Starting phenix.real_space_refine on Sat Mar 16 16:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8o_0374/03_2024/6n8o_0374.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8o_0374/03_2024/6n8o_0374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8o_0374/03_2024/6n8o_0374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8o_0374/03_2024/6n8o_0374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8o_0374/03_2024/6n8o_0374.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8o_0374/03_2024/6n8o_0374.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 3480 5.49 5 S 134 5.16 5 C 70575 2.51 5 N 24564 2.21 5 O 34700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y ARG 236": "NH1" <-> "NH2" Residue "Y PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 67": "NH1" <-> "NH2" Residue "L ARG 67": "NH1" <-> "NH2" Residue "W ARG 128": "NH1" <-> "NH2" Residue "W ARG 197": "NH1" <-> "NH2" Residue "W ARG 208": "NH1" <-> "NH2" Residue "W ARG 214": "NH1" <-> "NH2" Residue "W ARG 220": "NH1" <-> "NH2" Residue "W ARG 427": "NH1" <-> "NH2" Residue "W ARG 468": "NH1" <-> "NH2" Residue "W ARG 482": "NH1" <-> "NH2" Residue "W ARG 485": "NH1" <-> "NH2" Residue "V ARG 63": "NH1" <-> "NH2" Residue "V PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 110": "NH1" <-> "NH2" Residue "V ARG 111": "NH1" <-> "NH2" Residue "V ARG 113": "NH1" <-> "NH2" Residue "V ARG 148": "NH1" <-> "NH2" Residue "V ARG 162": "NH1" <-> "NH2" Residue "V ARG 303": "NH1" <-> "NH2" Residue "V PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 342": "NH1" <-> "NH2" Residue "V ARG 356": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 140": "NH1" <-> "NH2" Residue "G ARG 158": "NH1" <-> "NH2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "I PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "K ARG 23": "NH1" <-> "NH2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "Z ARG 4": "NH1" <-> "NH2" Residue "Z ARG 185": "NH1" <-> "NH2" Residue "M ARG 29": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 61": "NH1" <-> "NH2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "R ARG 36": "NH1" <-> "NH2" Residue "a ARG 20": "NH1" <-> "NH2" Residue "b PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 56": "NH1" <-> "NH2" Residue "c PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 126": "NH1" <-> "NH2" Residue "c ARG 128": "NH1" <-> "NH2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "c ARG 181": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 176": "NH1" <-> "NH2" Residue "d ARG 180": "NH1" <-> "NH2" Residue "e ARG 62": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 117": "NH1" <-> "NH2" Residue "f ARG 155": "NH1" <-> "NH2" Residue "g ARG 8": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 108": "NH1" <-> "NH2" Residue "g ARG 139": "NH1" <-> "NH2" Residue "g PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 32": "NH1" <-> "NH2" Residue "i ARG 88": "NH1" <-> "NH2" Residue "i PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 125": "NH1" <-> "NH2" Residue "k ARG 138": "NH1" <-> "NH2" Residue "l ARG 121": "NH1" <-> "NH2" Residue "m PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 84": "NH1" <-> "NH2" Residue "m PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 135": "NH1" <-> "NH2" Residue "p PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "s TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "v ARG 99": "NH1" <-> "NH2" Residue "w ARG 63": "NH1" <-> "NH2" Residue "x ARG 3": "NH1" <-> "NH2" Residue "x ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 133453 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 68470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3201, 68470 Classifications: {'RNA': 3201} Modifications used: {'rna2p_pur': 327, 'rna2p_pyr': 224, 'rna3p_pur': 1448, 'rna3p_pyr': 1202} Link IDs: {'rna2p': 551, 'rna3p': 2649} Chain breaks: 2 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "C" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 14, 'rna3p_pur': 62, 'rna3p_pyr': 66} Link IDs: {'rna2p': 29, 'rna3p': 128} Chain: "Y" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 119} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1710 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 817 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'UNK:plan-1': 92, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "W" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2976 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 24, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "V" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3034 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "E" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3059 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 369} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2315 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain: "H" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1217 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1770 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "J" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1762 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 214} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain: "Z" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1648 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 10, 'TRANS': 190} Chain breaks: 1 Chain: "M" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1344 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "N" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1539 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "Q" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 819 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "R" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 673 Classifications: {'peptide': 88} Link IDs: {'TRANS': 87} Chain: "S" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1050 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'TRANS': 209} Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 630 Unresolved non-hydrogen dihedrals: 210 Planarities with less than four sites: {'UNK:plan-1': 210} Unresolved non-hydrogen planarities: 210 Chain: "a" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "b" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "c" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1420 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "e" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1219 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain: "f" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "g" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "h" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "i" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "j" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 509 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "k" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "l" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "m" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "n" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "o" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "p" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "q" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 866 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1012 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "s" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "t" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 861 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "u" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "v" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 753 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "w" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 81} Chain: "x" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 408 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Time building chain proxies: 49.88, per 1000 atoms: 0.37 Number of scatterers: 133453 At special positions: 0 Unit cell: (237.6, 215.6, 259.6, 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 134 16.00 P 3480 15.00 O 34700 8.00 N 24564 7.00 C 70575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS Y 235 " - pdb=" SG CYS Y 307 " distance=2.05 Simple disulfide: pdb=" SG CYS Y 235 " - pdb=" SG CYS Y 310 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 280 " - pdb=" SG CYS Y 324 " distance=2.08 Simple disulfide: pdb=" SG CYS Y 280 " - pdb=" SG CYS Y 326 " distance=2.00 Simple disulfide: pdb=" SG CYS Y 307 " - pdb=" SG CYS Y 310 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 324 " - pdb=" SG CYS Y 326 " distance=2.01 Simple disulfide: pdb=" SG CYS V 58 " - pdb=" SG CYS V 61 " distance=2.04 Simple disulfide: pdb=" SG CYS V 61 " - pdb=" SG CYS V 146 " distance=2.04 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 57 " distance=2.04 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 60 " distance=2.03 Simple disulfide: pdb=" SG CYS R 57 " - pdb=" SG CYS R 60 " distance=2.85 Simple disulfide: pdb=" SG CYS t 47 " - pdb=" SG CYS t 81 " distance=2.04 Simple disulfide: pdb=" SG CYS t 47 " - pdb=" SG CYS t 84 " distance=2.04 Simple disulfide: pdb=" SG CYS t 81 " - pdb=" SG CYS t 84 " distance=2.06 Simple disulfide: pdb=" SG CYS w 19 " - pdb=" SG CYS w 22 " distance=2.01 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 34 " distance=2.03 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 37 " distance=2.03 Simple disulfide: pdb=" SG CYS w 34 " - pdb=" SG CYS w 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 46.66 Conformation dependent library (CDL) restraints added in 8.5 seconds 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14214 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 81 sheets defined 35.4% alpha, 14.8% beta 817 base pairs and 1885 stacking pairs defined. Time for finding SS restraints: 38.82 Creating SS restraints... Processing helix chain 'Y' and resid 291 through 297 Processing helix chain 'X' and resid 31 through 43 removed outlier: 3.566A pdb=" N TYR X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA X 37 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE X 38 " --> pdb=" O PHE X 34 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU X 41 " --> pdb=" O ALA X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 63 Processing helix chain 'X' and resid 77 through 88 removed outlier: 3.672A pdb=" N ASN X 86 " --> pdb=" O GLN X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 107 removed outlier: 3.584A pdb=" N VAL X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 103 through 107' Processing helix chain 'X' and resid 122 through 133 removed outlier: 3.630A pdb=" N LEU X 128 " --> pdb=" O GLU X 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP X 131 " --> pdb=" O GLU X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 178 removed outlier: 3.870A pdb=" N GLU X 172 " --> pdb=" O GLN X 168 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 197 removed outlier: 3.539A pdb=" N GLY X 196 " --> pdb=" O VAL X 192 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET X 197 " --> pdb=" O VAL X 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 192 through 197' Processing helix chain 'X' and resid 211 through 223 removed outlier: 3.522A pdb=" N VAL X 217 " --> pdb=" O PRO X 213 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE X 221 " --> pdb=" O VAL X 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 removed outlier: 3.901A pdb=" N UNK L 30 " --> pdb=" O UNK L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 50 removed outlier: 3.676A pdb=" N UNK L 43 " --> pdb=" O UNK L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 85 Processing helix chain 'L' and resid 106 through 118 removed outlier: 3.659A pdb=" N UNK L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 129 removed outlier: 3.566A pdb=" N UNK L 128 " --> pdb=" O UNK L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 137 Processing helix chain 'L' and resid 148 through 152 removed outlier: 3.646A pdb=" N UNK L 152 " --> pdb=" O UNK L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 162 Processing helix chain 'W' and resid 118 through 129 removed outlier: 3.857A pdb=" N ALA W 125 " --> pdb=" O GLY W 121 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN W 127 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG W 128 " --> pdb=" O ASN W 124 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA W 129 " --> pdb=" O ALA W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 134 removed outlier: 3.891A pdb=" N ASP W 133 " --> pdb=" O LEU W 130 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU W 134 " --> pdb=" O ALA W 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 130 through 134' Processing helix chain 'W' and resid 149 through 168 removed outlier: 3.754A pdb=" N GLU W 157 " --> pdb=" O ARG W 153 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA W 158 " --> pdb=" O GLN W 154 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE W 159 " --> pdb=" O GLU W 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 173 Processing helix chain 'W' and resid 184 through 198 removed outlier: 3.939A pdb=" N TRP W 188 " --> pdb=" O ASN W 184 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN W 190 " --> pdb=" O GLU W 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU W 191 " --> pdb=" O VAL W 187 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL W 194 " --> pdb=" O GLN W 190 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER W 198 " --> pdb=" O VAL W 194 " (cutoff:3.500A) Processing helix chain 'W' and resid 209 through 214 removed outlier: 3.873A pdb=" N PHE W 213 " --> pdb=" O ASN W 209 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG W 214 " --> pdb=" O PRO W 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 209 through 214' Processing helix chain 'W' and resid 216 through 223 removed outlier: 3.556A pdb=" N ARG W 220 " --> pdb=" O VAL W 216 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR W 221 " --> pdb=" O ASP W 217 " (cutoff:3.500A) Processing helix chain 'W' and resid 224 through 226 No H-bonds generated for 'chain 'W' and resid 224 through 226' Processing helix chain 'W' and resid 237 through 241 Processing helix chain 'W' and resid 242 through 257 removed outlier: 4.091A pdb=" N ARG W 246 " --> pdb=" O THR W 242 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE W 247 " --> pdb=" O LYS W 243 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS W 251 " --> pdb=" O ILE W 247 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR W 252 " --> pdb=" O ALA W 248 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE W 253 " --> pdb=" O TRP W 249 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE W 254 " --> pdb=" O ALA W 250 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER W 255 " --> pdb=" O LYS W 251 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 358 removed outlier: 3.972A pdb=" N ILE W 353 " --> pdb=" O LYS W 349 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER W 355 " --> pdb=" O SER W 351 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL W 357 " --> pdb=" O ILE W 353 " (cutoff:3.500A) Processing helix chain 'W' and resid 400 through 406 removed outlier: 4.269A pdb=" N VAL W 404 " --> pdb=" O LYS W 400 " (cutoff:3.500A) Processing helix chain 'W' and resid 410 through 414 removed outlier: 3.540A pdb=" N GLN W 413 " --> pdb=" O PRO W 410 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU W 414 " --> pdb=" O ILE W 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 410 through 414' Processing helix chain 'W' and resid 417 through 427 removed outlier: 3.717A pdb=" N VAL W 424 " --> pdb=" O PRO W 420 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA W 425 " --> pdb=" O ALA W 421 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU W 426 " --> pdb=" O GLY W 422 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG W 427 " --> pdb=" O LEU W 423 " (cutoff:3.500A) Processing helix chain 'W' and resid 429 through 437 removed outlier: 4.015A pdb=" N ILE W 433 " --> pdb=" O PRO W 429 " (cutoff:3.500A) Processing helix chain 'W' and resid 456 through 467 removed outlier: 3.691A pdb=" N LEU W 460 " --> pdb=" O THR W 456 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU W 461 " --> pdb=" O ALA W 457 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA W 463 " --> pdb=" O GLU W 459 " (cutoff:3.500A) Processing helix chain 'W' and resid 479 through 493 removed outlier: 3.729A pdb=" N ALA W 483 " --> pdb=" O ASP W 479 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG W 485 " --> pdb=" O PRO W 481 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR W 486 " --> pdb=" O ARG W 482 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP W 490 " --> pdb=" O TYR W 486 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 88 removed outlier: 3.527A pdb=" N ALA V 83 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N CYS V 85 " --> pdb=" O LEU V 81 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU V 86 " --> pdb=" O LEU V 82 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 181 removed outlier: 3.924A pdb=" N GLU V 175 " --> pdb=" O PHE V 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN V 176 " --> pdb=" O LEU V 172 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS V 181 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 204 through 218 removed outlier: 3.692A pdb=" N VAL V 208 " --> pdb=" O LYS V 204 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS V 209 " --> pdb=" O ASN V 205 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET V 210 " --> pdb=" O HIS V 206 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA V 216 " --> pdb=" O ASP V 212 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL V 217 " --> pdb=" O PHE V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 260 through 267 Processing helix chain 'V' and resid 297 through 302 Processing helix chain 'V' and resid 343 through 348 removed outlier: 4.652A pdb=" N GLY V 347 " --> pdb=" O THR V 343 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL V 348 " --> pdb=" O SER V 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 343 through 348' Processing helix chain 'V' and resid 375 through 377 No H-bonds generated for 'chain 'V' and resid 375 through 377' Processing helix chain 'V' and resid 381 through 386 Processing helix chain 'V' and resid 388 through 392 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 181 through 189 removed outlier: 3.860A pdb=" N ALA D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.612A pdb=" N ALA D 203 " --> pdb=" O ARG D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 118 removed outlier: 3.652A pdb=" N LYS E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 141 through 154 removed outlier: 3.630A pdb=" N GLU E 145 " --> pdb=" O GLY E 141 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 169 removed outlier: 3.547A pdb=" N THR E 169 " --> pdb=" O ILE E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 198 removed outlier: 3.693A pdb=" N VAL E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS E 198 " --> pdb=" O TRP E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 234 removed outlier: 3.740A pdb=" N TRP E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.541A pdb=" N HIS E 377 " --> pdb=" O PRO E 373 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 43 removed outlier: 4.015A pdb=" N SER F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 47 removed outlier: 3.651A pdb=" N ARG F 47 " --> pdb=" O LYS F 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 44 through 47' Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.536A pdb=" N ALA F 121 " --> pdb=" O GLU F 117 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.503A pdb=" N LEU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.568A pdb=" N GLY F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 184 removed outlier: 3.627A pdb=" N VAL F 181 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER F 184 " --> pdb=" O LYS F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 removed outlier: 3.770A pdb=" N LYS F 193 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR F 194 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG F 195 " --> pdb=" O GLY F 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 190 through 195' Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 252 through 263 removed outlier: 3.559A pdb=" N THR F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP F 259 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 removed outlier: 3.932A pdb=" N ILE F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 4.495A pdb=" N ALA F 298 " --> pdb=" O GLU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 327 removed outlier: 3.685A pdb=" N LEU F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 337 removed outlier: 4.414A pdb=" N VAL F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA F 336 " --> pdb=" O LYS F 332 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 360 removed outlier: 3.715A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 357 " --> pdb=" O ALA F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 15 removed outlier: 3.528A pdb=" N SER G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER G 14 " --> pdb=" O SER G 10 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG G 15 " --> pdb=" O ALA G 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 9 through 15' Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.522A pdb=" N GLU G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 38 removed outlier: 4.099A pdb=" N ARG G 35 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 86 Proline residue: G 84 - end of helix No H-bonds generated for 'chain 'G' and resid 81 through 86' Processing helix chain 'G' and resid 94 through 114 Processing helix chain 'G' and resid 158 through 170 removed outlier: 3.555A pdb=" N ALA G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY G 170 " --> pdb=" O ALA G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 200 removed outlier: 3.624A pdb=" N ILE G 199 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 3.533A pdb=" N TYR G 207 " --> pdb=" O HIS G 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU G 210 " --> pdb=" O GLN G 206 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 222 removed outlier: 3.697A pdb=" N GLU G 221 " --> pdb=" O GLU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 229 removed outlier: 3.729A pdb=" N LEU G 227 " --> pdb=" O PHE G 223 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA G 228 " --> pdb=" O LYS G 224 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G 229 " --> pdb=" O GLY G 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 223 through 229' Processing helix chain 'G' and resid 232 through 250 removed outlier: 3.721A pdb=" N LEU G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU G 245 " --> pdb=" O THR G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 270 Processing helix chain 'G' and resid 278 through 295 removed outlier: 3.551A pdb=" N ARG G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 287 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 289 " --> pdb=" O ARG G 285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE G 290 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY G 295 " --> pdb=" O ALA G 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 73 Processing helix chain 'H' and resid 97 through 101 removed outlier: 4.134A pdb=" N LYS H 100 " --> pdb=" O ASN H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 150 removed outlier: 3.930A pdb=" N VAL H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA H 144 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 161 removed outlier: 3.574A pdb=" N SER H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 73 removed outlier: 3.742A pdb=" N ALA I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 106 removed outlier: 3.501A pdb=" N VAL I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 130 removed outlier: 3.578A pdb=" N LEU I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE I 130 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 152 removed outlier: 3.540A pdb=" N VAL I 148 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 174 removed outlier: 4.280A pdb=" N ILE I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN I 172 " --> pdb=" O ILE I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 190 removed outlier: 3.749A pdb=" N LEU I 184 " --> pdb=" O SER I 180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR I 190 " --> pdb=" O HIS I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 200 Processing helix chain 'I' and resid 222 through 226 Processing helix chain 'I' and resid 235 through 244 removed outlier: 4.085A pdb=" N LEU I 239 " --> pdb=" O PHE I 235 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS I 241 " --> pdb=" O ASN I 237 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER I 242 " --> pdb=" O LYS I 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.848A pdb=" N VAL J 50 " --> pdb=" O SER J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 69 removed outlier: 3.528A pdb=" N LYS J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS J 63 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE J 67 " --> pdb=" O LYS J 63 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 95 removed outlier: 3.546A pdb=" N GLU J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.658A pdb=" N THR J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 144 removed outlier: 3.621A pdb=" N VAL J 140 " --> pdb=" O LEU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 165 through 173 removed outlier: 3.551A pdb=" N LYS J 171 " --> pdb=" O PRO J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 187 removed outlier: 3.565A pdb=" N LEU J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 191 removed outlier: 3.569A pdb=" N ASN J 191 " --> pdb=" O THR J 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 188 through 191' Processing helix chain 'J' and resid 206 through 219 removed outlier: 4.444A pdb=" N ALA J 210 " --> pdb=" O GLU J 206 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU J 214 " --> pdb=" O ALA J 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER J 216 " --> pdb=" O ALA J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 230 Processing helix chain 'J' and resid 239 through 250 Processing helix chain 'K' and resid 61 through 84 removed outlier: 3.839A pdb=" N LEU K 68 " --> pdb=" O HIS K 64 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 120 Processing helix chain 'K' and resid 150 through 164 removed outlier: 3.582A pdb=" N GLN K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN K 157 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 81 removed outlier: 3.556A pdb=" N TYR Z 75 " --> pdb=" O CYS Z 71 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET Z 76 " --> pdb=" O ALA Z 72 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR Z 78 " --> pdb=" O LYS Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 154 removed outlier: 3.548A pdb=" N GLU Z 150 " --> pdb=" O ASP Z 146 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 187 removed outlier: 3.866A pdb=" N LEU Z 182 " --> pdb=" O ARG Z 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS Z 183 " --> pdb=" O PRO Z 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Z 184 " --> pdb=" O GLU Z 180 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA Z 187 " --> pdb=" O LYS Z 183 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 212 removed outlier: 3.590A pdb=" N ARG Z 211 " --> pdb=" O GLU Z 207 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU Z 212 " --> pdb=" O ASN Z 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 207 through 212' Processing helix chain 'M' and resid 27 through 42 removed outlier: 3.503A pdb=" N THR M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER M 34 " --> pdb=" O LEU M 30 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS M 35 " --> pdb=" O THR M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 87 removed outlier: 3.840A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 3.876A pdb=" N ARG M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 166 removed outlier: 3.506A pdb=" N SER M 161 " --> pdb=" O GLU M 157 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN M 165 " --> pdb=" O SER M 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 20 removed outlier: 3.609A pdb=" N GLU N 20 " --> pdb=" O HIS N 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 17 through 20' Processing helix chain 'N' and resid 29 through 46 removed outlier: 3.886A pdb=" N VAL N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA N 38 " --> pdb=" O SER N 34 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS N 45 " --> pdb=" O THR N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 3.609A pdb=" N VAL N 80 " --> pdb=" O THR N 76 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 91 removed outlier: 3.895A pdb=" N ARG N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 94 No H-bonds generated for 'chain 'N' and resid 92 through 94' Processing helix chain 'N' and resid 105 through 122 removed outlier: 3.715A pdb=" N ALA N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU N 118 " --> pdb=" O GLN N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 Processing helix chain 'N' and resid 167 through 179 Processing helix chain 'N' and resid 179 through 193 removed outlier: 3.820A pdb=" N ARG N 183 " --> pdb=" O PHE N 179 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU N 184 " --> pdb=" O ARG N 180 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU N 189 " --> pdb=" O LYS N 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 89 removed outlier: 3.838A pdb=" N ALA O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 96 removed outlier: 3.598A pdb=" N ALA O 96 " --> pdb=" O GLU O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 111 removed outlier: 3.809A pdb=" N LYS O 102 " --> pdb=" O SER O 98 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA O 110 " --> pdb=" O ARG O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 138 removed outlier: 3.512A pdb=" N MET O 121 " --> pdb=" O ARG O 117 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS O 133 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA O 136 " --> pdb=" O LYS O 132 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 48 removed outlier: 4.103A pdb=" N SER Q 48 " --> pdb=" O ASP Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 15 removed outlier: 3.734A pdb=" N THR R 11 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS R 13 " --> pdb=" O ILE R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 35 removed outlier: 3.645A pdb=" N LYS R 28 " --> pdb=" O ARG R 24 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU R 29 " --> pdb=" O GLN R 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 removed outlier: 3.784A pdb=" N THR R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU R 88 " --> pdb=" O ARG R 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 15 removed outlier: 3.789A pdb=" N UNK S 7 " --> pdb=" O UNK S 3 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N UNK S 8 " --> pdb=" O UNK S 4 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N UNK S 9 " --> pdb=" O UNK S 5 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N UNK S 11 " --> pdb=" O UNK S 7 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N UNK S 12 " --> pdb=" O UNK S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 71 removed outlier: 3.596A pdb=" N UNK S 69 " --> pdb=" O UNK S 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N UNK S 70 " --> pdb=" O UNK S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 86 Processing helix chain 'S' and resid 90 through 99 Processing helix chain 'S' and resid 141 through 146 Processing helix chain 'S' and resid 178 through 183 removed outlier: 4.253A pdb=" N UNK S 182 " --> pdb=" O UNK S 178 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N UNK S 183 " --> pdb=" O UNK S 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 178 through 183' Processing helix chain 'a' and resid 3 through 11 removed outlier: 3.667A pdb=" N LEU a 7 " --> pdb=" O ALA a 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 32 removed outlier: 4.083A pdb=" N ARG a 24 " --> pdb=" O ARG a 20 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG a 31 " --> pdb=" O VAL a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 50 removed outlier: 3.589A pdb=" N ARG a 49 " --> pdb=" O PRO a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 79 removed outlier: 3.717A pdb=" N GLY a 78 " --> pdb=" O VAL a 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA a 79 " --> pdb=" O PRO a 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 75 through 79' Processing helix chain 'a' and resid 97 through 110 removed outlier: 3.665A pdb=" N ARG a 109 " --> pdb=" O ARG a 105 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA a 110 " --> pdb=" O VAL a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 144 Processing helix chain 'a' and resid 153 through 157 removed outlier: 3.558A pdb=" N LYS a 157 " --> pdb=" O PRO a 154 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 163 removed outlier: 3.860A pdb=" N ARG a 162 " --> pdb=" O HIS a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 173 removed outlier: 3.538A pdb=" N SER a 171 " --> pdb=" O THR a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 194 removed outlier: 3.759A pdb=" N GLN a 194 " --> pdb=" O THR a 190 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 30 removed outlier: 3.547A pdb=" N VAL b 22 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU b 28 " --> pdb=" O ALA b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 59 removed outlier: 3.568A pdb=" N ASN b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE b 57 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG b 59 " --> pdb=" O HIS b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 65 through 69 Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 92 through 100 Processing helix chain 'b' and resid 109 through 114 removed outlier: 4.841A pdb=" N LYS b 114 " --> pdb=" O PRO b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 124 through 129 Processing helix chain 'b' and resid 138 through 144 Processing helix chain 'b' and resid 149 through 185 removed outlier: 3.714A pdb=" N VAL b 153 " --> pdb=" O TYR b 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA b 158 " --> pdb=" O ALA b 154 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL b 162 " --> pdb=" O ALA b 158 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER b 163 " --> pdb=" O LYS b 159 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR b 167 " --> pdb=" O SER b 163 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA b 173 " --> pdb=" O ALA b 169 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS b 177 " --> pdb=" O ALA b 173 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 184 " --> pdb=" O SER b 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 197 Processing helix chain 'c' and resid 10 through 12 No H-bonds generated for 'chain 'c' and resid 10 through 12' Processing helix chain 'c' and resid 25 through 35 removed outlier: 4.024A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 52 removed outlier: 3.705A pdb=" N LYS c 46 " --> pdb=" O THR c 42 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU c 49 " --> pdb=" O GLN c 45 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN c 50 " --> pdb=" O LYS c 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 76 removed outlier: 3.944A pdb=" N GLY c 73 " --> pdb=" O THR c 70 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU c 75 " --> pdb=" O GLN c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 106 removed outlier: 3.571A pdb=" N PHE c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN c 96 " --> pdb=" O GLN c 92 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS c 105 " --> pdb=" O ASN c 101 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 110 No H-bonds generated for 'chain 'c' and resid 108 through 110' Processing helix chain 'c' and resid 132 through 134 No H-bonds generated for 'chain 'c' and resid 132 through 134' Processing helix chain 'c' and resid 169 through 183 removed outlier: 3.547A pdb=" N ARG c 175 " --> pdb=" O ARG c 171 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE c 176 " --> pdb=" O GLN c 172 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG c 181 " --> pdb=" O ALA c 177 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE c 182 " --> pdb=" O ALA c 178 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 40 removed outlier: 3.721A pdb=" N LEU d 29 " --> pdb=" O TYR d 25 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE d 35 " --> pdb=" O LYS d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 53 removed outlier: 3.874A pdb=" N VAL d 47 " --> pdb=" O PRO d 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 71 Processing helix chain 'd' and resid 107 through 118 removed outlier: 3.544A pdb=" N ALA d 112 " --> pdb=" O ALA d 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS d 116 " --> pdb=" O ALA d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 131 Processing helix chain 'd' and resid 147 through 152 Processing helix chain 'e' and resid 4 through 16 Processing helix chain 'e' and resid 18 through 22 removed outlier: 3.851A pdb=" N VAL e 22 " --> pdb=" O LYS e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 34 removed outlier: 3.587A pdb=" N ALA e 33 " --> pdb=" O THR e 29 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN e 34 " --> pdb=" O SER e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 47 removed outlier: 3.823A pdb=" N LYS e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 60 through 72 removed outlier: 3.561A pdb=" N SER e 69 " --> pdb=" O ALA e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 Processing helix chain 'e' and resid 90 through 112 removed outlier: 3.686A pdb=" N VAL e 101 " --> pdb=" O ARG e 97 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG e 110 " --> pdb=" O LEU e 106 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP e 111 " --> pdb=" O ALA e 107 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 130 removed outlier: 3.761A pdb=" N VAL e 122 " --> pdb=" O HIS e 118 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS e 125 " --> pdb=" O HIS e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 135 through 152 removed outlier: 3.984A pdb=" N HIS e 141 " --> pdb=" O ALA e 137 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN e 144 " --> pdb=" O GLU e 140 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 49 removed outlier: 3.520A pdb=" N TYR f 41 " --> pdb=" O ALA f 37 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR f 43 " --> pdb=" O SER f 39 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS f 47 " --> pdb=" O TYR f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 114 removed outlier: 3.588A pdb=" N VAL f 103 " --> pdb=" O ARG f 99 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR f 107 " --> pdb=" O VAL f 103 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN f 108 " --> pdb=" O GLU f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 119 No H-bonds generated for 'chain 'f' and resid 117 through 119' Processing helix chain 'f' and resid 137 through 142 removed outlier: 3.712A pdb=" N LYS f 141 " --> pdb=" O ARG f 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN f 142 " --> pdb=" O GLN f 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 137 through 142' Processing helix chain 'f' and resid 143 through 145 No H-bonds generated for 'chain 'f' and resid 143 through 145' Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.615A pdb=" N LYS g 32 " --> pdb=" O SER g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 58 removed outlier: 3.930A pdb=" N GLN g 58 " --> pdb=" O LYS g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 99 through 123 removed outlier: 3.558A pdb=" N GLN g 103 " --> pdb=" O SER g 99 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS g 110 " --> pdb=" O LEU g 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA g 121 " --> pdb=" O ALA g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.662A pdb=" N ASN h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 41 removed outlier: 3.506A pdb=" N TYR h 33 " --> pdb=" O ASP h 29 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE h 41 " --> pdb=" O LEU h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 87 Processing helix chain 'i' and resid 119 through 126 removed outlier: 3.804A pdb=" N LEU i 125 " --> pdb=" O GLU i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 133 removed outlier: 3.688A pdb=" N ALA i 130 " --> pdb=" O TRP i 126 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER i 131 " --> pdb=" O PRO i 127 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 42 removed outlier: 3.692A pdb=" N PHE j 40 " --> pdb=" O SER j 36 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN j 42 " --> pdb=" O SER j 38 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 59 Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 69 through 78 removed outlier: 3.670A pdb=" N LYS k 74 " --> pdb=" O GLU k 70 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS k 75 " --> pdb=" O THR k 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU k 77 " --> pdb=" O MET k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 3.505A pdb=" N LYS k 100 " --> pdb=" O LYS k 96 " (cutoff:3.500A) Processing helix chain 'k' and resid 131 through 140 removed outlier: 3.592A pdb=" N ILE k 135 " --> pdb=" O ASP k 131 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN k 137 " --> pdb=" O LEU k 133 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG k 138 " --> pdb=" O ASP k 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 21 removed outlier: 3.756A pdb=" N LYS l 17 " --> pdb=" O ARG l 13 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 31 removed outlier: 4.094A pdb=" N VAL l 29 " --> pdb=" O SER l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 44 removed outlier: 3.814A pdb=" N ALA l 41 " --> pdb=" O LYS l 37 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 102 No H-bonds generated for 'chain 'l' and resid 100 through 102' Processing helix chain 'l' and resid 112 through 122 removed outlier: 3.744A pdb=" N ALA l 117 " --> pdb=" O LYS l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 61 through 66 removed outlier: 3.700A pdb=" N THR m 66 " --> pdb=" O VAL m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 123 removed outlier: 4.001A pdb=" N GLU m 109 " --> pdb=" O SER m 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 132 removed outlier: 3.723A pdb=" N PHE m 131 " --> pdb=" O ASN m 127 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 46 Processing helix chain 'n' and resid 76 through 82 removed outlier: 4.310A pdb=" N TRP n 79 " --> pdb=" O ASP n 76 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU n 81 " --> pdb=" O LEU n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 92 removed outlier: 3.555A pdb=" N LYS n 92 " --> pdb=" O ASP n 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 142 removed outlier: 3.571A pdb=" N GLU n 136 " --> pdb=" O LYS n 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS n 137 " --> pdb=" O LEU n 133 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE n 138 " --> pdb=" O ALA n 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 17 removed outlier: 3.604A pdb=" N LYS o 15 " --> pdb=" O ASN o 11 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA o 16 " --> pdb=" O GLN o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 36 through 58 removed outlier: 3.525A pdb=" N ASN o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU o 47 " --> pdb=" O HIS o 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 21 removed outlier: 3.872A pdb=" N LEU p 16 " --> pdb=" O GLN p 12 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL p 17 " --> pdb=" O LYS p 13 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS p 19 " --> pdb=" O ALA p 15 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 36 removed outlier: 3.541A pdb=" N THR p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN p 36 " --> pdb=" O LYS p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 63 removed outlier: 3.510A pdb=" N ALA p 60 " --> pdb=" O LEU p 56 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 81 removed outlier: 3.594A pdb=" N GLY p 78 " --> pdb=" O ASN p 74 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR p 79 " --> pdb=" O ASN p 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 26 No H-bonds generated for 'chain 'q' and resid 24 through 26' Processing helix chain 'q' and resid 27 through 45 removed outlier: 3.588A pdb=" N VAL q 33 " --> pdb=" O ALA q 29 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS q 34 " --> pdb=" O PRO q 30 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS q 43 " --> pdb=" O PHE q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 52 through 60 removed outlier: 3.624A pdb=" N GLN q 57 " --> pdb=" O PRO q 53 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA q 58 " --> pdb=" O GLU q 54 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 63 No H-bonds generated for 'chain 'q' and resid 61 through 63' Processing helix chain 'r' and resid 54 through 58 Processing helix chain 'r' and resid 78 through 83 Processing helix chain 'r' and resid 84 through 86 No H-bonds generated for 'chain 'r' and resid 84 through 86' Processing helix chain 'r' and resid 101 through 116 removed outlier: 3.910A pdb=" N VAL r 106 " --> pdb=" O ALA r 102 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL r 107 " --> pdb=" O LYS r 103 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE r 108 " --> pdb=" O ASN r 104 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS r 113 " --> pdb=" O LEU r 109 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA r 114 " --> pdb=" O ALA r 110 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 45 removed outlier: 3.771A pdb=" N LEU s 45 " --> pdb=" O GLN s 42 " (cutoff:3.500A) Processing helix chain 't' and resid 58 through 64 removed outlier: 3.754A pdb=" N TYR t 62 " --> pdb=" O PRO t 59 " (cutoff:3.500A) Processing helix chain 't' and resid 81 through 110 removed outlier: 3.885A pdb=" N ARG t 88 " --> pdb=" O CYS t 84 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU t 96 " --> pdb=" O ALA t 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE t 100 " --> pdb=" O GLU t 96 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL t 101 " --> pdb=" O GLU t 97 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS t 106 " --> pdb=" O LYS t 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU t 107 " --> pdb=" O LYS t 103 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 10 removed outlier: 3.806A pdb=" N LEU u 9 " --> pdb=" O LYS u 5 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG u 10 " --> pdb=" O ALA u 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 5 through 10' Processing helix chain 'u' and resid 13 through 35 removed outlier: 3.694A pdb=" N VAL u 22 " --> pdb=" O ALA u 18 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP u 23 " --> pdb=" O SER u 19 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL u 33 " --> pdb=" O ALA u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 67 removed outlier: 4.051A pdb=" N VAL u 47 " --> pdb=" O LYS u 43 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA u 52 " --> pdb=" O ARG u 48 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS u 53 " --> pdb=" O LYS u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 77 through 81 Processing helix chain 'u' and resid 86 through 90 Processing helix chain 'u' and resid 93 through 98 removed outlier: 3.624A pdb=" N SER u 98 " --> pdb=" O LYS u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 103 through 111 Processing helix chain 'v' and resid 25 through 29 removed outlier: 3.708A pdb=" N TYR v 28 " --> pdb=" O LYS v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 35 through 49 removed outlier: 3.646A pdb=" N PHE v 39 " --> pdb=" O ASN v 35 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG v 45 " --> pdb=" O ARG v 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU v 46 " --> pdb=" O SER v 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE v 47 " --> pdb=" O LEU v 43 " (cutoff:3.500A) Processing helix chain 'v' and resid 52 through 64 removed outlier: 3.885A pdb=" N ARG v 56 " --> pdb=" O PRO v 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE v 58 " --> pdb=" O GLU v 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP v 59 " --> pdb=" O ARG v 55 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE v 61 " --> pdb=" O LEU v 57 " (cutoff:3.500A) Processing helix chain 'v' and resid 65 through 77 removed outlier: 3.935A pdb=" N LYS v 71 " --> pdb=" O LYS v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 98 removed outlier: 3.994A pdb=" N ALA v 85 " --> pdb=" O THR v 81 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS v 86 " --> pdb=" O ARG v 82 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN v 92 " --> pdb=" O GLU v 88 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE v 94 " --> pdb=" O MET v 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER v 97 " --> pdb=" O ILE v 93 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 56 removed outlier: 3.776A pdb=" N ARG w 55 " --> pdb=" O ALA w 51 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG w 56 " --> pdb=" O LYS w 52 " (cutoff:3.500A) Processing helix chain 'w' and resid 69 through 77 removed outlier: 3.629A pdb=" N ARG w 73 " --> pdb=" O HIS w 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN w 76 " --> pdb=" O ARG w 72 " (cutoff:3.500A) Processing helix chain 'x' and resid 7 through 15 removed outlier: 3.677A pdb=" N PHE x 11 " --> pdb=" O ASP x 7 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU x 13 " --> pdb=" O LYS x 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR x 15 " --> pdb=" O PHE x 11 " (cutoff:3.500A) Processing helix chain 'x' and resid 58 through 68 removed outlier: 3.631A pdb=" N LYS x 64 " --> pdb=" O GLY x 60 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU x 65 " --> pdb=" O LYS x 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN x 67 " --> pdb=" O LYS x 63 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER x 68 " --> pdb=" O LYS x 64 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 19 removed outlier: 3.608A pdb=" N LYS y 12 " --> pdb=" O ARG y 8 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS y 15 " --> pdb=" O GLN y 11 " (cutoff:3.500A) Processing helix chain 'y' and resid 26 through 30 removed outlier: 3.578A pdb=" N LEU y 29 " --> pdb=" O TRP y 26 " (cutoff:3.500A) Processing helix chain 'z' and resid 79 through 91 removed outlier: 3.760A pdb=" N LYS z 83 " --> pdb=" O GLU z 79 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS z 88 " --> pdb=" O ALA z 84 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR z 89 " --> pdb=" O LEU z 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 238 through 241 removed outlier: 6.951A pdb=" N VAL Y 230 " --> pdb=" O LEU Y 239 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU Y 241 " --> pdb=" O THR Y 228 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR Y 228 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 259 through 262 removed outlier: 3.540A pdb=" N LYS Y 262 " --> pdb=" O ASP Y 272 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP Y 272 " --> pdb=" O LYS Y 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 282 through 284 removed outlier: 3.570A pdb=" N GLY Y 316 " --> pdb=" O HIS Y 335 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN Y 337 " --> pdb=" O VAL Y 314 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL Y 314 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY Y 315 " --> pdb=" O PHE Y 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 2 through 4 removed outlier: 6.632A pdb=" N THR X 3 " --> pdb=" O THR X 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 17 through 19 Processing sheet with id=AA6, first strand: chain 'X' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'X' and resid 108 through 109 Processing sheet with id=AA8, first strand: chain 'X' and resid 152 through 154 Processing sheet with id=AA9, first strand: chain 'W' and resid 261 through 262 removed outlier: 6.742A pdb=" N VAL W 201 " --> pdb=" O LEU W 232 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LEU W 234 " --> pdb=" O VAL W 201 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN W 203 " --> pdb=" O LEU W 234 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU W 200 " --> pdb=" O GLY W 340 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL W 342 " --> pdb=" O LEU W 200 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL W 202 " --> pdb=" O VAL W 342 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN W 375 " --> pdb=" O ASP W 387 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 52 through 58 removed outlier: 6.502A pdb=" N ALA V 53 " --> pdb=" O ILE V 137 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE V 139 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE V 55 " --> pdb=" O ILE V 139 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N MET V 141 " --> pdb=" O ILE V 55 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE V 57 " --> pdb=" O MET V 141 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP V 99 " --> pdb=" O THR V 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'V' and resid 187 through 192 removed outlier: 4.008A pdb=" N SER V 189 " --> pdb=" O PHE V 200 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE V 199 " --> pdb=" O VAL V 159 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL V 159 " --> pdb=" O PHE V 199 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN V 160 " --> pdb=" O VAL V 246 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE V 248 " --> pdb=" O GLN V 160 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG V 162 " --> pdb=" O ILE V 248 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS V 223 " --> pdb=" O SER V 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'V' and resid 257 through 258 removed outlier: 6.561A pdb=" N GLN V 284 " --> pdb=" O SER V 277 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'V' and resid 353 through 357 removed outlier: 3.829A pdb=" N THR V 339 " --> pdb=" O ASP V 322 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP V 322 " --> pdb=" O THR V 339 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA V 341 " --> pdb=" O VAL V 320 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL V 320 " --> pdb=" O ALA V 341 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER V 368 " --> pdb=" O LYS V 400 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS V 400 " --> pdb=" O SER V 368 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET V 370 " --> pdb=" O VAL V 398 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 77 removed outlier: 3.532A pdb=" N ARG D 72 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU D 58 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE D 48 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS D 60 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG D 64 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ARG D 42 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 101 through 103 removed outlier: 3.573A pdb=" N LEU D 102 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG D 147 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N HIS D 139 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS D 145 " --> pdb=" O HIS D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB8, first strand: chain 'E' and resid 356 through 359 removed outlier: 6.773A pdb=" N VAL E 57 " --> pdb=" O LYS E 357 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE E 359 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR E 55 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE E 335 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL E 220 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA E 217 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE E 278 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA E 219 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR E 276 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS E 281 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET E 323 " --> pdb=" O TYR E 283 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL E 285 " --> pdb=" O PHE E 321 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE E 321 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP E 320 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 70 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ASP E 80 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS E 50 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 106 removed outlier: 6.927A pdb=" N GLY E 91 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR E 104 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL E 89 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TRP E 106 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 87 " --> pdb=" O TRP E 106 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL E 86 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS E 163 " --> pdb=" O VAL E 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 106 removed outlier: 6.927A pdb=" N GLY E 91 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR E 104 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL E 89 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TRP E 106 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 87 " --> pdb=" O TRP E 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 223 through 227 removed outlier: 3.621A pdb=" N GLY E 225 " --> pdb=" O ARG E 270 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 15 through 20 removed outlier: 4.101A pdb=" N VAL F 8 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN F 18 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL F 6 " --> pdb=" O ASN F 18 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL F 151 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU F 150 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU F 206 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 251 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL F 208 " --> pdb=" O THR F 251 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR F 209 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AC5, first strand: chain 'G' and resid 73 through 79 removed outlier: 5.892A pdb=" N VAL G 74 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER G 66 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP G 59 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 53 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 77 through 80 removed outlier: 6.725A pdb=" N SER H 66 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR H 54 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL H 39 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AC8, first strand: chain 'I' and resid 205 through 206 removed outlier: 4.482A pdb=" N SER I 113 " --> pdb=" O ARG I 88 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY I 137 " --> pdb=" O PHE I 85 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 134 " --> pdb=" O GLY I 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AD1, first strand: chain 'J' and resid 70 through 71 removed outlier: 3.817A pdb=" N GLY J 234 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 177 through 179 removed outlier: 6.500A pdb=" N VAL J 151 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU J 150 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 6 removed outlier: 7.014A pdb=" N ILE K 4 " --> pdb=" O ASN K 59 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.665A pdb=" N LEU K 52 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 17 through 20 removed outlier: 3.505A pdb=" N VAL K 28 " --> pdb=" O THR K 17 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.489A pdb=" N ARG K 91 " --> pdb=" O VAL K 181 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL K 181 " --> pdb=" O ARG K 91 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL K 93 " --> pdb=" O ILE K 179 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE K 179 " --> pdb=" O VAL K 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 100 through 104 Processing sheet with id=AD8, first strand: chain 'Z' and resid 35 through 37 removed outlier: 6.391A pdb=" N ILE Z 134 " --> pdb=" O SER Z 54 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER Z 54 " --> pdb=" O ILE Z 134 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE Z 136 " --> pdb=" O LEU Z 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE Z 166 " --> pdb=" O HIS Z 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 95 through 99 removed outlier: 6.602A pdb=" N HIS Z 95 " --> pdb=" O LEU Z 125 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU Z 125 " --> pdb=" O HIS Z 95 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU Z 97 " --> pdb=" O HIS Z 123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 191 through 192 removed outlier: 3.677A pdb=" N LYS Z 191 " --> pdb=" O LYS Z 198 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 46 through 48 removed outlier: 3.521A pdb=" N VAL M 67 " --> pdb=" O ILE M 21 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 22 through 24 removed outlier: 6.660A pdb=" N LYS N 23 " --> pdb=" O LEU a 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'N' and resid 57 through 58 Processing sheet with id=AE5, first strand: chain 'N' and resid 123 through 125 removed outlier: 3.573A pdb=" N ILE N 124 " --> pdb=" O ALA u 117 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA u 117 " --> pdb=" O ILE N 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'N' and resid 156 through 157 removed outlier: 6.391A pdb=" N VAL n 125 " --> pdb=" O GLU n 146 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 14 through 15 removed outlier: 3.606A pdb=" N PHE f 150 " --> pdb=" O VAL O 15 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 53 through 59 removed outlier: 5.089A pdb=" N GLY O 48 " --> pdb=" O PRO O 54 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LYS O 43 " --> pdb=" O ILE O 38 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE O 38 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU O 45 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL O 20 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 3 through 4 removed outlier: 3.807A pdb=" N VAL Q 4 " --> pdb=" O GLU Q 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'Q' and resid 7 through 11 removed outlier: 3.567A pdb=" N THR Q 26 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL Q 68 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'S' and resid 198 through 199 removed outlier: 4.051A pdb=" N UNK S 198 " --> pdb=" O UNK S 210 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 36 through 39 removed outlier: 4.464A pdb=" N ILE a 61 " --> pdb=" O ALA a 39 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR a 127 " --> pdb=" O ASN a 122 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASN a 122 " --> pdb=" O TYR a 127 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TYR a 129 " --> pdb=" O TRP a 120 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TRP a 120 " --> pdb=" O TYR a 129 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU a 131 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N SER a 118 " --> pdb=" O GLU a 131 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE a 133 " --> pdb=" O LEU a 116 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 6 through 10 removed outlier: 5.974A pdb=" N VAL b 7 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL b 36 " --> pdb=" O VAL b 7 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE b 9 " --> pdb=" O VAL b 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 42 through 44 Processing sheet with id=AF7, first strand: chain 'c' and resid 14 through 22 removed outlier: 3.584A pdb=" N TYR c 21 " --> pdb=" O SER c 144 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N SER c 144 " --> pdb=" O TYR c 21 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS c 145 " --> pdb=" O VAL c 119 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL c 119 " --> pdb=" O HIS c 145 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU c 147 " --> pdb=" O ILE c 117 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE c 117 " --> pdb=" O GLU c 147 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL c 149 " --> pdb=" O SER c 115 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 58 through 59 Processing sheet with id=AF9, first strand: chain 'c' and resid 128 through 130 removed outlier: 3.831A pdb=" N ASN c 137 " --> pdb=" O THR c 129 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 62 through 63 removed outlier: 3.782A pdb=" N LEU d 104 " --> pdb=" O VAL d 83 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY d 85 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE d 106 " --> pdb=" O GLY d 85 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL d 87 " --> pdb=" O PHE d 106 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL d 101 " --> pdb=" O ILE d 122 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 62 through 63 Processing sheet with id=AG3, first strand: chain 'e' and resid 23 through 24 removed outlier: 3.585A pdb=" N TRP e 23 " --> pdb=" O VAL e 51 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL e 51 " --> pdb=" O TRP e 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'f' and resid 25 through 31 removed outlier: 7.225A pdb=" N GLU f 6 " --> pdb=" O GLN f 63 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN f 63 " --> pdb=" O GLU f 6 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN f 8 " --> pdb=" O ILE f 61 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE f 61 " --> pdb=" O GLN f 8 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE f 10 " --> pdb=" O VAL f 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'f' and resid 87 through 96 removed outlier: 7.172A pdb=" N ASN f 74 " --> pdb=" O GLU f 128 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU f 128 " --> pdb=" O ASN f 74 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY f 76 " --> pdb=" O VAL f 126 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL f 126 " --> pdb=" O GLY f 76 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP f 78 " --> pdb=" O LEU f 124 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 83 through 92 removed outlier: 3.526A pdb=" N ARG g 83 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN g 66 " --> pdb=" O GLY g 73 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE g 75 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL g 64 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ASN g 77 " --> pdb=" O GLY g 62 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY g 62 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 54 through 58 removed outlier: 7.814A pdb=" N TYR h 103 " --> pdb=" O THR h 14 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR h 16 " --> pdb=" O TYR h 103 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU h 105 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP h 18 " --> pdb=" O LEU h 105 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'i' and resid 17 through 18 removed outlier: 3.810A pdb=" N LEU i 17 " --> pdb=" O ALA i 52 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'i' and resid 22 through 25 removed outlier: 7.046A pdb=" N ASN i 33 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS i 63 " --> pdb=" O ASN i 33 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET i 59 " --> pdb=" O ILE i 37 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL i 39 " --> pdb=" O MET i 57 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET i 57 " --> pdb=" O VAL i 39 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA i 99 " --> pdb=" O VAL i 79 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY i 100 " --> pdb=" O ILE i 22 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN i 24 " --> pdb=" O GLY i 100 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE i 102 " --> pdb=" O ASN i 24 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'i' and resid 85 through 86 removed outlier: 6.488A pdb=" N PHE i 92 " --> pdb=" O LEU j 20 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL j 22 " --> pdb=" O PHE i 92 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYR i 94 " --> pdb=" O VAL j 22 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS j 27 " --> pdb=" O ARG j 23 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'i' and resid 117 through 118 Processing sheet with id=AH3, first strand: chain 'j' and resid 4 through 5 removed outlier: 3.654A pdb=" N GLU j 4 " --> pdb=" O ILE j 13 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'k' and resid 63 through 66 removed outlier: 3.909A pdb=" N LYS k 120 " --> pdb=" O VAL k 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR k 119 " --> pdb=" O ARG k 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS k 109 " --> pdb=" O ARG k 125 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'l' and resid 32 through 34 Processing sheet with id=AH6, first strand: chain 'l' and resid 79 through 82 removed outlier: 7.100A pdb=" N ALA l 79 " --> pdb=" O VAL l 73 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL l 73 " --> pdb=" O ALA l 79 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLN l 81 " --> pdb=" O SER l 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU l 55 " --> pdb=" O THR l 107 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'l' and resid 86 through 87 Processing sheet with id=AH8, first strand: chain 'm' and resid 69 through 76 removed outlier: 6.601A pdb=" N LYS m 69 " --> pdb=" O GLU m 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS m 27 " --> pdb=" O LEU m 42 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA m 44 " --> pdb=" O ILE m 25 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE m 25 " --> pdb=" O ALA m 44 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE m 46 " --> pdb=" O VAL m 23 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL m 23 " --> pdb=" O ILE m 46 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N ARG m 48 " --> pdb=" O LYS m 21 " (cutoff:3.500A) removed outlier: 10.978A pdb=" N LYS m 21 " --> pdb=" O ARG m 48 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS m 21 " --> pdb=" O VAL m 13 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL m 10 " --> pdb=" O THR m 83 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 72 through 73 Processing sheet with id=AI1, first strand: chain 'p' and resid 23 through 25 removed outlier: 3.555A pdb=" N LEU p 41 " --> pdb=" O ILE p 92 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE p 42 " --> pdb=" O LYS p 66 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'q' and resid 9 through 11 removed outlier: 4.527A pdb=" N THR q 9 " --> pdb=" O VAL q 109 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'q' and resid 49 through 51 Processing sheet with id=AI4, first strand: chain 'r' and resid 72 through 76 Processing sheet with id=AI5, first strand: chain 's' and resid 8 through 18 removed outlier: 6.729A pdb=" N LEU s 29 " --> pdb=" O LEU s 14 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TYR s 16 " --> pdb=" O VAL s 27 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL s 27 " --> pdb=" O TYR s 16 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ARG s 18 " --> pdb=" O PRO s 25 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN s 26 " --> pdb=" O PHE s 85 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE s 85 " --> pdb=" O ASN s 26 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG s 73 " --> pdb=" O ARG s 82 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR s 84 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL s 71 " --> pdb=" O THR s 84 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG s 48 " --> pdb=" O PHE s 101 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL s 52 " --> pdb=" O SER s 97 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER s 97 " --> pdb=" O VAL s 52 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 't' and resid 19 through 24 removed outlier: 4.398A pdb=" N LYS t 19 " --> pdb=" O VAL t 35 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL t 35 " --> pdb=" O LYS t 19 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'w' and resid 16 through 17 Processing sheet with id=AI8, first strand: chain 'x' and resid 51 through 56 removed outlier: 5.228A pdb=" N THR x 22 " --> pdb=" O ARG x 46 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA x 23 " --> pdb=" O ASN x 76 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'z' and resid 102 through 103 1736 hydrogen bonds defined for protein. 4875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1907 hydrogen bonds 3126 hydrogen bond angles 0 basepair planarities 817 basepair parallelities 1885 stacking parallelities Total time for adding SS restraints: 178.25 Time building geometry restraints manager: 51.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 33910 1.34 - 1.48: 60812 1.48 - 1.62: 48439 1.62 - 1.76: 8 1.76 - 1.90: 200 Bond restraints: 143369 Sorted by residual: bond pdb=" N UNK S 107 " pdb=" CA UNK S 107 " ideal model delta sigma weight residual 1.458 1.555 -0.097 1.90e-02 2.77e+03 2.61e+01 bond pdb=" N ASN W 395 " pdb=" CA ASN W 395 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.01e+01 bond pdb=" CB CYS t 81 " pdb=" SG CYS t 81 " ideal model delta sigma weight residual 1.808 1.902 -0.094 3.30e-02 9.18e+02 8.10e+00 bond pdb=" N ASP L 107 " pdb=" CA ASP L 107 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.70e+00 bond pdb=" N ALA W 207 " pdb=" CA ALA W 207 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.33e+00 ... (remaining 143364 not shown) Histogram of bond angle deviations from ideal: 95.15 - 103.39: 8531 103.39 - 111.62: 79985 111.62 - 119.85: 61120 119.85 - 128.08: 55099 128.08 - 136.31: 5978 Bond angle restraints: 210713 Sorted by residual: angle pdb=" C UNK S 106 " pdb=" N UNK S 107 " pdb=" CA UNK S 107 " ideal model delta sigma weight residual 121.70 107.10 14.60 1.80e+00 3.09e-01 6.58e+01 angle pdb=" CA CYS t 81 " pdb=" CB CYS t 81 " pdb=" SG CYS t 81 " ideal model delta sigma weight residual 114.40 132.87 -18.47 2.30e+00 1.89e-01 6.45e+01 angle pdb=" N LEU F 182 " pdb=" CA LEU F 182 " pdb=" C LEU F 182 " ideal model delta sigma weight residual 114.62 105.65 8.97 1.14e+00 7.69e-01 6.19e+01 angle pdb=" C GLU G 257 " pdb=" N LYS G 258 " pdb=" CA LYS G 258 " ideal model delta sigma weight residual 121.54 135.96 -14.42 1.91e+00 2.74e-01 5.70e+01 angle pdb=" C LYS n 47 " pdb=" N TYR n 48 " pdb=" CA TYR n 48 " ideal model delta sigma weight residual 121.54 134.69 -13.15 1.91e+00 2.74e-01 4.74e+01 ... (remaining 210708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 82633 35.99 - 71.99: 7246 71.99 - 107.98: 860 107.98 - 143.98: 13 143.98 - 179.97: 57 Dihedral angle restraints: 90809 sinusoidal: 68809 harmonic: 22000 Sorted by residual: dihedral pdb=" CA ASN I 157 " pdb=" C ASN I 157 " pdb=" N LYS I 158 " pdb=" CA LYS I 158 " ideal model delta harmonic sigma weight residual -180.00 -105.38 -74.62 0 5.00e+00 4.00e-02 2.23e+02 dihedral pdb=" CA ASP V 44 " pdb=" C ASP V 44 " pdb=" N ILE V 45 " pdb=" CA ILE V 45 " ideal model delta harmonic sigma weight residual 180.00 120.56 59.44 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA ILE W 441 " pdb=" C ILE W 441 " pdb=" N GLN W 442 " pdb=" CA GLN W 442 " ideal model delta harmonic sigma weight residual 180.00 -121.99 -58.01 0 5.00e+00 4.00e-02 1.35e+02 ... (remaining 90806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 24295 0.077 - 0.154: 1928 0.154 - 0.231: 181 0.231 - 0.308: 33 0.308 - 0.385: 13 Chirality restraints: 26450 Sorted by residual: chirality pdb=" C3' G A2249 " pdb=" C4' G A2249 " pdb=" O3' G A2249 " pdb=" C2' G A2249 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.38 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C3' G C 85 " pdb=" C4' G C 85 " pdb=" O3' G C 85 " pdb=" C2' G C 85 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C3' C A 599 " pdb=" C4' C A 599 " pdb=" O3' C A 599 " pdb=" C2' C A 599 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 26447 not shown) Planarity restraints: 13806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG f 12 " 0.024 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C ARG f 12 " -0.082 2.00e-02 2.50e+03 pdb=" O ARG f 12 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG f 13 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS n 47 " 0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C LYS n 47 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS n 47 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR n 48 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 255 " 0.028 2.00e-02 2.50e+03 2.37e-02 1.41e+01 pdb=" CG TRP E 255 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP E 255 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP E 255 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 255 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 255 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 255 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 255 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 255 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 255 " -0.000 2.00e-02 2.50e+03 ... (remaining 13803 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 13 2.02 - 2.74: 17636 2.74 - 3.46: 163403 3.46 - 4.18: 385185 4.18 - 4.90: 567884 Nonbonded interactions: 1134121 Sorted by model distance: nonbonded pdb=" O UNK L 120 " pdb=" N UNK L 122 " model vdw 1.297 2.520 nonbonded pdb=" O GLY L 102 " pdb=" N UNK L 141 " model vdw 1.300 2.520 nonbonded pdb=" O2' C A1254 " pdb=" CB UNK L 135 " model vdw 1.376 3.440 nonbonded pdb=" O ASP V 390 " pdb=" CB UNK S 39 " model vdw 1.376 3.440 nonbonded pdb=" CA UNK S 47 " pdb=" O UNK S 149 " model vdw 1.377 3.470 ... (remaining 1134116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 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: 17.040 Check model and map are aligned: 1.460 Set scattering table: 0.930 Process input model: 410.010 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 438.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 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 : 0.007 0.097 143369 Z= 0.433 Angle : 0.894 18.469 210713 Z= 0.481 Chirality : 0.046 0.385 26450 Planarity : 0.006 0.067 13806 Dihedral : 21.347 179.975 76541 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.20 % Favored : 92.36 % Rotamer: Outliers : 0.56 % Allowed : 4.34 % Favored : 95.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.45 % 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: -4.60 (0.07), residues: 7190 helix: -4.54 (0.04), residues: 2084 sheet: -1.66 (0.15), residues: 1028 loop : -2.64 (0.08), residues: 4078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP E 255 HIS 0.014 0.002 HIS Z 92 PHE 0.031 0.003 PHE E 118 TYR 0.043 0.003 TYR c 130 ARG 0.021 0.001 ARG c 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2110 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 2076 time to evaluate : 6.970 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: Y 276 SER cc_start: 0.8990 (m) cc_final: 0.8599 (m) REVERT: Y 291 MET cc_start: 0.8075 (mtt) cc_final: 0.7851 (mtt) REVERT: X 23 TYR cc_start: 0.8916 (p90) cc_final: 0.8629 (p90) REVERT: X 101 LEU cc_start: 0.8818 (mp) cc_final: 0.8614 (mt) REVERT: X 108 ILE cc_start: 0.9207 (mt) cc_final: 0.9001 (mp) REVERT: W 173 ASN cc_start: 0.6043 (t0) cc_final: 0.5639 (t0) REVERT: W 220 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7223 (ttp-170) REVERT: W 374 PHE cc_start: 0.4936 (p90) cc_final: 0.4374 (t80) REVERT: W 432 TYR cc_start: 0.6301 (t80) cc_final: 0.6086 (t80) REVERT: V 26 ILE cc_start: 0.7319 (mp) cc_final: 0.6970 (tt) REVERT: V 117 THR cc_start: 0.8206 (m) cc_final: 0.7722 (t) REVERT: V 135 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6963 (mt-10) REVERT: V 194 LYS cc_start: 0.8644 (tptt) cc_final: 0.8201 (tptm) REVERT: V 201 TYR cc_start: 0.7439 (m-10) cc_final: 0.6985 (m-80) REVERT: V 203 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7682 (mp10) REVERT: V 286 MET cc_start: 0.7951 (ttm) cc_final: 0.7714 (ttp) REVERT: V 287 ASP cc_start: 0.8541 (t0) cc_final: 0.8275 (t0) REVERT: V 314 GLN cc_start: 0.8933 (mp-120) cc_final: 0.8710 (mp10) REVERT: V 354 TYR cc_start: 0.8879 (t80) cc_final: 0.8423 (t80) REVERT: V 364 HIS cc_start: 0.7974 (m90) cc_final: 0.7507 (m-70) REVERT: D 34 TYR cc_start: 0.9172 (t80) cc_final: 0.8634 (t80) REVERT: D 65 ASP cc_start: 0.9049 (t0) cc_final: 0.8841 (t0) REVERT: D 194 ASN cc_start: 0.8962 (t0) cc_final: 0.8584 (t0) REVERT: E 7 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7217 (mp0) REVERT: E 56 ILE cc_start: 0.9013 (tp) cc_final: 0.8799 (tp) REVERT: E 251 CYS cc_start: 0.8573 (t) cc_final: 0.8213 (t) REVERT: F 61 SER cc_start: 0.8251 (p) cc_final: 0.7999 (p) REVERT: F 148 ILE cc_start: 0.9156 (mt) cc_final: 0.8871 (mm) REVERT: F 226 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7300 (mt-10) REVERT: F 234 ASN cc_start: 0.8493 (t0) cc_final: 0.8130 (t0) REVERT: G 46 THR cc_start: 0.8735 (m) cc_final: 0.8489 (p) REVERT: G 59 ASP cc_start: 0.8273 (t70) cc_final: 0.7338 (t0) REVERT: G 133 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8063 (mm-30) REVERT: H 82 ARG cc_start: 0.8479 (mmt90) cc_final: 0.8270 (mmm-85) REVERT: H 92 SER cc_start: 0.8585 (t) cc_final: 0.8303 (p) REVERT: H 170 LYS cc_start: 0.8834 (mtmt) cc_final: 0.8472 (mttm) REVERT: H 173 MET cc_start: 0.8108 (mmm) cc_final: 0.7771 (mmt) REVERT: I 228 SER cc_start: 0.9237 (m) cc_final: 0.9031 (m) REVERT: J 79 GLN cc_start: 0.8245 (pp30) cc_final: 0.7854 (pp30) REVERT: K 115 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7600 (mtt-85) REVERT: K 171 ASP cc_start: 0.8875 (t70) cc_final: 0.8516 (t70) REVERT: Z 66 GLU cc_start: 0.8581 (tp30) cc_final: 0.8179 (tp30) REVERT: Z 180 GLU cc_start: 0.8891 (tp30) cc_final: 0.8407 (tp30) REVERT: M 81 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7827 (tm-30) REVERT: M 101 ASN cc_start: 0.8974 (m-40) cc_final: 0.8764 (m-40) REVERT: N 140 SER cc_start: 0.9011 (t) cc_final: 0.8765 (t) REVERT: a 32 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8681 (mm110) REVERT: a 151 ILE cc_start: 0.8926 (mm) cc_final: 0.8712 (mm) REVERT: a 169 LYS cc_start: 0.9101 (mttt) cc_final: 0.8868 (mttm) REVERT: a 175 ASN cc_start: 0.8443 (t0) cc_final: 0.8118 (m110) REVERT: b 174 PHE cc_start: 0.9005 (t80) cc_final: 0.8664 (t80) REVERT: c 20 SER cc_start: 0.9637 (m) cc_final: 0.9435 (m) REVERT: c 64 ASN cc_start: 0.8974 (p0) cc_final: 0.8657 (p0) REVERT: c 65 SER cc_start: 0.9307 (p) cc_final: 0.9088 (m) REVERT: c 78 VAL cc_start: 0.9270 (t) cc_final: 0.9045 (p) REVERT: c 144 SER cc_start: 0.9303 (m) cc_final: 0.9040 (p) REVERT: d 21 SER cc_start: 0.9483 (t) cc_final: 0.9258 (t) REVERT: e 13 SER cc_start: 0.9249 (t) cc_final: 0.9035 (t) REVERT: e 27 ASN cc_start: 0.9068 (m-40) cc_final: 0.8690 (m110) REVERT: e 124 TYR cc_start: 0.9047 (t80) cc_final: 0.8637 (t80) REVERT: f 91 TYR cc_start: 0.9282 (t80) cc_final: 0.8946 (t80) REVERT: h 35 LYS cc_start: 0.9409 (tptp) cc_final: 0.9165 (tptp) REVERT: h 36 TYR cc_start: 0.9165 (t80) cc_final: 0.8832 (t80) REVERT: h 40 HIS cc_start: 0.7804 (m90) cc_final: 0.7446 (m170) REVERT: i 59 MET cc_start: 0.7738 (mmt) cc_final: 0.7393 (mtt) REVERT: i 72 LYS cc_start: 0.8821 (ptpt) cc_final: 0.8562 (ptpp) REVERT: i 83 LYS cc_start: 0.8812 (tptt) cc_final: 0.8461 (tttm) REVERT: i 110 LYS cc_start: 0.8375 (mttm) cc_final: 0.8131 (mtpt) REVERT: j 5 ILE cc_start: 0.8727 (pp) cc_final: 0.8518 (mm) REVERT: k 80 ASN cc_start: 0.8589 (t0) cc_final: 0.8377 (t0) REVERT: o 33 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8215 (ptmm) REVERT: p 63 SER cc_start: 0.9248 (p) cc_final: 0.9029 (p) REVERT: q 34 LYS cc_start: 0.8774 (mttm) cc_final: 0.8435 (mttp) REVERT: r 111 ARG cc_start: 0.9034 (tpt170) cc_final: 0.8670 (tpt90) REVERT: s 44 TYR cc_start: 0.9050 (m-80) cc_final: 0.8810 (m-80) REVERT: t 11 ASN cc_start: 0.9351 (t0) cc_final: 0.8860 (t0) REVERT: t 14 ASN cc_start: 0.8743 (t0) cc_final: 0.8492 (t0) REVERT: t 18 ASN cc_start: 0.8934 (t0) cc_final: 0.8472 (t0) REVERT: t 20 ILE cc_start: 0.9440 (mm) cc_final: 0.9238 (mm) REVERT: t 95 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8571 (mp) REVERT: u 104 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7904 (tm-30) REVERT: x 9 LYS cc_start: 0.8872 (tppt) cc_final: 0.8609 (tppt) REVERT: y 28 ARG cc_start: 0.8353 (mtp85) cc_final: 0.8073 (mtt-85) REVERT: z 109 ASN cc_start: 0.9063 (m110) cc_final: 0.8840 (m-40) outliers start: 34 outliers final: 14 residues processed: 2096 average time/residue: 1.2948 time to fit residues: 4547.6966 Evaluate side-chains 1312 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1297 time to evaluate : 6.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain W residue 237 LYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain w residue 22 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 903 optimal weight: 2.9990 chunk 811 optimal weight: 3.9990 chunk 450 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 547 optimal weight: 0.9980 chunk 433 optimal weight: 5.9990 chunk 838 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 509 optimal weight: 2.9990 chunk 624 optimal weight: 1.9990 chunk 971 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 318 ASN Y 335 HIS Y 343 GLN X 50 HIS X 145 ASN X 162 HIS W 127 GLN W 168 HIS W 170 GLN W 190 GLN W 323 ASN W 413 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 458 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS D 218 HIS D 233 GLN E 243 HIS F 36 HIS F 43 ASN F 221 ASN ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN H 28 GLN H 172 HIS ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 244 ASN J 24 ASN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 ASN J 243 GLN K 8 GLN K 64 HIS K 162 GLN ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 133 GLN M 68 HIS M 109 HIS N 103 ASN N 137 GLN O 41 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 GLN Q 22 GLN Q 82 GLN R 33 GLN a 37 HIS b 55 HIS c 28 ASN c 96 GLN e 58 HIS f 8 GLN f 88 HIS f 89 ASN f 142 GLN ** g 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 ASN ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 ASN i 81 GLN i 98 ASN j 58 HIS l 4 GLN n 89 GLN o 11 ASN o 45 HIS p 36 GLN q 57 GLN ** r 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 5 HIS s 26 ASN s 77 ASN t 98 GLN ** u 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 48 ASN x 67 GLN y 19 GLN y 43 ASN y 50 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 143369 Z= 0.176 Angle : 0.632 15.084 210713 Z= 0.325 Chirality : 0.037 0.391 26450 Planarity : 0.005 0.065 13806 Dihedral : 22.722 179.912 62235 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.45 % Favored : 93.25 % Rotamer: Outliers : 3.15 % Allowed : 12.02 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.18 (0.08), residues: 7190 helix: -2.35 (0.09), residues: 2169 sheet: -1.16 (0.15), residues: 1023 loop : -2.26 (0.08), residues: 3998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 155 HIS 0.010 0.001 HIS X 162 PHE 0.036 0.002 PHE G 260 TYR 0.023 0.001 TYR V 136 ARG 0.008 0.001 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1442 time to evaluate : 7.126 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: Y 234 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7329 (ttpp) REVERT: Y 291 MET cc_start: 0.7897 (mtt) cc_final: 0.7613 (mtt) REVERT: X 23 TYR cc_start: 0.8910 (p90) cc_final: 0.8672 (p90) REVERT: L 61 GLN cc_start: 0.6461 (mm110) cc_final: 0.5960 (mp10) REVERT: W 220 ARG cc_start: 0.7637 (ttm110) cc_final: 0.7294 (ttp-170) REVERT: W 432 TYR cc_start: 0.6508 (t80) cc_final: 0.6042 (t80) REVERT: V 24 THR cc_start: 0.7204 (p) cc_final: 0.6562 (t) REVERT: V 26 ILE cc_start: 0.7383 (mp) cc_final: 0.7144 (tt) REVERT: V 34 MET cc_start: 0.6564 (mmp) cc_final: 0.6000 (mmp) REVERT: V 84 ILE cc_start: 0.9094 (tt) cc_final: 0.8818 (mm) REVERT: V 194 LYS cc_start: 0.8398 (tptt) cc_final: 0.8093 (tptm) REVERT: V 344 SER cc_start: 0.9054 (m) cc_final: 0.8686 (t) REVERT: V 364 HIS cc_start: 0.7873 (m90) cc_final: 0.7615 (m-70) REVERT: D 194 ASN cc_start: 0.8833 (t0) cc_final: 0.8502 (t0) REVERT: E 56 ILE cc_start: 0.8935 (tp) cc_final: 0.8683 (tp) REVERT: F 61 SER cc_start: 0.8158 (p) cc_final: 0.7922 (p) REVERT: G 59 ASP cc_start: 0.8059 (t70) cc_final: 0.6862 (t0) REVERT: G 80 SER cc_start: 0.8453 (p) cc_final: 0.8243 (p) REVERT: H 60 ASP cc_start: 0.8054 (p0) cc_final: 0.7812 (p0) REVERT: H 170 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8441 (mttm) REVERT: H 173 MET cc_start: 0.8041 (mmm) cc_final: 0.7744 (mmt) REVERT: I 149 TYR cc_start: 0.9061 (m-80) cc_final: 0.8845 (m-80) REVERT: I 228 SER cc_start: 0.9196 (m) cc_final: 0.8984 (m) REVERT: J 64 ILE cc_start: 0.9475 (mt) cc_final: 0.9097 (mm) REVERT: J 79 GLN cc_start: 0.8147 (pp30) cc_final: 0.7640 (pp30) REVERT: J 202 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7450 (mt-10) REVERT: J 247 ASP cc_start: 0.8301 (t0) cc_final: 0.8084 (t0) REVERT: K 156 GLN cc_start: 0.8692 (tp40) cc_final: 0.8375 (tp-100) REVERT: K 171 ASP cc_start: 0.8773 (t70) cc_final: 0.8403 (t70) REVERT: Z 56 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7240 (mt-10) REVERT: Z 66 GLU cc_start: 0.8056 (tp30) cc_final: 0.7737 (tp30) REVERT: Z 76 MET cc_start: 0.8461 (mtp) cc_final: 0.8245 (mtp) REVERT: Z 174 THR cc_start: 0.9319 (m) cc_final: 0.9016 (p) REVERT: M 32 ARG cc_start: 0.8649 (mtm110) cc_final: 0.8112 (ptp-110) REVERT: M 40 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8863 (tp) REVERT: M 71 VAL cc_start: 0.9316 (t) cc_final: 0.9080 (m) REVERT: M 74 PRO cc_start: 0.9117 (Cg_endo) cc_final: 0.8597 (Cg_exo) REVERT: M 78 GLU cc_start: 0.8141 (mp0) cc_final: 0.7865 (mp0) REVERT: M 117 ASP cc_start: 0.7931 (t0) cc_final: 0.7691 (t70) REVERT: M 165 GLN cc_start: 0.8494 (tt0) cc_final: 0.8038 (tm-30) REVERT: N 140 SER cc_start: 0.8641 (t) cc_final: 0.8189 (p) REVERT: a 175 ASN cc_start: 0.8516 (t0) cc_final: 0.8169 (m110) REVERT: b 65 ASN cc_start: 0.9206 (t0) cc_final: 0.9005 (t0) REVERT: b 174 PHE cc_start: 0.8965 (t80) cc_final: 0.8561 (t80) REVERT: c 64 ASN cc_start: 0.8911 (p0) cc_final: 0.8417 (p0) REVERT: c 78 VAL cc_start: 0.9313 (t) cc_final: 0.9081 (p) REVERT: d 31 LYS cc_start: 0.9329 (ttmt) cc_final: 0.9122 (ttmm) REVERT: e 25 ASP cc_start: 0.8065 (p0) cc_final: 0.7144 (p0) REVERT: e 28 GLU cc_start: 0.7765 (mp0) cc_final: 0.7152 (mp0) REVERT: f 134 ASP cc_start: 0.8756 (m-30) cc_final: 0.8554 (m-30) REVERT: i 72 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8568 (ptpp) REVERT: i 83 LYS cc_start: 0.8833 (tptt) cc_final: 0.8476 (tttm) REVERT: i 106 LYS cc_start: 0.9174 (mttt) cc_final: 0.8952 (tttm) REVERT: i 110 LYS cc_start: 0.8473 (mttm) cc_final: 0.8203 (mtpt) REVERT: i 128 ARG cc_start: 0.8215 (tpp80) cc_final: 0.7958 (tpp80) REVERT: j 56 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8760 (mtp180) REVERT: j 57 LYS cc_start: 0.8602 (ttmm) cc_final: 0.8204 (tptp) REVERT: k 80 ASN cc_start: 0.8684 (t0) cc_final: 0.8410 (t0) REVERT: m 106 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: m 121 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8325 (tpp-160) REVERT: n 126 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8143 (mttt) REVERT: o 11 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8521 (t0) REVERT: o 21 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7573 (mt) REVERT: o 33 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8198 (ptmm) REVERT: p 40 LYS cc_start: 0.8463 (mptm) cc_final: 0.8165 (mmtm) REVERT: q 34 LYS cc_start: 0.8692 (mttm) cc_final: 0.8349 (mttp) REVERT: s 26 ASN cc_start: 0.8971 (m-40) cc_final: 0.8758 (m-40) REVERT: s 44 TYR cc_start: 0.9110 (m-80) cc_final: 0.8771 (m-80) REVERT: t 14 ASN cc_start: 0.8829 (t0) cc_final: 0.8407 (t0) REVERT: t 20 ILE cc_start: 0.9468 (mm) cc_final: 0.9253 (mm) REVERT: u 28 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9343 (tp) REVERT: u 104 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7717 (tm-30) REVERT: u 116 TYR cc_start: 0.9067 (p90) cc_final: 0.8177 (p90) REVERT: v 40 VAL cc_start: 0.9348 (t) cc_final: 0.9139 (p) REVERT: w 76 ASN cc_start: 0.8909 (m-40) cc_final: 0.8622 (m110) REVERT: y 23 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8597 (tt) REVERT: y 28 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7637 (mtp85) REVERT: y 36 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7272 (mmm160) REVERT: z 109 ASN cc_start: 0.9062 (m110) cc_final: 0.8840 (m-40) outliers start: 191 outliers final: 107 residues processed: 1556 average time/residue: 1.1864 time to fit residues: 3230.3777 Evaluate side-chains 1357 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1244 time to evaluate : 6.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 141 THR Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 168 HIS Chi-restraints excluded: chain W residue 237 LYS Chi-restraints excluded: chain W residue 261 THR Chi-restraints excluded: chain W residue 269 ASN Chi-restraints excluded: chain W residue 349 LYS Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 458 GLN Chi-restraints excluded: chain W residue 460 LEU Chi-restraints excluded: chain W residue 462 VAL Chi-restraints excluded: chain V residue 36 TYR Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 188 ILE Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 389 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 237 ILE Chi-restraints excluded: chain J residue 245 LYS Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 146 ASP Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 4 GLN Chi-restraints excluded: chain m residue 106 GLN Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain n residue 76 ASP Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain o residue 11 ASN Chi-restraints excluded: chain o residue 13 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain t residue 6 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain y residue 23 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 540 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 808 optimal weight: 7.9990 chunk 661 optimal weight: 0.0470 chunk 268 optimal weight: 10.0000 chunk 973 optimal weight: 7.9990 chunk 1051 optimal weight: 3.9990 chunk 866 optimal weight: 10.0000 chunk 965 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 780 optimal weight: 2.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 343 GLN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 164 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 233 GLN E 3 HIS ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS F 221 ASN ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 225 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN K 9 GLN ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 GLN Q 53 GLN R 25 GLN b 122 GLN c 28 ASN c 96 GLN f 8 GLN ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 ASN m 36 HIS ** p 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 17 HIS r 71 HIS y 50 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 143369 Z= 0.313 Angle : 0.636 15.360 210713 Z= 0.326 Chirality : 0.038 0.391 26450 Planarity : 0.005 0.068 13806 Dihedral : 22.607 179.967 62231 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.44 % Favored : 92.32 % Rotamer: Outliers : 4.47 % Allowed : 14.02 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.39 (0.09), residues: 7190 helix: -1.10 (0.10), residues: 2181 sheet: -0.93 (0.15), residues: 1040 loop : -2.10 (0.09), residues: 3969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 155 HIS 0.011 0.001 HIS W 168 PHE 0.019 0.002 PHE W 149 TYR 0.022 0.002 TYR G 44 ARG 0.007 0.001 ARG j 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1545 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1274 time to evaluate : 6.951 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: Y 291 MET cc_start: 0.7866 (mtt) cc_final: 0.7593 (mtt) REVERT: X 12 GLU cc_start: 0.7882 (mp0) cc_final: 0.7673 (mp0) REVERT: X 23 TYR cc_start: 0.8911 (p90) cc_final: 0.8639 (p90) REVERT: X 171 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: L 61 GLN cc_start: 0.6494 (mm110) cc_final: 0.6230 (mm110) REVERT: W 362 VAL cc_start: 0.8331 (t) cc_final: 0.8081 (p) REVERT: W 364 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7355 (m) REVERT: W 432 TYR cc_start: 0.6675 (t80) cc_final: 0.5989 (t80) REVERT: V 141 MET cc_start: 0.8278 (ptm) cc_final: 0.8036 (ptm) REVERT: V 194 LYS cc_start: 0.8320 (tptt) cc_final: 0.8060 (tptm) REVERT: V 209 LYS cc_start: 0.8333 (tptt) cc_final: 0.8050 (tptt) REVERT: V 344 SER cc_start: 0.8957 (m) cc_final: 0.8566 (t) REVERT: V 364 HIS cc_start: 0.7859 (m90) cc_final: 0.7655 (m-70) REVERT: V 370 MET cc_start: 0.8994 (mmm) cc_final: 0.8750 (mmt) REVERT: D 60 LYS cc_start: 0.9148 (mmtp) cc_final: 0.8835 (mttm) REVERT: D 72 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8258 (mmt90) REVERT: D 194 ASN cc_start: 0.8899 (t0) cc_final: 0.8562 (t0) REVERT: E 56 ILE cc_start: 0.9003 (tp) cc_final: 0.8733 (tp) REVERT: F 288 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8135 (ttm110) REVERT: G 59 ASP cc_start: 0.8080 (t70) cc_final: 0.6927 (t0) REVERT: G 185 PHE cc_start: 0.7122 (t80) cc_final: 0.6908 (t80) REVERT: G 264 GLN cc_start: 0.9171 (mp10) cc_final: 0.8804 (mt0) REVERT: H 60 ASP cc_start: 0.8115 (p0) cc_final: 0.7785 (p0) REVERT: H 170 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8440 (mttp) REVERT: H 173 MET cc_start: 0.8138 (mmm) cc_final: 0.7797 (mmt) REVERT: I 64 GLN cc_start: 0.8526 (tp40) cc_final: 0.8263 (tp40) REVERT: J 79 GLN cc_start: 0.8179 (pp30) cc_final: 0.7662 (pp30) REVERT: J 247 ASP cc_start: 0.8357 (t0) cc_final: 0.8152 (t0) REVERT: K 171 ASP cc_start: 0.8919 (t70) cc_final: 0.8607 (t70) REVERT: Z 174 THR cc_start: 0.9349 (m) cc_final: 0.8933 (p) REVERT: M 74 PRO cc_start: 0.9000 (Cg_endo) cc_final: 0.8453 (Cg_exo) REVERT: M 117 ASP cc_start: 0.8165 (t0) cc_final: 0.7961 (t70) REVERT: M 165 GLN cc_start: 0.8639 (tt0) cc_final: 0.8072 (tm-30) REVERT: N 140 SER cc_start: 0.8766 (t) cc_final: 0.8439 (p) REVERT: a 175 ASN cc_start: 0.8605 (t0) cc_final: 0.8201 (m110) REVERT: b 58 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9103 (mp) REVERT: b 174 PHE cc_start: 0.8967 (t80) cc_final: 0.8592 (t80) REVERT: c 49 GLU cc_start: 0.8107 (tp30) cc_final: 0.7894 (tp30) REVERT: c 64 ASN cc_start: 0.8925 (p0) cc_final: 0.8319 (p0) REVERT: e 25 ASP cc_start: 0.8082 (p0) cc_final: 0.7215 (p0) REVERT: e 28 GLU cc_start: 0.7825 (mp0) cc_final: 0.7257 (mp0) REVERT: f 138 GLN cc_start: 0.8685 (tp40) cc_final: 0.8157 (tp-100) REVERT: i 74 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8041 (ptp) REVERT: i 83 LYS cc_start: 0.8982 (tptt) cc_final: 0.8607 (tttm) REVERT: i 128 ARG cc_start: 0.8268 (tpp80) cc_final: 0.8011 (tpp80) REVERT: j 56 ARG cc_start: 0.9045 (mtp-110) cc_final: 0.8761 (mtp180) REVERT: j 57 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8169 (tptp) REVERT: k 80 ASN cc_start: 0.8726 (t0) cc_final: 0.8499 (t0) REVERT: k 134 ASP cc_start: 0.7772 (m-30) cc_final: 0.7373 (m-30) REVERT: l 4 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8790 (mm110) REVERT: m 46 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8991 (pt) REVERT: m 121 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8279 (tpp-160) REVERT: n 86 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8725 (mtpp) REVERT: o 33 LYS cc_start: 0.8458 (ttpp) cc_final: 0.8192 (ptmm) REVERT: p 23 TYR cc_start: 0.9148 (p90) cc_final: 0.8939 (p90) REVERT: q 34 LYS cc_start: 0.8763 (mttm) cc_final: 0.8424 (mttm) REVERT: s 24 ASN cc_start: 0.9055 (t0) cc_final: 0.8851 (t0) REVERT: s 26 ASN cc_start: 0.9024 (m-40) cc_final: 0.8815 (m-40) REVERT: s 44 TYR cc_start: 0.9105 (m-80) cc_final: 0.8703 (m-80) REVERT: t 11 ASN cc_start: 0.9371 (t0) cc_final: 0.8849 (t0) REVERT: t 14 ASN cc_start: 0.8972 (t0) cc_final: 0.8490 (t0) REVERT: t 18 ASN cc_start: 0.8950 (t0) cc_final: 0.8473 (t0) REVERT: u 104 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8148 (tm-30) REVERT: w 76 ASN cc_start: 0.8975 (m-40) cc_final: 0.8684 (m110) REVERT: y 28 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7837 (mtp85) REVERT: z 108 THR cc_start: 0.9342 (p) cc_final: 0.9090 (p) REVERT: z 109 ASN cc_start: 0.9098 (m110) cc_final: 0.8783 (m-40) outliers start: 271 outliers final: 182 residues processed: 1423 average time/residue: 1.1506 time to fit residues: 2875.3708 Evaluate side-chains 1364 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1176 time to evaluate : 8.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 301 LEU Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 141 THR Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 168 HIS Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 237 LYS Chi-restraints excluded: chain W residue 261 THR Chi-restraints excluded: chain W residue 269 ASN Chi-restraints excluded: chain W residue 317 PHE Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 399 ASN Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 460 LEU Chi-restraints excluded: chain W residue 462 VAL Chi-restraints excluded: chain W residue 487 ILE Chi-restraints excluded: chain V residue 36 TYR Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 225 SER Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 267 MET Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 290 THR Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 103 ASN Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 145 ASP Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 148 ASP Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 128 GLU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 4 SER Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 4 GLN Chi-restraints excluded: chain l residue 5 SER Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 126 LEU Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 76 ASP Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain p residue 81 VAL Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain q residue 14 ILE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 91 THR Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain r residue 120 THR Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 58 GLU Chi-restraints excluded: chain s residue 105 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 64 THR Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 13 SER Chi-restraints excluded: chain u residue 98 SER Chi-restraints excluded: chain u residue 109 ILE Chi-restraints excluded: chain v residue 7 ILE Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 71 SER Chi-restraints excluded: chain x residue 53 THR Chi-restraints excluded: chain x residue 66 ILE Chi-restraints excluded: chain z residue 88 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 961 optimal weight: 5.9990 chunk 731 optimal weight: 10.0000 chunk 505 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 464 optimal weight: 0.8980 chunk 653 optimal weight: 9.9990 chunk 976 optimal weight: 6.9990 chunk 1034 optimal weight: 0.0040 chunk 510 optimal weight: 2.9990 chunk 925 optimal weight: 0.3980 chunk 278 optimal weight: 10.0000 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 277 GLN Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 157 GLN ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 164 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 231 ASN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 458 GLN W 504 HIS D 38 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN F 36 HIS F 221 ASN ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 80 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN K 157 ASN ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 194 GLN c 28 ASN d 58 ASN l 4 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 56 ASN s 39 GLN w 20 ASN y 50 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 143369 Z= 0.134 Angle : 0.544 14.727 210713 Z= 0.282 Chirality : 0.034 0.275 26450 Planarity : 0.004 0.071 13806 Dihedral : 22.559 179.899 62230 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.45 % Favored : 93.38 % Rotamer: Outliers : 3.10 % Allowed : 16.83 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.80 (0.09), residues: 7190 helix: -0.33 (0.11), residues: 2158 sheet: -0.70 (0.16), residues: 1042 loop : -1.88 (0.09), residues: 3990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 155 HIS 0.011 0.001 HIS W 168 PHE 0.020 0.001 PHE f 30 TYR 0.024 0.001 TYR b 168 ARG 0.008 0.000 ARG j 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1506 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1318 time to evaluate : 6.306 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: X 23 TYR cc_start: 0.8838 (p90) cc_final: 0.8539 (p90) REVERT: X 171 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: W 331 PRO cc_start: 0.5931 (Cg_exo) cc_final: 0.5719 (Cg_endo) REVERT: W 364 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.7389 (m) REVERT: V 177 LEU cc_start: 0.9133 (tp) cc_final: 0.8846 (tp) REVERT: V 194 LYS cc_start: 0.8372 (tptt) cc_final: 0.8131 (tptm) REVERT: V 203 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8044 (mm-40) REVERT: V 344 SER cc_start: 0.8926 (m) cc_final: 0.8469 (t) REVERT: V 370 MET cc_start: 0.9043 (mmm) cc_final: 0.8823 (mmt) REVERT: D 72 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8178 (mmt90) REVERT: D 194 ASN cc_start: 0.8820 (t0) cc_final: 0.8504 (t0) REVERT: E 7 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7002 (mp0) REVERT: E 56 ILE cc_start: 0.8947 (tp) cc_final: 0.8662 (tp) REVERT: F 285 ASP cc_start: 0.8155 (p0) cc_final: 0.7569 (p0) REVERT: G 59 ASP cc_start: 0.7846 (t70) cc_final: 0.6929 (t0) REVERT: G 264 GLN cc_start: 0.9101 (mp10) cc_final: 0.8685 (mt0) REVERT: H 60 ASP cc_start: 0.7863 (p0) cc_final: 0.7603 (p0) REVERT: H 170 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8366 (mttp) REVERT: H 173 MET cc_start: 0.8026 (mmm) cc_final: 0.7661 (mmt) REVERT: I 64 GLN cc_start: 0.8613 (tp40) cc_final: 0.8112 (tp40) REVERT: I 149 TYR cc_start: 0.9076 (m-80) cc_final: 0.8789 (m-80) REVERT: J 64 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9017 (mm) REVERT: K 171 ASP cc_start: 0.8764 (t70) cc_final: 0.8447 (t70) REVERT: Z 141 LYS cc_start: 0.8379 (mmtp) cc_final: 0.8157 (mmmt) REVERT: Z 150 GLU cc_start: 0.7727 (tp30) cc_final: 0.7316 (tp30) REVERT: Z 174 THR cc_start: 0.9286 (m) cc_final: 0.8934 (p) REVERT: M 74 PRO cc_start: 0.8830 (Cg_endo) cc_final: 0.8600 (Cg_exo) REVERT: M 165 GLN cc_start: 0.8781 (tt0) cc_final: 0.8155 (tm-30) REVERT: N 140 SER cc_start: 0.8707 (t) cc_final: 0.8378 (p) REVERT: Q 83 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8911 (mp) REVERT: a 119 TYR cc_start: 0.9484 (p90) cc_final: 0.9283 (p90) REVERT: a 175 ASN cc_start: 0.8552 (t0) cc_final: 0.8196 (m110) REVERT: c 64 ASN cc_start: 0.8743 (p0) cc_final: 0.8138 (p0) REVERT: c 78 VAL cc_start: 0.9320 (t) cc_final: 0.9073 (p) REVERT: e 25 ASP cc_start: 0.7666 (p0) cc_final: 0.6766 (p0) REVERT: e 28 GLU cc_start: 0.7857 (mp0) cc_final: 0.7517 (mp0) REVERT: f 66 GLU cc_start: 0.8377 (tp30) cc_final: 0.7944 (tt0) REVERT: f 96 ASP cc_start: 0.7518 (t0) cc_final: 0.7307 (t0) REVERT: g 139 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7552 (ptt90) REVERT: h 27 VAL cc_start: 0.8786 (m) cc_final: 0.8580 (p) REVERT: i 33 ASN cc_start: 0.9128 (p0) cc_final: 0.8901 (p0) REVERT: i 74 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8106 (ptp) REVERT: i 131 SER cc_start: 0.9385 (t) cc_final: 0.9021 (p) REVERT: j 30 ARG cc_start: 0.8035 (mtt-85) cc_final: 0.7742 (mtt90) REVERT: j 56 ARG cc_start: 0.9000 (mtp-110) cc_final: 0.8719 (mtp180) REVERT: j 57 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8248 (tptp) REVERT: m 46 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8828 (pt) REVERT: m 121 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8109 (tpp-160) REVERT: n 44 ASN cc_start: 0.8831 (t0) cc_final: 0.8558 (t0) REVERT: o 11 ASN cc_start: 0.9310 (t0) cc_final: 0.8778 (t0) REVERT: o 21 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7624 (mt) REVERT: p 18 ILE cc_start: 0.9108 (tp) cc_final: 0.8629 (tp) REVERT: s 24 ASN cc_start: 0.8811 (t0) cc_final: 0.8601 (t0) REVERT: s 26 ASN cc_start: 0.8970 (m-40) cc_final: 0.8750 (m-40) REVERT: s 44 TYR cc_start: 0.9044 (m-80) cc_final: 0.8615 (m-80) REVERT: t 11 ASN cc_start: 0.9297 (t0) cc_final: 0.8884 (t0) REVERT: t 14 ASN cc_start: 0.8962 (t0) cc_final: 0.8526 (t0) REVERT: u 28 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9260 (tp) REVERT: u 34 GLN cc_start: 0.8310 (mt0) cc_final: 0.8088 (tt0) REVERT: u 116 TYR cc_start: 0.9064 (p90) cc_final: 0.8523 (p90) REVERT: y 28 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7826 (mtp85) REVERT: z 108 THR cc_start: 0.9343 (p) cc_final: 0.9078 (p) REVERT: z 109 ASN cc_start: 0.9053 (m110) cc_final: 0.8735 (m-40) outliers start: 188 outliers final: 111 residues processed: 1435 average time/residue: 1.1021 time to fit residues: 2783.1917 Evaluate side-chains 1323 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1203 time to evaluate : 6.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain Y residue 301 LEU Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 237 LYS Chi-restraints excluded: chain W residue 261 THR Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 384 MET Chi-restraints excluded: chain W residue 399 ASN Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 454 ILE Chi-restraints excluded: chain W residue 462 VAL Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 97 LEU Chi-restraints excluded: chain V residue 115 LYS Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 225 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 335 LEU Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 297 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 180 SER Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain g residue 142 SER Chi-restraints excluded: chain h residue 11 ILE Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 57 LEU Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain u residue 13 SER Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain z residue 88 LYS Chi-restraints excluded: chain z residue 127 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 861 optimal weight: 2.9990 chunk 587 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 770 optimal weight: 6.9990 chunk 426 optimal weight: 10.0000 chunk 882 optimal weight: 9.9990 chunk 714 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 chunk 928 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 277 GLN Y 292 GLN Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 145 ASN X 162 HIS X 164 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 458 GLN D 83 HIS ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 187 HIS D 233 GLN E 165 GLN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS F 221 ASN G 40 HIS G 178 ASN H 138 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN K 50 ASN K 157 ASN ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 GLN a 123 GLN c 54 HIS e 27 ASN e 47 ASN e 134 HIS g 98 HIS l 98 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN t 18 ASN x 40 GLN ** x 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 143369 Z= 0.406 Angle : 0.673 15.267 210713 Z= 0.340 Chirality : 0.039 0.315 26450 Planarity : 0.005 0.060 13806 Dihedral : 22.499 179.842 62228 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.91 % Favored : 91.91 % Rotamer: Outliers : 4.92 % Allowed : 16.55 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.20 % 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 (0.09), residues: 7190 helix: -0.18 (0.11), residues: 2195 sheet: -0.80 (0.16), residues: 1061 loop : -1.90 (0.09), residues: 3934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 85 HIS 0.010 0.002 HIS c 145 PHE 0.020 0.002 PHE m 101 TYR 0.022 0.002 TYR F 120 ARG 0.009 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1197 time to evaluate : 7.028 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: Y 291 MET cc_start: 0.7804 (mtt) cc_final: 0.7488 (mtt) REVERT: X 23 TYR cc_start: 0.8890 (p90) cc_final: 0.8588 (p90) REVERT: X 171 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: W 364 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7409 (m) REVERT: V 177 LEU cc_start: 0.9281 (tp) cc_final: 0.8993 (tp) REVERT: V 194 LYS cc_start: 0.8337 (tptt) cc_final: 0.8060 (tptm) REVERT: V 344 SER cc_start: 0.9019 (m) cc_final: 0.8637 (t) REVERT: D 72 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8101 (mmt90) REVERT: F 285 ASP cc_start: 0.8027 (p0) cc_final: 0.7732 (p0) REVERT: F 288 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7760 (mtm110) REVERT: G 46 THR cc_start: 0.8733 (m) cc_final: 0.8188 (p) REVERT: G 59 ASP cc_start: 0.8038 (t70) cc_final: 0.7004 (t0) REVERT: G 264 GLN cc_start: 0.9199 (mp10) cc_final: 0.8780 (mt0) REVERT: H 60 ASP cc_start: 0.8108 (p0) cc_final: 0.7838 (p0) REVERT: H 170 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8448 (mttp) REVERT: H 173 MET cc_start: 0.8092 (mmm) cc_final: 0.7728 (mmt) REVERT: I 124 LEU cc_start: 0.9339 (mm) cc_final: 0.9119 (mt) REVERT: I 149 TYR cc_start: 0.9202 (m-80) cc_final: 0.8952 (m-80) REVERT: K 171 ASP cc_start: 0.8909 (t70) cc_final: 0.8636 (t70) REVERT: Z 144 ASN cc_start: 0.8760 (t0) cc_final: 0.8554 (t0) REVERT: Z 150 GLU cc_start: 0.8059 (tp30) cc_final: 0.7680 (tp30) REVERT: Z 174 THR cc_start: 0.9320 (m) cc_final: 0.8895 (p) REVERT: M 74 PRO cc_start: 0.8923 (Cg_endo) cc_final: 0.8362 (Cg_exo) REVERT: M 78 GLU cc_start: 0.8073 (mp0) cc_final: 0.7825 (mp0) REVERT: M 165 GLN cc_start: 0.8846 (tt0) cc_final: 0.8124 (tm-30) REVERT: N 140 SER cc_start: 0.8832 (t) cc_final: 0.8489 (p) REVERT: Q 53 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8592 (tp-100) REVERT: Q 83 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8925 (mp) REVERT: a 175 ASN cc_start: 0.8639 (t0) cc_final: 0.8239 (m110) REVERT: c 64 ASN cc_start: 0.8910 (p0) cc_final: 0.8277 (p0) REVERT: e 25 ASP cc_start: 0.8045 (p0) cc_final: 0.7206 (p0) REVERT: e 28 GLU cc_start: 0.7868 (mp0) cc_final: 0.7255 (mp0) REVERT: f 138 GLN cc_start: 0.8750 (tp40) cc_final: 0.8193 (tp-100) REVERT: h 104 ARG cc_start: 0.8352 (ptt-90) cc_final: 0.8076 (ptt-90) REVERT: i 74 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8244 (ptp) REVERT: j 12 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7436 (mmmt) REVERT: j 57 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8234 (tptp) REVERT: k 134 ASP cc_start: 0.7752 (m-30) cc_final: 0.7375 (m-30) REVERT: m 46 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9021 (pt) REVERT: n 44 ASN cc_start: 0.9093 (t0) cc_final: 0.8839 (t0) REVERT: n 84 GLU cc_start: 0.7899 (tp30) cc_final: 0.7652 (tp30) REVERT: o 11 ASN cc_start: 0.9391 (t0) cc_final: 0.9092 (t0) REVERT: o 21 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7960 (mt) REVERT: r 100 ILE cc_start: 0.9099 (mm) cc_final: 0.8861 (mm) REVERT: s 24 ASN cc_start: 0.9143 (t0) cc_final: 0.8875 (t0) REVERT: s 26 ASN cc_start: 0.9066 (m-40) cc_final: 0.8862 (m-40) REVERT: s 44 TYR cc_start: 0.9113 (m-80) cc_final: 0.8632 (m-80) REVERT: t 11 ASN cc_start: 0.9332 (t0) cc_final: 0.8934 (t0) REVERT: t 14 ASN cc_start: 0.9040 (t0) cc_final: 0.8531 (t0) REVERT: u 28 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9323 (tp) REVERT: u 35 LYS cc_start: 0.8820 (tttt) cc_final: 0.8439 (tptp) REVERT: u 104 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8106 (tm-30) REVERT: v 66 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: x 13 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: y 28 ARG cc_start: 0.8498 (mtp85) cc_final: 0.7924 (mtp85) REVERT: z 108 THR cc_start: 0.9369 (p) cc_final: 0.8969 (t) REVERT: z 109 ASN cc_start: 0.9162 (m110) cc_final: 0.8923 (m-40) outliers start: 298 outliers final: 226 residues processed: 1366 average time/residue: 1.1129 time to fit residues: 2684.2386 Evaluate side-chains 1404 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1169 time to evaluate : 6.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain Y residue 270 ILE Chi-restraints excluded: chain Y residue 277 GLN Chi-restraints excluded: chain Y residue 301 LEU Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 141 THR Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 237 LYS Chi-restraints excluded: chain W residue 317 PHE Chi-restraints excluded: chain W residue 349 LYS Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 384 MET Chi-restraints excluded: chain W residue 399 ASN Chi-restraints excluded: chain W residue 428 ILE Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 447 ASP Chi-restraints excluded: chain W residue 458 GLN Chi-restraints excluded: chain W residue 462 VAL Chi-restraints excluded: chain W residue 487 ILE Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 225 SER Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 335 LEU Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 146 ASP Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain Z residue 190 VAL Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 145 ASP Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 190 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 180 SER Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 105 LEU Chi-restraints excluded: chain e residue 148 ASP Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 128 GLU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 91 ASP Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 139 ILE Chi-restraints excluded: chain l residue 4 GLN Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 76 ASP Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain n residue 123 VAL Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain p residue 9 SER Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 14 ILE Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 81 ASP Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain r residue 108 ILE Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain r residue 120 THR Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 22 VAL Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 105 SER Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 64 THR Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 98 SER Chi-restraints excluded: chain u residue 109 ILE Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 66 GLU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 71 SER Chi-restraints excluded: chain x residue 13 GLU Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain z residue 88 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 347 optimal weight: 9.9990 chunk 931 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 607 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 1035 optimal weight: 7.9990 chunk 859 optimal weight: 0.9980 chunk 479 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 342 optimal weight: 8.9990 chunk 543 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 277 GLN Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 164 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS F 237 GLN H 138 GLN I 80 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 GLN K 157 ASN ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 194 GLN c 28 ASN e 47 ASN g 131 GLN h 87 ASN r 52 GLN ** t 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 143369 Z= 0.305 Angle : 0.618 15.038 210713 Z= 0.315 Chirality : 0.037 0.459 26450 Planarity : 0.004 0.083 13806 Dihedral : 22.499 179.984 62228 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.20 % Favored : 92.61 % Rotamer: Outliers : 4.74 % Allowed : 17.49 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.62 (0.09), residues: 7190 helix: 0.09 (0.11), residues: 2176 sheet: -0.83 (0.16), residues: 1067 loop : -1.87 (0.09), residues: 3947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 155 HIS 0.007 0.001 HIS E 3 PHE 0.019 0.002 PHE g 56 TYR 0.022 0.002 TYR j 14 ARG 0.009 0.000 ARG j 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1204 time to evaluate : 7.188 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: X 23 TYR cc_start: 0.8869 (p90) cc_final: 0.8521 (p90) REVERT: X 171 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: L 61 GLN cc_start: 0.6460 (mm110) cc_final: 0.5898 (mp10) REVERT: W 134 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7914 (pp) REVERT: W 364 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7391 (m) REVERT: V 177 LEU cc_start: 0.9252 (tp) cc_final: 0.8988 (tp) REVERT: V 194 LYS cc_start: 0.8377 (tptt) cc_final: 0.8121 (tptm) REVERT: V 344 SER cc_start: 0.9063 (m) cc_final: 0.8642 (t) REVERT: D 72 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8315 (mmt90) REVERT: G 59 ASP cc_start: 0.8013 (t70) cc_final: 0.6995 (t0) REVERT: G 264 GLN cc_start: 0.9158 (mp10) cc_final: 0.8779 (mt0) REVERT: H 31 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7893 (mtt180) REVERT: H 60 ASP cc_start: 0.8133 (p0) cc_final: 0.7867 (p0) REVERT: H 170 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8423 (mttp) REVERT: H 173 MET cc_start: 0.8083 (mmm) cc_final: 0.7705 (mmt) REVERT: I 124 LEU cc_start: 0.9320 (mm) cc_final: 0.9112 (mt) REVERT: I 149 TYR cc_start: 0.9176 (m-80) cc_final: 0.8881 (m-80) REVERT: K 171 ASP cc_start: 0.8883 (t70) cc_final: 0.8624 (t70) REVERT: Z 150 GLU cc_start: 0.7978 (tp30) cc_final: 0.7420 (tp30) REVERT: Z 153 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8029 (mtm-85) REVERT: Z 174 THR cc_start: 0.9290 (m) cc_final: 0.8861 (p) REVERT: M 74 PRO cc_start: 0.8818 (Cg_endo) cc_final: 0.8549 (Cg_exo) REVERT: M 165 GLN cc_start: 0.8881 (tt0) cc_final: 0.8189 (tm-30) REVERT: N 140 SER cc_start: 0.8860 (t) cc_final: 0.8576 (p) REVERT: Q 83 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8984 (mp) REVERT: a 175 ASN cc_start: 0.8631 (t0) cc_final: 0.8245 (m110) REVERT: c 64 ASN cc_start: 0.8902 (p0) cc_final: 0.8289 (p0) REVERT: c 126 ARG cc_start: 0.7423 (ttp-170) cc_final: 0.7198 (ttp-170) REVERT: e 25 ASP cc_start: 0.7885 (p0) cc_final: 0.7026 (p0) REVERT: e 28 GLU cc_start: 0.7875 (mp0) cc_final: 0.7308 (mp0) REVERT: f 138 GLN cc_start: 0.8782 (tp40) cc_final: 0.8226 (tp-100) REVERT: i 74 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8273 (ptp) REVERT: j 12 LYS cc_start: 0.7840 (ptpt) cc_final: 0.7379 (mmmt) REVERT: j 57 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8234 (tptp) REVERT: k 40 LEU cc_start: 0.8691 (tp) cc_final: 0.8338 (mt) REVERT: k 134 ASP cc_start: 0.7733 (m-30) cc_final: 0.7321 (m-30) REVERT: m 46 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8958 (pt) REVERT: n 44 ASN cc_start: 0.9086 (t0) cc_final: 0.8797 (t0) REVERT: n 84 GLU cc_start: 0.7976 (tp30) cc_final: 0.7719 (tp30) REVERT: o 11 ASN cc_start: 0.9416 (t0) cc_final: 0.9078 (t0) REVERT: o 21 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7824 (mt) REVERT: s 24 ASN cc_start: 0.9092 (t0) cc_final: 0.8868 (t0) REVERT: s 26 ASN cc_start: 0.9053 (m-40) cc_final: 0.8847 (m-40) REVERT: s 44 TYR cc_start: 0.9099 (m-80) cc_final: 0.8631 (m-80) REVERT: t 11 ASN cc_start: 0.9353 (t0) cc_final: 0.8955 (t0) REVERT: t 14 ASN cc_start: 0.9059 (t0) cc_final: 0.8553 (t0) REVERT: u 28 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9305 (tp) REVERT: u 35 LYS cc_start: 0.8758 (tttt) cc_final: 0.8417 (tptp) REVERT: u 104 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8049 (tm-30) REVERT: v 66 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: y 28 ARG cc_start: 0.8490 (mtp85) cc_final: 0.7902 (mtp85) REVERT: z 108 THR cc_start: 0.9355 (p) cc_final: 0.8951 (t) REVERT: z 109 ASN cc_start: 0.9171 (m110) cc_final: 0.8934 (m-40) outliers start: 287 outliers final: 222 residues processed: 1368 average time/residue: 1.2322 time to fit residues: 3003.7416 Evaluate side-chains 1415 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1182 time to evaluate : 6.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain Y residue 270 ILE Chi-restraints excluded: chain Y residue 301 LEU Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 141 THR Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 168 HIS Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 317 PHE Chi-restraints excluded: chain W residue 349 LYS Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 384 MET Chi-restraints excluded: chain W residue 399 ASN Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 458 GLN Chi-restraints excluded: chain W residue 462 VAL Chi-restraints excluded: chain W residue 487 ILE Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 225 SER Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 335 LEU Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 146 ASP Chi-restraints excluded: chain Z residue 153 ARG Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain Z residue 190 VAL Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 53 LYS Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 22 ASP Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain e residue 148 ASP Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 128 GLU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain h residue 11 ILE Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain k residue 31 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 139 ILE Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain p residue 9 SER Chi-restraints excluded: chain p residue 17 VAL Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 14 ILE Chi-restraints excluded: chain q residue 25 PHE Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 81 ASP Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain r residue 120 THR Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 19 SER Chi-restraints excluded: chain s residue 49 ILE Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain s residue 105 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 64 THR Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 68 THR Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 34 GLN Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 66 GLU Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 71 SER Chi-restraints excluded: chain x residue 8 ILE Chi-restraints excluded: chain x residue 13 GLU Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain y residue 27 ILE Chi-restraints excluded: chain z residue 88 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 998 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 589 optimal weight: 7.9990 chunk 756 optimal weight: 40.0000 chunk 585 optimal weight: 0.3980 chunk 871 optimal weight: 4.9990 chunk 578 optimal weight: 0.7980 chunk 1031 optimal weight: 7.9990 chunk 645 optimal weight: 4.9990 chunk 628 optimal weight: 2.9990 chunk 476 optimal weight: 0.6980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 164 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 458 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN J 38 GLN ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 GLN N 137 GLN ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 GLN c 28 ASN e 47 ASN h 87 ASN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 ASN t 18 ASN y 50 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 143369 Z= 0.164 Angle : 0.545 14.787 210713 Z= 0.280 Chirality : 0.034 0.356 26450 Planarity : 0.004 0.069 13806 Dihedral : 22.474 179.908 62224 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.97 % Favored : 92.88 % Rotamer: Outliers : 3.76 % Allowed : 18.64 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.33 (0.10), residues: 7190 helix: 0.41 (0.12), residues: 2165 sheet: -0.64 (0.16), residues: 1082 loop : -1.75 (0.09), residues: 3943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 155 HIS 0.007 0.001 HIS q 21 PHE 0.021 0.001 PHE g 56 TYR 0.020 0.001 TYR Z 75 ARG 0.014 0.000 ARG F 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1480 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1252 time to evaluate : 6.965 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: Y 234 LYS cc_start: 0.7701 (ttmm) cc_final: 0.7228 (tttm) REVERT: X 23 TYR cc_start: 0.8806 (p90) cc_final: 0.8445 (p90) REVERT: X 171 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: W 331 PRO cc_start: 0.6345 (Cg_exo) cc_final: 0.6099 (Cg_endo) REVERT: V 34 MET cc_start: 0.6270 (mmt) cc_final: 0.5958 (mmt) REVERT: V 194 LYS cc_start: 0.8371 (tptt) cc_final: 0.8170 (tptp) REVERT: V 210 MET cc_start: 0.7920 (ttt) cc_final: 0.7429 (ttt) REVERT: V 344 SER cc_start: 0.8990 (m) cc_final: 0.8572 (t) REVERT: D 72 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8252 (mmt90) REVERT: D 194 ASN cc_start: 0.8864 (t0) cc_final: 0.8468 (t0) REVERT: G 59 ASP cc_start: 0.7897 (t70) cc_final: 0.6936 (t0) REVERT: G 264 GLN cc_start: 0.9051 (mp10) cc_final: 0.8680 (mt0) REVERT: H 31 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7997 (mtt180) REVERT: H 94 GLU cc_start: 0.8269 (pp20) cc_final: 0.7855 (pp20) REVERT: H 133 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: H 170 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8361 (mttm) REVERT: H 173 MET cc_start: 0.8091 (mmm) cc_final: 0.7711 (mmt) REVERT: I 124 LEU cc_start: 0.9262 (mm) cc_final: 0.9050 (mt) REVERT: I 149 TYR cc_start: 0.9174 (m-80) cc_final: 0.8885 (m-80) REVERT: J 64 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9002 (mm) REVERT: K 136 PHE cc_start: 0.8146 (m-80) cc_final: 0.7488 (m-80) REVERT: K 171 ASP cc_start: 0.8807 (t70) cc_final: 0.8509 (t70) REVERT: Z 66 GLU cc_start: 0.8007 (tp30) cc_final: 0.7657 (tp30) REVERT: Z 174 THR cc_start: 0.9276 (m) cc_final: 0.8893 (p) REVERT: M 165 GLN cc_start: 0.8863 (tt0) cc_final: 0.8174 (tm-30) REVERT: N 140 SER cc_start: 0.8800 (t) cc_final: 0.8472 (p) REVERT: Q 18 ARG cc_start: 0.8761 (mtt90) cc_final: 0.8365 (mtt90) REVERT: Q 83 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9075 (mp) REVERT: a 119 TYR cc_start: 0.9499 (p90) cc_final: 0.9265 (p90) REVERT: a 175 ASN cc_start: 0.8570 (t0) cc_final: 0.8255 (m110) REVERT: c 64 ASN cc_start: 0.8801 (p0) cc_final: 0.8114 (p0) REVERT: c 126 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.7205 (ttp-170) REVERT: e 25 ASP cc_start: 0.7686 (p0) cc_final: 0.6724 (p0) REVERT: e 28 GLU cc_start: 0.7785 (mp0) cc_final: 0.7395 (mp0) REVERT: f 96 ASP cc_start: 0.7626 (t0) cc_final: 0.7407 (t0) REVERT: f 138 GLN cc_start: 0.8755 (tp40) cc_final: 0.8166 (tp-100) REVERT: g 139 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7718 (ptt90) REVERT: i 74 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8373 (ptp) REVERT: i 131 SER cc_start: 0.9387 (t) cc_final: 0.9117 (p) REVERT: j 57 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8289 (tptp) REVERT: k 134 ASP cc_start: 0.7734 (m-30) cc_final: 0.7319 (m-30) REVERT: l 114 ASP cc_start: 0.8257 (m-30) cc_final: 0.8046 (m-30) REVERT: m 46 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8734 (pt) REVERT: m 105 SER cc_start: 0.9193 (t) cc_final: 0.8964 (m) REVERT: n 44 ASN cc_start: 0.9084 (t0) cc_final: 0.8820 (t0) REVERT: o 11 ASN cc_start: 0.9390 (t0) cc_final: 0.9124 (t0) REVERT: o 18 ARG cc_start: 0.7746 (tpp80) cc_final: 0.7508 (mmt90) REVERT: o 21 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7847 (mt) REVERT: p 22 LYS cc_start: 0.8321 (tptt) cc_final: 0.8042 (tptt) REVERT: s 24 ASN cc_start: 0.8992 (t0) cc_final: 0.8790 (t0) REVERT: s 26 ASN cc_start: 0.9025 (m-40) cc_final: 0.8807 (m-40) REVERT: t 11 ASN cc_start: 0.9236 (t0) cc_final: 0.9004 (t0) REVERT: t 14 ASN cc_start: 0.9074 (t0) cc_final: 0.8605 (t0) REVERT: u 28 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9268 (tp) REVERT: u 34 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: u 35 LYS cc_start: 0.8765 (tttt) cc_final: 0.8418 (tptp) REVERT: u 108 GLN cc_start: 0.8814 (mt0) cc_final: 0.8559 (mt0) REVERT: u 116 TYR cc_start: 0.9010 (p90) cc_final: 0.8765 (p90) REVERT: y 28 ARG cc_start: 0.8451 (mtp85) cc_final: 0.7876 (mtp85) REVERT: z 108 THR cc_start: 0.9369 (p) cc_final: 0.9008 (t) REVERT: z 109 ASN cc_start: 0.9108 (m110) cc_final: 0.8892 (m-40) outliers start: 228 outliers final: 169 residues processed: 1386 average time/residue: 1.1151 time to fit residues: 2723.5798 Evaluate side-chains 1347 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1167 time to evaluate : 6.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 141 THR Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 168 HIS Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 349 LYS Chi-restraints excluded: chain W residue 384 MET Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 458 GLN Chi-restraints excluded: chain W residue 462 VAL Chi-restraints excluded: chain W residue 487 ILE Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 290 THR Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 335 LEU Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain Z residue 190 VAL Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 180 SER Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain h residue 11 ILE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 67 SER Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain j residue 59 HIS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 76 ASP Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain q residue 14 ILE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 57 LEU Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 34 GLN Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 109 ILE Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 71 SER Chi-restraints excluded: chain x residue 13 GLU Chi-restraints excluded: chain x residue 66 ILE Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain z residue 88 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 638 optimal weight: 0.9990 chunk 411 optimal weight: 8.9990 chunk 615 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 655 optimal weight: 7.9990 chunk 702 optimal weight: 6.9990 chunk 509 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 810 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 458 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN F 36 HIS ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 ASN d 58 ASN e 47 ASN ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 ASN l 98 ASN ** t 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 143369 Z= 0.316 Angle : 0.615 15.122 210713 Z= 0.312 Chirality : 0.037 0.332 26450 Planarity : 0.005 0.087 13806 Dihedral : 22.436 179.932 62224 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.87 % Favored : 91.99 % Rotamer: Outliers : 4.46 % Allowed : 18.61 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.17 % 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: -1.36 (0.10), residues: 7190 helix: 0.42 (0.12), residues: 2175 sheet: -0.73 (0.16), residues: 1106 loop : -1.78 (0.09), residues: 3909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 155 HIS 0.008 0.001 HIS E 3 PHE 0.017 0.002 PHE I 229 TYR 0.031 0.002 TYR E 123 ARG 0.014 0.001 ARG F 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1178 time to evaluate : 9.344 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: X 23 TYR cc_start: 0.8817 (p90) cc_final: 0.8503 (p90) REVERT: X 171 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: W 331 PRO cc_start: 0.6343 (Cg_exo) cc_final: 0.6128 (Cg_endo) REVERT: W 364 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7405 (m) REVERT: W 455 PRO cc_start: 0.5732 (Cg_exo) cc_final: 0.5516 (Cg_endo) REVERT: V 210 MET cc_start: 0.8041 (ttt) cc_final: 0.7472 (ttt) REVERT: V 344 SER cc_start: 0.9089 (m) cc_final: 0.8667 (t) REVERT: D 72 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8170 (mmt90) REVERT: E 119 TYR cc_start: 0.8714 (m-80) cc_final: 0.8397 (m-80) REVERT: F 285 ASP cc_start: 0.8161 (p0) cc_final: 0.7908 (p0) REVERT: G 46 THR cc_start: 0.8728 (m) cc_final: 0.8156 (p) REVERT: G 59 ASP cc_start: 0.8024 (t70) cc_final: 0.7045 (t0) REVERT: G 168 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: G 264 GLN cc_start: 0.9110 (mp10) cc_final: 0.8707 (mt0) REVERT: H 31 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7874 (mtt180) REVERT: H 94 GLU cc_start: 0.8339 (pp20) cc_final: 0.7951 (pp20) REVERT: H 133 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: H 170 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8396 (mttp) REVERT: H 173 MET cc_start: 0.8105 (mmm) cc_final: 0.7717 (mmt) REVERT: I 124 LEU cc_start: 0.9325 (mm) cc_final: 0.9105 (mt) REVERT: I 149 TYR cc_start: 0.9226 (m-80) cc_final: 0.8910 (m-80) REVERT: K 168 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7897 (mtp85) REVERT: K 171 ASP cc_start: 0.8843 (t70) cc_final: 0.8595 (t70) REVERT: Z 150 GLU cc_start: 0.7660 (tp30) cc_final: 0.7286 (tp30) REVERT: Z 153 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8041 (mtm-85) REVERT: Z 174 THR cc_start: 0.9298 (m) cc_final: 0.8899 (p) REVERT: M 165 GLN cc_start: 0.8876 (tt0) cc_final: 0.8149 (tm-30) REVERT: N 140 SER cc_start: 0.8844 (t) cc_final: 0.8544 (p) REVERT: Q 18 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8438 (mtt90) REVERT: Q 83 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9035 (mp) REVERT: a 175 ASN cc_start: 0.8618 (t0) cc_final: 0.8268 (m110) REVERT: c 64 ASN cc_start: 0.8876 (p0) cc_final: 0.8167 (p0) REVERT: c 126 ARG cc_start: 0.7582 (ttp-170) cc_final: 0.7306 (ttp-170) REVERT: e 25 ASP cc_start: 0.7851 (p0) cc_final: 0.6929 (p0) REVERT: e 28 GLU cc_start: 0.7844 (mp0) cc_final: 0.7378 (mp0) REVERT: f 138 GLN cc_start: 0.8780 (tp40) cc_final: 0.8467 (tp-100) REVERT: i 74 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8351 (ptp) REVERT: i 128 ARG cc_start: 0.8368 (tpp80) cc_final: 0.8065 (tpp80) REVERT: j 12 LYS cc_start: 0.7904 (ptpt) cc_final: 0.7450 (mmmt) REVERT: j 57 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8311 (tptp) REVERT: k 134 ASP cc_start: 0.7777 (m-30) cc_final: 0.7351 (m-30) REVERT: m 46 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8885 (pt) REVERT: m 105 SER cc_start: 0.9212 (t) cc_final: 0.8973 (m) REVERT: m 121 ARG cc_start: 0.8413 (tpp80) cc_final: 0.7946 (tpp-160) REVERT: n 44 ASN cc_start: 0.9133 (t0) cc_final: 0.8861 (t0) REVERT: n 75 LEU cc_start: 0.9258 (mt) cc_final: 0.8910 (mt) REVERT: n 84 GLU cc_start: 0.8060 (tp30) cc_final: 0.7841 (tp30) REVERT: o 11 ASN cc_start: 0.9403 (t0) cc_final: 0.9068 (t0) REVERT: o 18 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7631 (tpp80) REVERT: o 21 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7927 (mt) REVERT: s 24 ASN cc_start: 0.9077 (t0) cc_final: 0.8861 (t0) REVERT: s 26 ASN cc_start: 0.9046 (m-40) cc_final: 0.8834 (m-40) REVERT: t 11 ASN cc_start: 0.9366 (t0) cc_final: 0.9047 (t0) REVERT: t 14 ASN cc_start: 0.9108 (t0) cc_final: 0.8645 (t0) REVERT: t 18 ASN cc_start: 0.8931 (t0) cc_final: 0.8662 (t0) REVERT: u 28 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9285 (tp) REVERT: u 35 LYS cc_start: 0.8746 (tttt) cc_final: 0.8405 (tptp) REVERT: u 104 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8206 (tm-30) REVERT: u 116 TYR cc_start: 0.9026 (p90) cc_final: 0.8723 (p90) REVERT: y 28 ARG cc_start: 0.8465 (mtp85) cc_final: 0.7904 (mtp85) REVERT: z 108 THR cc_start: 0.9370 (p) cc_final: 0.8982 (t) REVERT: z 109 ASN cc_start: 0.9150 (m110) cc_final: 0.8910 (m-40) outliers start: 270 outliers final: 223 residues processed: 1341 average time/residue: 1.1016 time to fit residues: 2610.8511 Evaluate side-chains 1391 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1157 time to evaluate : 6.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 291 MET Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 141 THR Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 168 HIS Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 384 MET Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 487 ILE Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 225 SER Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 290 THR Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 333 ARG Chi-restraints excluded: chain V residue 335 LEU Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 111 ILE Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 152 GLU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 153 ARG Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain Z residue 190 VAL Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 121 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 145 ASP Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 190 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 143 THR Chi-restraints excluded: chain b residue 180 SER Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 128 GLU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 96 ILE Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain h residue 11 ILE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 67 SER Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 23 MET Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 76 ASP Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain p residue 9 SER Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain p residue 89 VAL Chi-restraints excluded: chain q residue 14 ILE Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 25 PHE Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain s residue 105 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 64 THR Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 98 SER Chi-restraints excluded: chain u residue 109 ILE Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 71 SER Chi-restraints excluded: chain x residue 13 GLU Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain y residue 27 ILE Chi-restraints excluded: chain z residue 88 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 938 optimal weight: 10.0000 chunk 988 optimal weight: 0.3980 chunk 901 optimal weight: 0.3980 chunk 961 optimal weight: 5.9990 chunk 987 optimal weight: 6.9990 chunk 578 optimal weight: 0.9990 chunk 418 optimal weight: 6.9990 chunk 754 optimal weight: 40.0000 chunk 294 optimal weight: 10.0000 chunk 868 optimal weight: 0.8980 chunk 908 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 277 GLN Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 458 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 137 GLN O 126 GLN ** Q 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 ASN d 58 ASN e 47 ASN ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 ASN l 98 ASN m 57 HIS m 106 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 ASN ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN u 59 ASN y 19 GLN y 50 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 143369 Z= 0.150 Angle : 0.545 14.498 210713 Z= 0.280 Chirality : 0.033 0.360 26450 Planarity : 0.004 0.078 13806 Dihedral : 22.435 179.842 62224 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.88 % Favored : 92.96 % Rotamer: Outliers : 3.62 % Allowed : 19.68 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.16 (0.10), residues: 7190 helix: 0.66 (0.12), residues: 2164 sheet: -0.60 (0.16), residues: 1099 loop : -1.69 (0.09), residues: 3927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 155 HIS 0.011 0.001 HIS F 311 PHE 0.017 0.001 PHE g 56 TYR 0.038 0.001 TYR E 123 ARG 0.016 0.000 ARG F 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1432 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1213 time to evaluate : 6.166 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: X 23 TYR cc_start: 0.8810 (p90) cc_final: 0.8504 (p90) REVERT: X 171 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: W 331 PRO cc_start: 0.6531 (Cg_exo) cc_final: 0.6302 (Cg_endo) REVERT: W 364 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7414 (m) REVERT: W 384 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5521 (tmm) REVERT: W 393 PHE cc_start: 0.6469 (m-80) cc_final: 0.6191 (m-80) REVERT: V 210 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7507 (ttt) REVERT: V 344 SER cc_start: 0.8998 (m) cc_final: 0.8594 (t) REVERT: D 72 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8299 (mmt90) REVERT: D 194 ASN cc_start: 0.8864 (t0) cc_final: 0.8454 (t0) REVERT: E 213 GLU cc_start: 0.6730 (tt0) cc_final: 0.6509 (tt0) REVERT: G 35 ARG cc_start: 0.8996 (mtt90) cc_final: 0.8679 (mtt90) REVERT: G 46 THR cc_start: 0.8731 (m) cc_final: 0.8207 (p) REVERT: G 59 ASP cc_start: 0.7900 (t70) cc_final: 0.6929 (t0) REVERT: G 168 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: G 264 GLN cc_start: 0.9008 (mp10) cc_final: 0.8639 (mt0) REVERT: H 31 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7988 (mtt180) REVERT: H 94 GLU cc_start: 0.8310 (pp20) cc_final: 0.8043 (pp20) REVERT: H 133 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: H 170 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8338 (mttm) REVERT: H 173 MET cc_start: 0.8087 (mmm) cc_final: 0.7707 (mmt) REVERT: I 124 LEU cc_start: 0.9260 (mm) cc_final: 0.9053 (mt) REVERT: I 149 TYR cc_start: 0.9174 (m-80) cc_final: 0.8901 (m-80) REVERT: K 171 ASP cc_start: 0.8818 (t70) cc_final: 0.8529 (t70) REVERT: Z 150 GLU cc_start: 0.7623 (tp30) cc_final: 0.7175 (tp30) REVERT: Z 153 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8091 (mtm-85) REVERT: Z 174 THR cc_start: 0.9301 (m) cc_final: 0.8987 (p) REVERT: M 165 GLN cc_start: 0.8931 (tt0) cc_final: 0.8181 (tm-30) REVERT: N 140 SER cc_start: 0.8784 (t) cc_final: 0.8491 (p) REVERT: O 105 GLN cc_start: 0.8857 (tt0) cc_final: 0.8591 (tp40) REVERT: Q 18 ARG cc_start: 0.8756 (mtt90) cc_final: 0.8365 (mtt90) REVERT: a 175 ASN cc_start: 0.8542 (t0) cc_final: 0.8223 (m110) REVERT: c 64 ASN cc_start: 0.8802 (p0) cc_final: 0.8102 (p0) REVERT: c 126 ARG cc_start: 0.7396 (ttp-170) cc_final: 0.7129 (ttp-170) REVERT: c 182 ILE cc_start: 0.9336 (mm) cc_final: 0.9126 (mm) REVERT: e 25 ASP cc_start: 0.7660 (p0) cc_final: 0.6695 (p0) REVERT: e 28 GLU cc_start: 0.7715 (mp0) cc_final: 0.7395 (mp0) REVERT: f 96 ASP cc_start: 0.7686 (t0) cc_final: 0.7457 (t0) REVERT: f 138 GLN cc_start: 0.8759 (tp40) cc_final: 0.8440 (tp-100) REVERT: g 139 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7757 (ptt90) REVERT: i 74 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8397 (ptp) REVERT: i 106 LYS cc_start: 0.9226 (mttt) cc_final: 0.8867 (tttm) REVERT: i 128 ARG cc_start: 0.8255 (tpp80) cc_final: 0.8009 (tpp80) REVERT: k 134 ASP cc_start: 0.7800 (m-30) cc_final: 0.7381 (m-30) REVERT: l 4 GLN cc_start: 0.8783 (mm110) cc_final: 0.8474 (mm110) REVERT: l 114 ASP cc_start: 0.8236 (m-30) cc_final: 0.8023 (m-30) REVERT: m 46 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8722 (pt) REVERT: m 105 SER cc_start: 0.9162 (t) cc_final: 0.8937 (m) REVERT: m 121 ARG cc_start: 0.8396 (tpp80) cc_final: 0.7943 (tpp-160) REVERT: n 44 ASN cc_start: 0.9045 (t0) cc_final: 0.8759 (t0) REVERT: n 84 GLU cc_start: 0.7937 (tp30) cc_final: 0.7716 (tp30) REVERT: o 11 ASN cc_start: 0.9394 (t0) cc_final: 0.9121 (t0) REVERT: o 21 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7829 (mt) REVERT: s 24 ASN cc_start: 0.8945 (t0) cc_final: 0.8729 (t0) REVERT: s 26 ASN cc_start: 0.9017 (m-40) cc_final: 0.8797 (m-40) REVERT: t 14 ASN cc_start: 0.9106 (t0) cc_final: 0.8651 (t0) REVERT: u 28 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9271 (tp) REVERT: u 34 GLN cc_start: 0.8255 (mt0) cc_final: 0.8040 (tt0) REVERT: u 35 LYS cc_start: 0.8724 (tttt) cc_final: 0.8401 (tptp) REVERT: u 116 TYR cc_start: 0.8974 (p90) cc_final: 0.8773 (p90) REVERT: v 66 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: v 90 MET cc_start: 0.8658 (mmt) cc_final: 0.8402 (mmm) REVERT: y 28 ARG cc_start: 0.8443 (mtp85) cc_final: 0.7880 (mtp85) REVERT: z 108 THR cc_start: 0.9374 (p) cc_final: 0.9010 (t) REVERT: z 109 ASN cc_start: 0.9097 (m110) cc_final: 0.8879 (m-40) outliers start: 219 outliers final: 182 residues processed: 1343 average time/residue: 1.1213 time to fit residues: 2659.3997 Evaluate side-chains 1373 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1177 time to evaluate : 6.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 331 ILE Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 141 THR Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 384 MET Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 454 ILE Chi-restraints excluded: chain W residue 487 ILE Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 333 ARG Chi-restraints excluded: chain V residue 335 LEU Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 153 ARG Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain Z residue 190 VAL Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 47 ASP Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 126 GLN Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 41 PHE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 180 SER Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 128 GLU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 71 SER Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain h residue 11 ILE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 55 THR Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 74 MET Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain j residue 59 HIS Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain s residue 105 SER Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 57 LEU Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 109 ILE Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 66 GLU Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 71 SER Chi-restraints excluded: chain x residue 13 GLU Chi-restraints excluded: chain z residue 88 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 957 optimal weight: 7.9990 chunk 631 optimal weight: 10.0000 chunk 1016 optimal weight: 6.9990 chunk 620 optimal weight: 3.9990 chunk 482 optimal weight: 10.0000 chunk 706 optimal weight: 7.9990 chunk 1065 optimal weight: 4.9990 chunk 981 optimal weight: 0.5980 chunk 848 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 655 optimal weight: 0.3980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 277 GLN Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS I 80 GLN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 150 ASN ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN N 137 GLN ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 ASN ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 98 ASN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 143369 Z= 0.225 Angle : 0.569 14.647 210713 Z= 0.290 Chirality : 0.035 0.318 26450 Planarity : 0.004 0.063 13806 Dihedral : 22.398 179.785 62224 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.44 % Favored : 92.42 % Rotamer: Outliers : 3.65 % Allowed : 19.91 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.10), residues: 7190 helix: 0.68 (0.12), residues: 2172 sheet: -0.57 (0.16), residues: 1096 loop : -1.70 (0.09), residues: 3922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP V 155 HIS 0.008 0.001 HIS F 36 PHE 0.018 0.001 PHE V 64 TYR 0.035 0.002 TYR E 123 ARG 0.015 0.000 ARG F 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14380 Ramachandran restraints generated. 7190 Oldfield, 0 Emsley, 7190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1184 time to evaluate : 6.854 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: X 23 TYR cc_start: 0.8798 (p90) cc_final: 0.8491 (p90) REVERT: X 171 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: W 331 PRO cc_start: 0.6547 (Cg_exo) cc_final: 0.6321 (Cg_endo) REVERT: W 393 PHE cc_start: 0.6406 (m-80) cc_final: 0.6107 (m-80) REVERT: V 173 PHE cc_start: 0.8445 (t80) cc_final: 0.8228 (t80) REVERT: V 210 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7486 (ttt) REVERT: V 344 SER cc_start: 0.9071 (m) cc_final: 0.8652 (t) REVERT: D 72 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8313 (mmt90) REVERT: E 213 GLU cc_start: 0.6565 (tt0) cc_final: 0.6323 (tt0) REVERT: G 46 THR cc_start: 0.8696 (m) cc_final: 0.8128 (p) REVERT: G 59 ASP cc_start: 0.7918 (t70) cc_final: 0.6965 (t0) REVERT: G 264 GLN cc_start: 0.9087 (mp10) cc_final: 0.8691 (mt0) REVERT: H 31 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7944 (mtt180) REVERT: H 94 GLU cc_start: 0.8339 (pp20) cc_final: 0.8081 (pp20) REVERT: H 133 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: H 170 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8358 (mttp) REVERT: H 173 MET cc_start: 0.8135 (mmm) cc_final: 0.7742 (mmt) REVERT: I 124 LEU cc_start: 0.9295 (mm) cc_final: 0.9094 (mt) REVERT: I 149 TYR cc_start: 0.9192 (m-80) cc_final: 0.8952 (m-80) REVERT: K 171 ASP cc_start: 0.8798 (t70) cc_final: 0.8496 (t70) REVERT: Z 39 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8964 (ptmm) REVERT: Z 66 GLU cc_start: 0.8016 (tp30) cc_final: 0.7660 (tp30) REVERT: Z 150 GLU cc_start: 0.7701 (tp30) cc_final: 0.7202 (tp30) REVERT: Z 153 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8091 (mtm-85) REVERT: Z 174 THR cc_start: 0.9315 (m) cc_final: 0.9008 (p) REVERT: Z 180 GLU cc_start: 0.8914 (tp30) cc_final: 0.8623 (tp30) REVERT: M 165 GLN cc_start: 0.8896 (tt0) cc_final: 0.8186 (tm-30) REVERT: N 140 SER cc_start: 0.8761 (t) cc_final: 0.8502 (p) REVERT: Q 18 ARG cc_start: 0.8809 (mtt90) cc_final: 0.8518 (mtt90) REVERT: a 175 ASN cc_start: 0.8596 (t0) cc_final: 0.8280 (m110) REVERT: c 64 ASN cc_start: 0.8842 (p0) cc_final: 0.8122 (p0) REVERT: c 126 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.7281 (ttp-170) REVERT: c 182 ILE cc_start: 0.9337 (mm) cc_final: 0.9128 (mm) REVERT: e 25 ASP cc_start: 0.7715 (p0) cc_final: 0.6690 (p0) REVERT: e 28 GLU cc_start: 0.7754 (mp0) cc_final: 0.7373 (mp0) REVERT: f 96 ASP cc_start: 0.7678 (t0) cc_final: 0.7477 (t0) REVERT: f 138 GLN cc_start: 0.8766 (tp40) cc_final: 0.8449 (tp-100) REVERT: g 139 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7780 (ptt90) REVERT: i 106 LYS cc_start: 0.9223 (mttt) cc_final: 0.8872 (tttm) REVERT: i 128 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7998 (tpp80) REVERT: j 12 LYS cc_start: 0.7669 (ptpt) cc_final: 0.7158 (mmmt) REVERT: k 134 ASP cc_start: 0.7818 (m-30) cc_final: 0.7395 (m-30) REVERT: l 114 ASP cc_start: 0.8246 (m-30) cc_final: 0.8021 (m-30) REVERT: m 46 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8817 (pt) REVERT: m 105 SER cc_start: 0.9166 (t) cc_final: 0.8948 (m) REVERT: m 121 ARG cc_start: 0.8412 (tpp80) cc_final: 0.7942 (tpp-160) REVERT: n 44 ASN cc_start: 0.9109 (t0) cc_final: 0.8820 (t0) REVERT: n 84 GLU cc_start: 0.7957 (tp30) cc_final: 0.7713 (tp30) REVERT: o 11 ASN cc_start: 0.9425 (t0) cc_final: 0.9125 (t0) REVERT: o 21 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7974 (mt) REVERT: s 26 ASN cc_start: 0.9014 (m-40) cc_final: 0.8802 (m-40) REVERT: t 14 ASN cc_start: 0.9131 (t0) cc_final: 0.8625 (t0) REVERT: u 28 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9261 (tp) REVERT: u 34 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: u 35 LYS cc_start: 0.8704 (tttt) cc_final: 0.8401 (tptp) REVERT: u 116 TYR cc_start: 0.8983 (p90) cc_final: 0.8763 (p90) REVERT: v 66 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: y 28 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7839 (mtp85) REVERT: z 108 THR cc_start: 0.9381 (p) cc_final: 0.9016 (t) REVERT: z 109 ASN cc_start: 0.9106 (m110) cc_final: 0.8883 (m-40) outliers start: 221 outliers final: 196 residues processed: 1318 average time/residue: 1.1861 time to fit residues: 2783.4491 Evaluate side-chains 1368 residues out of total 6143 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1160 time to evaluate : 6.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 242 SER Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 277 GLN Chi-restraints excluded: chain Y residue 291 MET Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 331 ILE Chi-restraints excluded: chain Y residue 346 LEU Chi-restraints excluded: chain X residue 78 ASP Chi-restraints excluded: chain X residue 171 GLU Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 179 THR Chi-restraints excluded: chain W residue 211 LEU Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 384 MET Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 454 ILE Chi-restraints excluded: chain W residue 458 GLN Chi-restraints excluded: chain W residue 487 ILE Chi-restraints excluded: chain V residue 72 ILE Chi-restraints excluded: chain V residue 126 THR Chi-restraints excluded: chain V residue 127 ILE Chi-restraints excluded: chain V residue 186 ASP Chi-restraints excluded: chain V residue 210 MET Chi-restraints excluded: chain V residue 230 SER Chi-restraints excluded: chain V residue 266 SER Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 335 LEU Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 357 SER Chi-restraints excluded: chain V residue 390 ASP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain G residue 95 TRP Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 133 GLU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 18 VAL Chi-restraints excluded: chain K residue 23 ARG Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain Z residue 39 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 48 LEU Chi-restraints excluded: chain Z residue 153 ARG Chi-restraints excluded: chain Z residue 164 LYS Chi-restraints excluded: chain Z residue 190 VAL Chi-restraints excluded: chain M residue 57 PHE Chi-restraints excluded: chain M residue 107 ASP Chi-restraints excluded: chain M residue 129 VAL Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 168 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 39 CYS Chi-restraints excluded: chain R residue 41 PHE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 151 ILE Chi-restraints excluded: chain a residue 167 THR Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain a residue 190 THR Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 180 SER Chi-restraints excluded: chain c residue 22 LEU Chi-restraints excluded: chain c residue 75 GLU Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 107 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 128 ARG Chi-restraints excluded: chain c residue 165 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain d residue 63 SER Chi-restraints excluded: chain d residue 123 THR Chi-restraints excluded: chain e residue 59 SER Chi-restraints excluded: chain e residue 142 ILE Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 45 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 87 THR Chi-restraints excluded: chain f residue 128 GLU Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 18 ASP Chi-restraints excluded: chain g residue 71 SER Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain h residue 11 ILE Chi-restraints excluded: chain h residue 16 THR Chi-restraints excluded: chain h residue 55 THR Chi-restraints excluded: chain h residue 76 LEU Chi-restraints excluded: chain i residue 13 ILE Chi-restraints excluded: chain i residue 61 THR Chi-restraints excluded: chain i residue 102 ILE Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 36 SER Chi-restraints excluded: chain j residue 38 SER Chi-restraints excluded: chain j residue 59 HIS Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 59 SER Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 36 SER Chi-restraints excluded: chain l residue 59 VAL Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 89 VAL Chi-restraints excluded: chain m residue 132 SER Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 78 LEU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain p residue 87 VAL Chi-restraints excluded: chain q residue 14 ILE Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 40 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 115 LEU Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain s residue 105 SER Chi-restraints excluded: chain t residue 23 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 64 THR Chi-restraints excluded: chain t residue 66 SER Chi-restraints excluded: chain t residue 71 THR Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 34 GLN Chi-restraints excluded: chain u residue 36 LEU Chi-restraints excluded: chain u residue 62 GLN Chi-restraints excluded: chain u residue 109 ILE Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 57 LEU Chi-restraints excluded: chain v residue 66 GLU Chi-restraints excluded: chain v residue 72 VAL Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain w residue 7 SER Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 71 SER Chi-restraints excluded: chain z residue 88 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1070 random chunks: chunk 520 optimal weight: 0.7980 chunk 674 optimal weight: 3.9990 chunk 904 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 782 optimal weight: 0.4980 chunk 125 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 850 optimal weight: 0.9990 chunk 355 optimal weight: 5.9990 chunk 873 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 343 GLN ** X 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 HIS ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN O 126 GLN ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 ASN ** g 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 ASN l 98 ASN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.076556 restraints weight = 268737.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.078733 restraints weight = 100704.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.080072 restraints weight = 58631.817| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 143369 Z= 0.185 Angle : 0.556 14.537 210713 Z= 0.284 Chirality : 0.034 0.313 26450 Planarity : 0.004 0.089 13806 Dihedral : 22.405 179.964 62224 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.26 % Favored : 92.60 % Rotamer: Outliers : 3.48 % Allowed : 20.16 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.10), residues: 7190 helix: 0.76 (0.12), residues: 2169 sheet: -0.55 (0.16), residues: 1085 loop : -1.70 (0.09), residues: 3936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 155 HIS 0.008 0.001 HIS F 36 PHE 0.031 0.001 PHE V 64 TYR 0.033 0.002 TYR E 123 ARG 0.015 0.000 ARG F 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38205.25 seconds wall clock time: 664 minutes 37.78 seconds (39877.78 seconds total)