ILE Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 52 ILE Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 92 ASN Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain X residue 20 GLN Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 77 ASN Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 38 SER Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Z residue 95 PHE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 94 VAL Chi-restraints excluded: chain b residue 3 ILE Chi-restraints excluded: chain b residue 15 SER Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 17 ARG Chi-restraints excluded: chain d residue 37 CYS Chi-restraints excluded: chain d residue 53 TYR Chi-restraints excluded: chain e residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 366 optimal weight: 0.9990 chunk 491 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 462 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 474 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN I 88 ASN I 162 GLN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 HIS ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN m 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101586 restraints weight = 121240.136| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.47 r_work: 0.3059 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 73591 Z= 0.404 Angle : 0.736 12.763 107052 Z= 0.369 Chirality : 0.042 0.293 13312 Planarity : 0.006 0.055 7623 Dihedral : 23.130 179.357 29804 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.22 % Favored : 90.94 % Rotamer: Outliers : 5.13 % Allowed : 25.06 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % Twisted Proline : 0.57 % 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: -1.48 (0.13), residues: 4283 helix: 0.24 (0.14), residues: 1419 sheet: -0.63 (0.20), residues: 684 loop : -1.98 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP S 129 HIS 0.010 0.002 HIS P 133 PHE 0.036 0.003 PHE G 50 TYR 0.045 0.003 TYR a 59 ARG 0.011 0.001 ARG H 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21783.70 seconds wall clock time: 380 minutes 22.48 seconds (22822.48 seconds total)