Starting phenix.real_space_refine on Sat Mar 16 12:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8n_0373/03_2024/6n8n_0373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8n_0373/03_2024/6n8n_0373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8n_0373/03_2024/6n8n_0373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8n_0373/03_2024/6n8n_0373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8n_0373/03_2024/6n8n_0373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8n_0373/03_2024/6n8n_0373.pdb" } resolution = 3.8 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 3482 5.49 5 S 129 5.16 5 C 69522 2.51 5 N 24257 2.21 5 O 34423 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 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X 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 PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 318": "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 50": "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 "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 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 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 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" Residue "L ARG 67": "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: 131813 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 68513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3203, 68513 Classifications: {'RNA': 3203} Modifications used: {'rna2p_pur': 331, 'rna2p_pyr': 222, 'rna3p_pur': 1445, 'rna3p_pyr': 1205} Link IDs: {'rna2p': 553, '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: "W" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2972 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 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': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 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: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2280 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, 'TRANS': 272} 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: "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} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 821 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 133 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 Time building chain proxies: 48.81, per 1000 atoms: 0.37 Number of scatterers: 131813 At special positions: 0 Unit cell: (236.5, 215.6, 261.8, 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 129 16.00 P 3482 15.00 O 34423 8.00 N 24257 7.00 C 69522 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 57 " distance=2.05 Simple disulfide: pdb=" SG CYS R 42 " - pdb=" SG CYS R 60 " distance=2.01 Simple disulfide: pdb=" SG CYS R 57 " - pdb=" SG CYS R 60 " distance=2.80 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=2.01 Simple disulfide: pdb=" SG CYS t 81 " - pdb=" SG CYS t 84 " distance=2.05 Simple disulfide: pdb=" SG CYS w 19 " - pdb=" SG CYS w 22 " distance=2.02 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 34 " distance=2.02 Simple disulfide: pdb=" SG CYS w 22 " - pdb=" SG CYS w 37 " distance=2.00 Simple disulfide: pdb=" SG CYS w 34 " - pdb=" SG CYS w 37 " distance=1.99 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: 46.24 Conformation dependent library (CDL) restraints added in 8.0 seconds 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13824 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 78 sheets defined 36.6% alpha, 14.9% beta 735 base pairs and 1729 stacking pairs defined. Time for finding SS restraints: 38.60 Creating SS restraints... Processing helix chain 'Y' and resid 291 through 297 removed outlier: 3.658A pdb=" N GLY Y 297 " --> pdb=" O PRO Y 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 43 removed outlier: 3.628A pdb=" N ALA X 37 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE X 38 " --> pdb=" O PHE X 34 " (cutoff:3.500A) removed outlier: 3.825A 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: 3.520A pdb=" N HIS X 83 " --> pdb=" O GLN X 79 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU X 84 " --> pdb=" O GLU X 80 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER X 87 " --> pdb=" O HIS X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 107 removed outlier: 3.627A 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 134 removed outlier: 3.507A pdb=" N GLU X 127 " --> pdb=" O ARG X 123 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU X 128 " --> pdb=" O GLU X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 178 Processing helix chain 'X' and resid 211 through 223 removed outlier: 3.565A pdb=" N ILE X 221 " --> pdb=" O VAL X 217 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 130 removed outlier: 4.007A pdb=" N ALA W 125 " --> pdb=" O GLY W 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS W 126 " --> pdb=" O ASN W 122 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG W 128 " --> pdb=" O ASN W 124 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA W 129 " --> pdb=" O ALA W 125 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU W 130 " --> pdb=" O LYS W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 135 removed outlier: 3.852A pdb=" N LEU W 134 " --> pdb=" O ALA W 131 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE W 135 " --> pdb=" O LYS W 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 131 through 135' Processing helix chain 'W' and resid 149 through 173 removed outlier: 3.904A pdb=" N GLU W 157 " --> pdb=" O ARG W 153 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA W 158 " --> pdb=" O GLN W 154 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE W 159 " --> pdb=" O GLU W 155 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU W 169 " --> pdb=" O LYS W 165 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU W 171 " --> pdb=" O ALA W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 198 removed outlier: 4.027A pdb=" N TRP W 188 " --> pdb=" O ASN W 184 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL W 194 " --> pdb=" O GLN W 190 " (cutoff:3.500A) Processing helix chain 'W' and resid 209 through 214 removed outlier: 3.603A pdb=" N PHE W 213 " --> pdb=" O ASN W 209 " (cutoff:3.500A) removed outlier: 3.612A 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 217 through 223 removed outlier: 3.846A pdb=" N TYR W 221 " --> pdb=" O ASP W 217 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS W 223 " --> pdb=" O GLU W 219 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 241 Processing helix chain 'W' and resid 242 through 257 removed outlier: 3.596A pdb=" N ARG W 246 " --> pdb=" O THR W 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE W 247 " --> pdb=" O LYS W 243 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA W 248 " --> pdb=" O LYS W 244 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS W 251 " --> pdb=" O ILE W 247 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR W 252 " --> pdb=" O ALA W 248 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE W 253 " --> pdb=" O TRP W 249 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE W 254 " --> pdb=" O ALA W 250 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 310 Processing helix chain 'W' and resid 319 through 324 removed outlier: 3.606A pdb=" N ASN W 323 " --> pdb=" O SER W 319 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 358 removed outlier: 3.820A pdb=" N ILE W 353 " --> pdb=" O LYS W 349 " (cutoff:3.500A) Processing helix chain 'W' and resid 400 through 406 removed outlier: 4.464A pdb=" N VAL W 404 " --> pdb=" O LYS W 400 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS W 405 " --> pdb=" O GLY W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 417 through 427 removed outlier: 3.582A pdb=" N LEU W 423 " --> pdb=" O GLY W 419 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL W 424 " --> pdb=" O PRO W 420 " (cutoff:3.500A) Processing helix chain 'W' and resid 429 through 437 Processing helix chain 'W' and resid 456 through 467 removed outlier: 3.511A pdb=" N LEU W 460 " --> pdb=" O THR W 456 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU W 461 " --> pdb=" O ALA W 457 " (cutoff:3.500A) Processing helix chain 'W' and resid 479 through 493 removed outlier: 3.846A pdb=" N ALA W 483 " --> pdb=" O ASP W 479 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG W 485 " --> pdb=" O PRO W 481 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR W 486 " --> pdb=" O ARG W 482 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP W 490 " --> pdb=" O TYR W 486 " (cutoff:3.500A) Processing helix chain 'V' and resid 36 through 42 removed outlier: 4.181A pdb=" N LEU V 41 " --> pdb=" O ASP V 37 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 88 removed outlier: 3.893A pdb=" N ALA V 83 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE V 84 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS V 85 " --> pdb=" O LEU V 81 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU V 86 " --> pdb=" O LEU V 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 148 removed outlier: 3.647A pdb=" N ARG V 148 " --> pdb=" O PRO V 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 169 through 181 removed outlier: 3.739A pdb=" N LEU V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS V 180 " --> pdb=" O GLN V 176 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS V 181 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 218 removed outlier: 3.710A pdb=" N ALA V 207 " --> pdb=" O GLN V 203 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET V 210 " --> pdb=" O HIS V 206 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE V 211 " --> pdb=" O ALA V 207 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA V 216 " --> pdb=" O ASP V 212 " (cutoff:3.500A) removed outlier: 3.913A 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 303 removed outlier: 3.890A pdb=" N ARG V 303 " --> pdb=" O SER V 299 " (cutoff:3.500A) Processing helix chain 'V' and resid 343 through 348 removed outlier: 4.583A pdb=" N GLY V 347 " --> pdb=" O THR V 343 " (cutoff:3.500A) removed outlier: 4.199A 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 381 through 386 Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.514A pdb=" N ARG D 9 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS D 10 " --> pdb=" O ARG D 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5 through 10' Processing helix chain 'D' and resid 173 through 177 removed outlier: 3.969A pdb=" N ASP D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 173 through 177' Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'E' and resid 111 through 118 removed outlier: 3.549A pdb=" N LYS E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 removed outlier: 4.357A pdb=" N TYR E 137 " --> pdb=" O TYR E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 154 removed outlier: 3.568A pdb=" N GLU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 188 through 198 Processing helix chain 'E' and resid 228 through 234 removed outlier: 3.564A pdb=" N TRP E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.799A pdb=" N HIS E 377 " --> pdb=" O PRO E 373 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 44 removed outlier: 3.645A pdb=" N SER F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 114 through 130 removed outlier: 3.652A pdb=" N THR F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.517A pdb=" N VAL F 135 " --> pdb=" O VAL F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 157 Processing helix chain 'F' and resid 161 through 173 removed outlier: 3.554A pdb=" N ALA F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 184 removed outlier: 3.699A pdb=" N VAL F 181 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 removed outlier: 3.711A pdb=" N LYS F 193 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR F 194 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 240 through 243 removed outlier: 3.779A pdb=" N HIS F 243 " --> pdb=" O PRO F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 240 through 243' Processing helix chain 'F' and resid 252 through 263 removed outlier: 4.367A pdb=" N ASP F 259 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN F 260 " --> pdb=" O THR F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 removed outlier: 3.902A pdb=" N ILE F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 3.556A pdb=" N SER F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 327 removed outlier: 3.722A pdb=" N LEU F 327 " --> pdb=" O VAL F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 338 removed outlier: 4.345A pdb=" N VAL F 333 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA F 336 " --> pdb=" O LYS F 332 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 360 removed outlier: 3.655A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 15 Processing helix chain 'G' and resid 20 through 26 Processing helix chain 'G' and resid 29 through 38 removed outlier: 4.017A pdb=" N ARG G 35 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 44 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 removed outlier: 3.560A pdb=" N ALA G 106 " --> pdb=" O GLY G 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 113 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 170 removed outlier: 3.588A pdb=" N GLY G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY G 165 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 200 removed outlier: 3.632A pdb=" N TYR G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 199 " --> pdb=" O LEU G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 removed outlier: 4.103A pdb=" N ASP G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 222 removed outlier: 3.616A pdb=" N PHE G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU G 221 " --> pdb=" O GLU G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 232 through 250 removed outlier: 3.558A pdb=" N LEU G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP G 238 " --> pdb=" O ASP G 234 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU G 245 " --> pdb=" O THR G 241 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 273 removed outlier: 4.043A pdb=" N TYR G 265 " --> pdb=" O THR G 261 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 270 " --> pdb=" O ALA G 266 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR G 272 " --> pdb=" O GLU G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 289 removed outlier: 3.537A pdb=" N VAL G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 73 Processing helix chain 'H' and resid 80 through 82 No H-bonds generated for 'chain 'H' and resid 80 through 82' Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.502A pdb=" N LYS H 100 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE H 101 " --> pdb=" O VAL H 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 97 through 101' Processing helix chain 'H' and resid 131 through 150 removed outlier: 3.657A pdb=" N VAL H 135 " --> pdb=" O LYS H 131 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA H 144 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 161 Processing helix chain 'I' and resid 26 through 73 removed outlier: 3.539A pdb=" N ALA I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN I 61 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 106 Processing helix chain 'I' and resid 120 through 130 removed outlier: 3.794A pdb=" N LEU I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE I 130 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 152 removed outlier: 3.536A pdb=" N LEU I 147 " --> pdb=" O THR I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 173 removed outlier: 3.826A pdb=" N ILE I 169 " --> pdb=" O ASP I 165 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN I 172 " --> pdb=" O ILE I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 177 removed outlier: 4.028A pdb=" N GLY I 177 " --> pdb=" O GLY I 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 174 through 177' Processing helix chain 'I' and resid 180 through 190 Processing helix chain 'I' and resid 194 through 202 Processing helix chain 'I' and resid 222 through 226 Processing helix chain 'I' and resid 235 through 244 removed outlier: 3.796A pdb=" N LEU I 239 " --> pdb=" O PHE I 235 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS I 241 " --> pdb=" O ASN I 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 69 removed outlier: 3.820A pdb=" N LYS J 63 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE J 67 " --> pdb=" O LYS J 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 95 removed outlier: 3.794A pdb=" N GLU J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 120 removed outlier: 3.674A pdb=" N THR J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 144 removed outlier: 3.606A pdb=" N LEU J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 164 through 173 removed outlier: 4.577A pdb=" N ALA J 168 " --> pdb=" O VAL J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 189 removed outlier: 3.601A pdb=" N LEU J 186 " --> pdb=" O GLY J 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 188 " --> pdb=" O ALA J 184 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 222 removed outlier: 4.243A pdb=" N ALA J 209 " --> pdb=" O ALA J 205 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA J 210 " --> pdb=" O GLU J 206 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU J 214 " --> pdb=" O ALA J 210 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 230 Processing helix chain 'J' and resid 239 through 250 removed outlier: 3.572A pdb=" N ALA J 244 " --> pdb=" O ASN J 240 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS J 245 " --> pdb=" O LYS J 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 84 removed outlier: 3.757A pdb=" N VAL K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU K 68 " --> pdb=" O HIS K 64 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 165 removed outlier: 3.632A pdb=" N GLN K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN K 157 " --> pdb=" O ASP K 153 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 42 removed outlier: 3.773A pdb=" N LYS M 35 " --> pdb=" O THR M 31 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 37 " --> pdb=" O ALA M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 87 removed outlier: 3.900A pdb=" N GLU M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU M 78 " --> pdb=" O PRO M 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE M 79 " --> pdb=" O LYS M 75 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 112 removed outlier: 3.613A pdb=" N LEU M 112 " --> pdb=" O HIS M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 4.106A pdb=" N ARG M 140 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 166 removed outlier: 3.740A pdb=" N GLN M 165 " --> pdb=" O SER M 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 20 removed outlier: 3.523A 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 27 through 46 removed outlier: 3.900A pdb=" N VAL N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA N 43 " --> pdb=" O ARG N 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS N 45 " --> pdb=" O THR N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 84 removed outlier: 3.524A pdb=" N VAL N 80 " --> pdb=" O THR N 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS N 81 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 92 removed outlier: 3.625A pdb=" N ARG N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 122 removed outlier: 3.638A pdb=" N GLN N 114 " --> pdb=" O ASP N 110 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER N 121 " --> pdb=" O LYS N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 145 removed outlier: 3.603A pdb=" N THR N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 179 removed outlier: 3.801A pdb=" N LEU N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 193 removed outlier: 3.894A pdb=" N ARG N 183 " --> pdb=" O PHE N 179 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU N 184 " --> pdb=" O ARG N 180 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 88 removed outlier: 3.700A pdb=" N ALA O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 96 Processing helix chain 'O' and resid 97 through 111 removed outlier: 3.539A pdb=" N ALA O 110 " --> pdb=" O ARG O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 138 removed outlier: 3.570A pdb=" N TYR O 129 " --> pdb=" O LYS O 125 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA O 138 " --> pdb=" O ALA O 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 48 removed outlier: 3.518A pdb=" N SER Q 48 " --> pdb=" O ASP Q 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 15 removed outlier: 3.532A pdb=" N THR R 11 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY R 12 " --> pdb=" O GLY R 9 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS R 13 " --> pdb=" O ILE R 10 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 35 removed outlier: 3.506A pdb=" N LEU R 29 " --> pdb=" O GLN R 25 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE R 31 " --> pdb=" O LYS R 27 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 removed outlier: 3.512A pdb=" N ALA R 77 " --> pdb=" O THR R 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 15 removed outlier: 3.927A pdb=" N UNK S 10 " --> pdb=" O UNK S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 71 removed outlier: 3.705A pdb=" N UNK S 69 " --> pdb=" O UNK S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 86 Processing helix chain 'S' and resid 90 through 98 Processing helix chain 'S' and resid 111 through 116 Processing helix chain 'S' and resid 139 through 145 Processing helix chain 'S' and resid 169 through 184 removed outlier: 3.826A pdb=" N UNK S 175 " --> pdb=" O UNK S 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N UNK S 176 " --> pdb=" O UNK S 172 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK S 179 " --> pdb=" O UNK S 175 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N UNK S 183 " --> pdb=" O UNK S 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 13 removed outlier: 3.590A pdb=" N ARG a 12 " --> pdb=" O GLU a 8 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS a 13 " --> pdb=" O GLU a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 32 removed outlier: 3.694A pdb=" N ARG a 24 " --> pdb=" O ARG a 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 27 " --> pdb=" O GLN a 23 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 50 removed outlier: 3.667A pdb=" N ARG a 49 " --> pdb=" O PRO a 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 79 removed outlier: 4.011A pdb=" N GLY a 78 " --> pdb=" O VAL a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 110 removed outlier: 3.682A pdb=" N VAL a 106 " --> pdb=" O ALA a 102 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG a 109 " --> pdb=" O ARG a 105 " (cutoff:3.500A) removed outlier: 3.525A 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 148 through 152 Processing helix chain 'a' and resid 153 through 157 removed outlier: 3.610A pdb=" N LYS a 157 " --> pdb=" O PRO a 154 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 163 removed outlier: 3.684A pdb=" N ARG a 162 " --> pdb=" O HIS a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 173 removed outlier: 3.568A pdb=" N LYS a 170 " --> pdb=" O ALA a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 194 removed outlier: 3.720A pdb=" N GLN a 194 " --> pdb=" O THR a 190 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 30 removed outlier: 3.645A pdb=" N GLN b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU b 28 " --> pdb=" O ALA b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 40 removed outlier: 3.841A pdb=" N GLU b 40 " --> pdb=" O ARG b 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 37 through 40' Processing helix chain 'b' and resid 46 through 59 removed outlier: 3.522A pdb=" N ASN b 50 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU b 52 " --> pdb=" O PHE b 48 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE b 57 " --> pdb=" O LYS b 53 " (cutoff:3.500A) removed outlier: 3.778A 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 88 removed outlier: 3.519A pdb=" N PHE b 80 " --> pdb=" O PRO b 76 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 100 Processing helix chain 'b' and resid 120 through 123 removed outlier: 3.655A pdb=" N ALA b 123 " --> pdb=" O VAL b 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 120 through 123' Processing helix chain 'b' and resid 124 through 129 Processing helix chain 'b' and resid 138 through 145 removed outlier: 3.540A pdb=" N THR b 143 " --> pdb=" O GLY b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 186 removed outlier: 3.581A pdb=" N VAL b 153 " --> pdb=" O TYR b 149 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS b 155 " --> pdb=" O ASP b 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL b 162 " --> pdb=" O ALA b 158 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER b 163 " --> pdb=" O LYS b 159 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA b 173 " --> pdb=" O ALA b 169 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS b 177 " --> pdb=" O ALA b 173 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL b 178 " --> pdb=" O PHE b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 188 through 197 removed outlier: 3.921A pdb=" N LEU b 194 " --> pdb=" O VAL b 190 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA b 195 " --> pdb=" O ALA b 191 " (cutoff:3.500A) 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: 3.637A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR c 32 " --> pdb=" O ASN c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 53 removed outlier: 4.104A pdb=" N LYS c 46 " --> pdb=" O THR c 42 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP c 53 " --> pdb=" O GLU c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 70 through 74 removed outlier: 3.644A pdb=" N GLY c 73 " --> pdb=" O THR c 70 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 106 removed outlier: 3.579A pdb=" N PHE c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY c 93 " --> pdb=" O LYS c 89 " (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 Processing helix chain 'd' and resid 23 through 40 removed outlier: 3.718A pdb=" N LEU d 29 " --> pdb=" O TYR d 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE d 35 " --> pdb=" O LYS d 31 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG d 38 " --> pdb=" O THR d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 52 removed outlier: 3.537A pdb=" N VAL d 47 " --> pdb=" O PRO d 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS d 50 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 71 Processing helix chain 'd' and resid 107 through 118 Processing helix chain 'd' and resid 123 through 131 removed outlier: 3.524A pdb=" N VAL d 129 " --> pdb=" O ASP d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 152 removed outlier: 3.585A pdb=" N VAL d 150 " --> pdb=" O ARG d 147 " (cutoff:3.500A) Processing helix chain 'e' and resid 4 through 16 removed outlier: 3.581A pdb=" N ARG e 9 " --> pdb=" O ARG e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 18 through 22 removed outlier: 4.072A pdb=" N VAL e 22 " --> pdb=" O LYS e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 34 removed outlier: 3.940A pdb=" N ALA e 33 " --> pdb=" O THR e 29 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN e 34 " --> pdb=" O SER e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 47 removed outlier: 3.903A pdb=" N LYS e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 60 through 73 removed outlier: 3.533A pdb=" N SER e 69 " --> pdb=" O ALA e 65 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 Processing helix chain 'e' and resid 90 through 113 removed outlier: 3.895A pdb=" N VAL e 101 " --> pdb=" O ARG e 97 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR e 109 " --> pdb=" O LEU e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 116 through 130 removed outlier: 3.886A pdb=" N VAL e 122 " --> pdb=" O HIS e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 151 Processing helix chain 'f' and resid 33 through 49 removed outlier: 3.587A pdb=" N TYR f 41 " --> pdb=" O ALA f 37 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP f 42 " --> pdb=" O LYS f 38 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS f 47 " --> pdb=" O TYR f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 98 through 114 removed outlier: 3.633A pdb=" N GLU f 104 " --> pdb=" O VAL f 100 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR f 105 " --> pdb=" O ALA f 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU f 106 " --> pdb=" O ALA f 102 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR f 107 " --> pdb=" O VAL f 103 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN f 108 " --> pdb=" O GLU f 104 " (cutoff:3.500A) Processing helix chain 'f' and resid 137 through 142 removed outlier: 4.015A pdb=" N LYS f 141 " --> pdb=" O ARG f 137 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 58 removed outlier: 3.799A pdb=" N GLN g 58 " --> pdb=" O LYS g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 99 through 123 removed outlier: 3.593A pdb=" N PHE g 105 " --> pdb=" O CYS g 101 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS g 110 " --> pdb=" O LEU g 106 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU g 118 " --> pdb=" O ALA g 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 26 removed outlier: 3.970A pdb=" N ASN h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 41 removed outlier: 4.036A pdb=" N TYR h 33 " --> pdb=" O ASP h 29 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP h 39 " --> pdb=" O LYS h 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS h 40 " --> pdb=" O TYR h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 87 Processing helix chain 'i' and resid 119 through 126 Processing helix chain 'i' and resid 126 through 132 Processing helix chain 'j' and resid 33 through 42 removed outlier: 3.514A pdb=" N PHE j 40 " --> pdb=" O SER j 36 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS j 41 " --> pdb=" O ALA j 37 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN j 42 " --> pdb=" O SER j 38 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 60 removed outlier: 3.697A pdb=" N ARG j 56 " --> pdb=" O THR j 52 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 69 through 78 removed outlier: 3.868A pdb=" N LYS k 75 " --> pdb=" O THR k 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU k 77 " --> pdb=" O MET k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 104 Processing helix chain 'k' and resid 131 through 140 removed outlier: 3.864A pdb=" N ARG k 138 " --> pdb=" O ASP k 134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE k 139 " --> pdb=" O ILE k 135 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 21 removed outlier: 3.515A pdb=" N LYS l 17 " --> pdb=" O ARG l 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR l 19 " --> pdb=" O ALA l 15 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 31 removed outlier: 3.590A pdb=" N LEU l 30 " --> pdb=" O GLN l 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 43 removed outlier: 3.538A pdb=" N GLN l 42 " --> pdb=" O GLU l 38 " (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 Processing helix chain 'm' and resid 60 through 66 removed outlier: 3.769A pdb=" N THR m 66 " --> pdb=" O VAL m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 123 removed outlier: 4.005A pdb=" N GLU m 109 " --> pdb=" O SER m 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL m 113 " --> pdb=" O GLU m 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 132 removed outlier: 4.121A 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 81 removed outlier: 4.295A pdb=" N TRP n 79 " --> pdb=" O ASP n 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU n 81 " --> pdb=" O LEU n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 92 removed outlier: 4.287A pdb=" N ASP n 88 " --> pdb=" O GLU n 84 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN n 89 " --> pdb=" O ASP n 85 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS n 92 " --> pdb=" O ASP n 88 " (cutoff:3.500A) Processing helix chain 'n' and resid 104 through 108 Processing helix chain 'n' and resid 131 through 142 removed outlier: 3.904A pdb=" N LYS n 137 " --> pdb=" O LEU n 133 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE n 138 " --> pdb=" O ALA n 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 17 Processing helix chain 'o' and resid 36 through 58 removed outlier: 4.026A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU o 47 " --> pdb=" O HIS o 43 " (cutoff:3.500A) Processing helix chain 'p' and resid 10 through 21 removed outlier: 3.917A pdb=" N LEU p 16 " --> pdb=" O GLN p 12 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL p 17 " --> pdb=" O LYS p 13 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE p 18 " --> pdb=" O LEU p 14 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS p 19 " --> pdb=" O ALA p 15 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER p 20 " --> pdb=" O LEU p 16 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 36 removed outlier: 3.516A pdb=" N SER p 33 " --> pdb=" O SER p 29 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN p 36 " --> pdb=" O LYS p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 64 removed outlier: 3.594A pdb=" N LEU p 56 " --> pdb=" O ARG p 52 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU p 62 " --> pdb=" O TYR p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 82 removed outlier: 3.503A pdb=" N THR p 79 " --> pdb=" O ASN p 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 20 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 HIS q 43 " --> pdb=" O PHE q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 52 through 60 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 101 through 116 removed outlier: 3.613A pdb=" N ARG r 105 " --> pdb=" O SER r 101 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL r 106 " --> pdb=" O ALA r 102 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL r 107 " --> pdb=" O LYS r 103 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 45 removed outlier: 3.626A pdb=" N PHE s 43 " --> pdb=" O ASP s 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU s 45 " --> pdb=" O GLN s 42 " (cutoff:3.500A) Processing helix chain 't' and resid 60 through 64 Processing helix chain 't' and resid 66 through 70 removed outlier: 3.565A pdb=" N HIS t 69 " --> pdb=" O SER t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 81 through 110 removed outlier: 3.784A pdb=" N ARG t 88 " --> pdb=" O CYS t 84 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU t 96 " --> pdb=" O ALA t 92 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL t 101 " --> pdb=" O GLU t 97 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 10 removed outlier: 3.899A pdb=" N LEU u 9 " --> pdb=" O LYS u 5 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 38 removed outlier: 3.561A pdb=" N ALA u 18 " --> pdb=" O LYS u 14 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER u 19 " --> pdb=" O GLU u 15 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP u 23 " --> pdb=" O SER u 19 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU u 36 " --> pdb=" O LYS u 32 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER u 37 " --> pdb=" O VAL u 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG u 38 " --> pdb=" O GLN u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 67 removed outlier: 3.833A pdb=" N VAL u 47 " --> pdb=" O LYS u 43 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG u 48 " --> pdb=" O ILE u 44 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL u 57 " --> pdb=" O CYS u 53 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL u 66 " --> pdb=" O GLN u 62 " (cutoff:3.500A) Processing helix chain 'u' and resid 85 through 91 removed outlier: 3.760A pdb=" N ARG u 89 " --> pdb=" O THR u 85 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG u 90 " --> pdb=" O ARG u 86 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 99 removed outlier: 3.549A pdb=" N SER u 98 " --> pdb=" O LYS u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 111 removed outlier: 3.637A pdb=" N LYS u 106 " --> pdb=" O GLU u 102 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 31 removed outlier: 3.546A pdb=" N LYS v 30 " --> pdb=" O SER v 27 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY v 31 " --> pdb=" O TYR v 28 " (cutoff:3.500A) Processing helix chain 'v' and resid 35 through 49 removed outlier: 4.018A pdb=" N PHE v 39 " --> pdb=" O ASN v 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU v 46 " --> pdb=" O SER v 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE v 47 " --> pdb=" O LEU v 43 " (cutoff:3.500A) Processing helix chain 'v' and resid 51 through 63 removed outlier: 3.513A pdb=" N ARG v 56 " --> pdb=" O PRO v 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP v 59 " --> pdb=" O ARG v 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE v 61 " --> pdb=" O LEU v 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN v 63 " --> pdb=" O ASP v 59 " (cutoff:3.500A) Processing helix chain 'v' and resid 65 through 77 removed outlier: 3.638A pdb=" N LYS v 71 " --> pdb=" O LYS v 67 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL v 72 " --> pdb=" O ARG v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 80 through 97 removed outlier: 3.832A pdb=" N ALA v 85 " --> pdb=" O THR v 81 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN v 92 " --> pdb=" O GLU v 88 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE v 93 " --> pdb=" O GLU v 89 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE v 94 " --> pdb=" O MET v 90 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA v 95 " --> pdb=" O ASN v 91 " (cutoff:3.500A) Processing helix chain 'w' and resid 6 through 11 removed outlier: 3.671A pdb=" N LYS w 10 " --> pdb=" O SER w 7 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG w 11 " --> pdb=" O PHE w 8 " (cutoff:3.500A) Processing helix chain 'w' and resid 50 through 56 Processing helix chain 'w' and resid 69 through 77 removed outlier: 3.567A pdb=" N LYS w 75 " --> pdb=" O SER w 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 7 through 15 removed outlier: 3.925A pdb=" N PHE x 11 " --> pdb=" O ASP x 7 " (cutoff:3.500A) Processing helix chain 'x' and resid 58 through 68 removed outlier: 3.633A pdb=" N GLN x 67 " --> pdb=" O LYS x 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER x 68 " --> pdb=" O LYS x 64 " (cutoff:3.500A) Processing helix chain 'y' and resid 6 through 20 removed outlier: 3.766A pdb=" N LYS y 12 " --> pdb=" O ARG y 8 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET y 13 " --> pdb=" O ILE y 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS y 15 " --> pdb=" O GLN y 11 " (cutoff:3.500A) Processing helix chain 'y' and resid 24 through 28 Processing helix chain 'z' and resid 79 through 88 removed outlier: 3.831A pdb=" N LYS z 83 " --> pdb=" O GLU z 79 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS z 88 " --> pdb=" O ALA z 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 32 removed outlier: 3.753A pdb=" N UNK L 29 " --> pdb=" O UNK L 25 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N UNK L 30 " --> pdb=" O UNK L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 50 removed outlier: 3.691A pdb=" N UNK L 43 " --> pdb=" O UNK L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 85 removed outlier: 3.571A pdb=" N LEU L 85 " --> pdb=" O VAL L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 118 removed outlier: 4.420A pdb=" N ILE L 109 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N UNK L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 137 removed outlier: 3.544A pdb=" N UNK L 131 " --> pdb=" O UNK L 127 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N UNK L 132 " --> pdb=" O UNK L 128 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N UNK L 133 " --> pdb=" O UNK L 129 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N UNK L 134 " --> pdb=" O UNK L 130 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N UNK L 135 " --> pdb=" O UNK L 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N UNK L 137 " --> pdb=" O UNK L 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 238 through 240 removed outlier: 6.923A pdb=" N VAL Y 230 " --> pdb=" O LEU Y 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 259 through 262 removed outlier: 3.803A pdb=" N ASP Y 272 " --> pdb=" O LYS Y 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 302 through 306 removed outlier: 3.986A pdb=" N GLY Y 315 " --> pdb=" O PHE Y 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 3 through 4 removed outlier: 6.597A 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 removed outlier: 6.709A pdb=" N CYS X 24 " --> pdb=" O VAL X 49 " (cutoff:3.500A) 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 110 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 263 removed outlier: 8.558A pdb=" N THR W 261 " --> pdb=" O ASN W 231 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU W 233 " --> pdb=" O THR W 261 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR W 263 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL W 235 " --> pdb=" O TYR W 263 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL W 201 " --> pdb=" O LEU W 232 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU W 234 " --> pdb=" O VAL W 201 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN W 203 " --> pdb=" O LEU W 234 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASN W 236 " --> pdb=" O GLN W 203 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL W 205 " --> pdb=" O ASN W 236 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP W 387 " --> pdb=" O GLN W 375 " (cutoff:3.500A) removed outlier: 4.568A 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: 6.606A pdb=" N ALA V 53 " --> pdb=" O ILE V 137 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE V 139 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE V 55 " --> pdb=" O ILE V 139 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET V 141 " --> pdb=" O ILE V 55 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE V 57 " --> pdb=" O MET V 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE V 132 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 3.629A 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: 7.068A pdb=" N PHE V 200 " --> pdb=" O ILE V 188 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE V 190 " --> pdb=" O ASP V 198 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP V 198 " --> pdb=" O ILE V 190 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU V 192 " --> pdb=" O GLY V 196 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY V 196 " --> pdb=" O GLU V 192 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR V 158 " --> pdb=" O TYR V 244 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL V 246 " --> pdb=" O THR V 158 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN V 160 " --> pdb=" O VAL V 246 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE V 248 " --> pdb=" O GLN V 160 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG V 162 " --> pdb=" O ILE V 248 " (cutoff:3.500A) removed outlier: 3.503A 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: 6.641A 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: 6.436A pdb=" N ASP V 337 " --> pdb=" O VAL V 323 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL V 323 " --> pdb=" O ASP V 337 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR V 339 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS V 399 " --> pdb=" O MET V 370 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR V 372 " --> pdb=" O LEU V 397 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU V 397 " --> pdb=" O TYR V 372 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 77 removed outlier: 3.902A pdb=" N GLN D 47 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL D 62 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL D 45 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ARG D 64 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLY D 43 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 101 through 103 removed outlier: 3.635A pdb=" N ILE D 135 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG D 147 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HIS D 139 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.707A 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: 6.984A pdb=" N VAL E 57 " --> pdb=" O LYS E 357 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE E 359 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N THR E 55 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE E 335 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL E 220 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA E 217 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE E 278 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA E 219 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THR E 276 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS E 281 " --> pdb=" O LYS E 325 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET E 323 " --> pdb=" O TYR E 283 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL E 285 " --> pdb=" O PHE E 321 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE E 321 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG E 70 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 52 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP E 80 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LYS E 50 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 106 removed outlier: 7.086A pdb=" N GLY E 91 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR E 104 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 89 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP E 106 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL E 87 " --> pdb=" O TRP E 106 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL E 86 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS E 163 " --> pdb=" O VAL E 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 99 through 106 removed outlier: 7.086A pdb=" N GLY E 91 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N THR E 104 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL E 89 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP E 106 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 8.430A 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: 3.706A 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: 4.259A pdb=" N VAL F 8 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASN F 18 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 6 " --> pdb=" O ASN F 18 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL F 151 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU F 206 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR F 251 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL F 208 " --> pdb=" O THR F 251 " (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: 6.780A pdb=" N ILE G 64 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA G 77 " --> pdb=" O CYS G 62 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N CYS G 62 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TYR G 79 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE G 60 " --> pdb=" O TYR G 79 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP G 59 " --> pdb=" O THR G 56 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.513A pdb=" N ARG H 77 " --> pdb=" O ILE H 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE H 65 " --> pdb=" O ARG H 77 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER H 66 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N TYR H 54 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS H 50 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 5.231A 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: 4.492A pdb=" N SER I 113 " --> pdb=" O ARG I 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY I 230 " --> pdb=" O VAL I 134 " (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: 3.966A 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 180 removed outlier: 6.465A pdb=" N VAL J 151 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL J 180 " --> pdb=" O VAL J 151 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE J 153 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 3.901A 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 11 removed outlier: 7.061A pdb=" N ILE K 4 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN K 8 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU K 52 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 17 through 20 removed outlier: 3.590A pdb=" N VAL K 28 " --> pdb=" O THR K 17 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 132 through 136 removed outlier: 7.248A pdb=" N LYS K 87 " --> pdb=" O LYS K 184 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS K 184 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS K 89 " --> pdb=" O SER K 182 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 100 through 104 Processing sheet with id=AD7, first strand: chain 'M' and resid 46 through 48 removed outlier: 3.793A pdb=" N ALA M 66 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL M 67 " --> pdb=" O ILE M 21 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE M 102 " --> pdb=" O VAL M 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 22 through 24 removed outlier: 6.623A pdb=" N LYS N 23 " --> pdb=" O LEU a 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'N' and resid 57 through 58 Processing sheet with id=AE1, first strand: chain 'N' and resid 123 through 125 Processing sheet with id=AE2, first strand: chain 'N' and resid 156 through 157 removed outlier: 7.690A pdb=" N LYS n 126 " --> pdb=" O PRO n 100 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE n 102 " --> pdb=" O LYS n 126 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL n 125 " --> pdb=" O GLU n 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 14 through 15 removed outlier: 3.505A pdb=" N PHE f 150 " --> pdb=" O VAL O 15 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 53 through 59 removed outlier: 4.936A pdb=" N GLY O 48 " --> pdb=" O PRO O 54 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LYS O 43 " --> pdb=" O ILE O 38 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE O 38 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU O 45 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA O 34 " --> pdb=" O ASP O 47 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG O 19 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL O 20 " --> pdb=" O THR O 66 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 3 through 4 Processing sheet with id=AE6, first strand: chain 'Q' and resid 7 through 11 Processing sheet with id=AE7, first strand: chain 'R' and resid 37 through 38 Processing sheet with id=AE8, first strand: chain 'S' and resid 198 through 199 removed outlier: 3.947A pdb=" N UNK S 198 " --> pdb=" O UNK S 210 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 36 through 39 removed outlier: 4.283A pdb=" N ILE a 61 " --> pdb=" O ALA a 39 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N TYR a 127 " --> pdb=" O ASN a 122 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASN a 122 " --> pdb=" O TYR a 127 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TYR a 129 " --> pdb=" O TRP a 120 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TRP a 120 " --> pdb=" O TYR a 129 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU a 131 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER a 118 " --> pdb=" O GLU a 131 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE a 133 " --> pdb=" O LEU a 116 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'b' and resid 6 through 10 removed outlier: 6.303A pdb=" N VAL b 7 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL b 36 " --> pdb=" O VAL b 7 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE b 9 " --> pdb=" O VAL b 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 42 through 44 Processing sheet with id=AF3, first strand: chain 'c' and resid 14 through 22 removed outlier: 7.372A pdb=" N SER c 14 " --> pdb=" O GLU c 152 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N GLU c 152 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER c 16 " --> pdb=" O VAL c 150 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL c 150 " --> pdb=" O SER c 16 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG c 18 " --> pdb=" O LEU c 148 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU c 148 " --> pdb=" O ARG c 18 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER c 20 " --> pdb=" O ILE c 146 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE c 146 " --> pdb=" O SER c 20 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR c 151 " --> pdb=" O VAL c 114 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL c 114 " --> pdb=" O THR c 151 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 58 through 59 Processing sheet with id=AF5, first strand: chain 'c' and resid 128 through 130 removed outlier: 3.687A pdb=" N ASN c 137 " --> pdb=" O THR c 129 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 62 through 63 removed outlier: 3.760A pdb=" N LEU d 104 " --> pdb=" O VAL d 83 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY d 85 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHE d 106 " --> pdb=" O GLY d 85 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL d 87 " --> pdb=" O PHE d 106 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 62 through 63 Processing sheet with id=AF8, first strand: chain 'e' and resid 23 through 24 removed outlier: 3.678A pdb=" N TRP e 23 " --> pdb=" O VAL e 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL e 51 " --> pdb=" O TRP e 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'f' and resid 26 through 31 Processing sheet with id=AG1, first strand: chain 'f' and resid 87 through 96 removed outlier: 7.165A pdb=" N ASN f 74 " --> pdb=" O GLU f 128 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU f 128 " --> pdb=" O ASN f 74 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY f 76 " --> pdb=" O VAL f 126 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL f 126 " --> pdb=" O GLY f 76 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TRP f 78 " --> pdb=" O LEU f 124 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 83 through 92 removed outlier: 3.940A pdb=" N ASN g 66 " --> pdb=" O GLY g 73 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE g 75 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL g 64 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ASN g 77 " --> pdb=" O GLY g 62 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N GLY g 62 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 54 through 58 removed outlier: 7.946A pdb=" N TYR h 103 " --> pdb=" O THR h 14 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR h 16 " --> pdb=" O TYR h 103 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU h 105 " --> pdb=" O THR h 16 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP h 18 " --> pdb=" O LEU h 105 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU h 102 " --> pdb=" O THR h 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'i' and resid 17 through 18 removed outlier: 3.626A pdb=" N LEU i 17 " --> pdb=" O ALA i 52 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 22 through 25 removed outlier: 6.756A pdb=" N MET i 59 " --> pdb=" O ILE i 37 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL i 39 " --> pdb=" O MET i 57 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N MET i 57 " --> pdb=" O VAL i 39 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA i 99 " --> pdb=" O VAL i 79 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N GLY i 100 " --> pdb=" O ILE i 22 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN i 24 " --> pdb=" O GLY i 100 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE i 102 " --> pdb=" O ASN i 24 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'i' and resid 85 through 86 removed outlier: 6.466A pdb=" N PHE i 92 " --> pdb=" O LEU j 20 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL j 22 " --> pdb=" O PHE i 92 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR i 94 " --> pdb=" O VAL j 22 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'i' and resid 114 through 118 removed outlier: 6.113A pdb=" N SER i 133 " --> pdb=" O ILE i 114 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLY i 116 " --> pdb=" O SER i 133 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL i 135 " --> pdb=" O GLY i 116 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'j' and resid 4 through 5 removed outlier: 3.573A pdb=" N GLU j 4 " --> pdb=" O ILE j 13 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'k' and resid 63 through 66 removed outlier: 3.526A pdb=" N GLN k 65 " --> pdb=" O GLN k 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS k 120 " --> pdb=" O VAL k 86 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'l' and resid 32 through 34 Processing sheet with id=AH2, first strand: chain 'l' and resid 79 through 82 removed outlier: 7.015A pdb=" N ALA l 79 " --> pdb=" O VAL l 73 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL l 73 " --> pdb=" O ALA l 79 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLN l 81 " --> pdb=" O SER l 71 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU l 55 " --> pdb=" O THR l 107 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'l' and resid 86 through 88 Processing sheet with id=AH4, first strand: chain 'm' and resid 69 through 76 removed outlier: 6.678A pdb=" N LYS m 69 " --> pdb=" O GLU m 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL m 75 " --> pdb=" O ALA m 41 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS m 40 " --> pdb=" O PRO m 28 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU m 42 " --> pdb=" O VAL m 26 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL m 24 " --> pdb=" O ALA m 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE m 46 " --> pdb=" O LYS m 22 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS m 22 " --> pdb=" O ILE m 46 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS m 21 " --> pdb=" O VAL m 13 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL m 13 " --> pdb=" O LYS m 21 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 72 through 74 removed outlier: 5.895A pdb=" N LEU n 73 " --> pdb=" O LEU n 113 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'p' and resid 23 through 25 removed outlier: 3.627A pdb=" N LEU p 41 " --> pdb=" O ILE p 92 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 10 through 11 removed outlier: 3.616A pdb=" N VAL q 107 " --> pdb=" O GLU q 11 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 13 through 15 removed outlier: 3.526A pdb=" N ILE q 14 " --> pdb=" O LEU q 71 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'r' and resid 72 through 73 removed outlier: 6.320A pdb=" N LYS r 72 " --> pdb=" O ALA r 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 's' and resid 8 through 18 removed outlier: 9.946A pdb=" N VAL s 9 " --> pdb=" O ILE s 32 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE s 32 " --> pdb=" O VAL s 9 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY s 11 " --> pdb=" O ILE s 30 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE s 30 " --> pdb=" O GLY s 11 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N HIS s 13 " --> pdb=" O SER s 28 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N SER s 28 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N SER s 15 " --> pdb=" O ASN s 26 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ASN s 26 " --> pdb=" O SER s 15 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN s 17 " --> pdb=" O ASN s 24 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASN s 26 " --> pdb=" O PHE s 85 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE s 85 " --> pdb=" O ASN s 26 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG s 73 " --> pdb=" O ARG s 82 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR s 84 " --> pdb=" O VAL s 71 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL s 71 " --> pdb=" O THR s 84 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG s 48 " --> pdb=" O PHE s 101 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL s 52 " --> pdb=" O SER s 97 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N SER s 97 " --> pdb=" O VAL s 52 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 't' and resid 19 through 24 removed outlier: 4.488A pdb=" N LYS t 19 " --> pdb=" O VAL t 35 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL t 35 " --> pdb=" O LYS t 19 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'w' and resid 16 through 17 Processing sheet with id=AI4, first strand: chain 'x' and resid 51 through 56 removed outlier: 5.095A pdb=" N THR x 22 " --> pdb=" O ARG x 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA x 23 " --> pdb=" O ASN x 76 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'z' and resid 102 through 103 Processing sheet with id=AI6, first strand: chain 'L' and resid 13 through 17 removed outlier: 4.845A pdb=" N UNK L 13 " --> pdb=" O GLN L 65 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN L 65 " --> pdb=" O UNK L 13 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N UNK L 15 " --> pdb=" O LYS L 63 " (cutoff:3.500A) 1773 hydrogen bonds defined for protein. 5049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1707 hydrogen bonds 2806 hydrogen bond angles 0 basepair planarities 735 basepair parallelities 1729 stacking parallelities Total time for adding SS restraints: 187.93 Time building geometry restraints manager: 50.55 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: 33309 1.34 - 1.48: 60713 1.48 - 1.62: 47474 1.62 - 1.76: 9 1.76 - 1.90: 193 Bond restraints: 141698 Sorted by residual: bond pdb=" C1' A A2259 " pdb=" N9 A A2259 " ideal model delta sigma weight residual 1.475 1.384 0.091 1.50e-02 4.44e+03 3.67e+01 bond pdb=" N UNK S 107 " pdb=" CA UNK S 107 " ideal model delta sigma weight residual 1.458 1.553 -0.095 1.90e-02 2.77e+03 2.52e+01 bond pdb=" C ILE W 428 " pdb=" N PRO W 429 " ideal model delta sigma weight residual 1.329 1.369 -0.041 1.20e-02 6.94e+03 1.16e+01 bond pdb=" C ARG t 58 " pdb=" N PRO t 59 " ideal model delta sigma weight residual 1.335 1.372 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N ALA W 207 " pdb=" CA ALA W 207 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.68e+00 ... (remaining 141693 not shown) Histogram of bond angle deviations from ideal: 89.38 - 98.83: 10 98.83 - 108.28: 38152 108.28 - 117.73: 90117 117.73 - 127.18: 71797 127.18 - 136.63: 8404 Bond angle restraints: 208480 Sorted by residual: angle pdb=" CA CYS t 81 " pdb=" CB CYS t 81 " pdb=" SG CYS t 81 " ideal model delta sigma weight residual 114.40 133.76 -19.36 2.30e+00 1.89e-01 7.09e+01 angle pdb=" C UNK S 106 " pdb=" N UNK S 107 " pdb=" CA UNK S 107 " ideal model delta sigma weight residual 121.70 106.59 15.11 1.80e+00 3.09e-01 7.05e+01 angle pdb=" C ILE W 337 " pdb=" N ASN W 338 " pdb=" CA ASN W 338 " ideal model delta sigma weight residual 121.54 135.61 -14.07 1.91e+00 2.74e-01 5.42e+01 angle pdb=" C LYS G 258 " pdb=" N LYS G 259 " pdb=" CA LYS G 259 " ideal model delta sigma weight residual 121.54 135.37 -13.83 1.91e+00 2.74e-01 5.24e+01 angle pdb=" CG1 ILE Y 331 " pdb=" CB ILE Y 331 " pdb=" CG2 ILE Y 331 " ideal model delta sigma weight residual 110.70 89.38 21.32 3.00e+00 1.11e-01 5.05e+01 ... (remaining 208475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 81289 35.98 - 71.96: 7540 71.96 - 107.94: 881 107.94 - 143.93: 14 143.93 - 179.91: 63 Dihedral angle restraints: 89787 sinusoidal: 68391 harmonic: 21396 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 -106.33 -73.67 0 5.00e+00 4.00e-02 2.17e+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 180.00 119.74 60.26 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LEU W 134 " pdb=" C LEU W 134 " pdb=" N ILE W 135 " pdb=" CA ILE W 135 " ideal model delta harmonic sigma weight residual -180.00 -124.00 -56.00 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 89784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 23957 0.075 - 0.150: 2006 0.150 - 0.225: 197 0.225 - 0.300: 40 0.300 - 0.375: 18 Chirality restraints: 26218 Sorted by residual: 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 -2.10 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB VAL Y 330 " pdb=" CA VAL Y 330 " pdb=" CG1 VAL Y 330 " pdb=" CG2 VAL Y 330 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" C3' U A1716 " pdb=" C4' U A1716 " pdb=" O3' U A1716 " pdb=" C2' U A1716 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 26215 not shown) Planarity restraints: 13510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG f 12 " 0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C ARG f 12 " -0.085 2.00e-02 2.50e+03 pdb=" O ARG f 12 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG f 13 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS n 47 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C LYS n 47 " -0.069 2.00e-02 2.50e+03 pdb=" O LYS n 47 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR n 48 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE X 7 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C PHE X 7 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE X 7 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU X 8 " 0.020 2.00e-02 2.50e+03 ... (remaining 13507 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 13 2.02 - 2.74: 16776 2.74 - 3.46: 165832 3.46 - 4.18: 379098 4.18 - 4.90: 552328 Nonbonded interactions: 1114047 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=" O ASP V 390 " pdb=" CB UNK S 39 " model vdw 1.375 3.440 nonbonded pdb=" CA UNK S 47 " pdb=" O UNK S 149 " model vdw 1.378 3.470 nonbonded pdb=" O ILE L 104 " pdb=" C UNK L 142 " model vdw 1.384 3.270 ... (remaining 1114042 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 16.390 Check model and map are aligned: 1.440 Set scattering table: 0.860 Process input model: 411.460 Find NCS groups from input model: 2.870 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:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 437.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 141698 Z= 0.390 Angle : 0.889 21.317 208480 Z= 0.471 Chirality : 0.046 0.375 26218 Planarity : 0.006 0.066 13510 Dihedral : 21.734 179.908 75909 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.74 % Favored : 92.76 % Rotamer: Outliers : 0.49 % Allowed : 4.44 % Favored : 95.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.72 % Twisted General : 0.67 % 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: -3.90 (0.08), residues: 6987 helix: -3.90 (0.05), residues: 1998 sheet: -1.02 (0.16), residues: 950 loop : -2.31 (0.08), residues: 4039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP E 255 HIS 0.016 0.002 HIS r 20 PHE 0.029 0.003 PHE X 16 TYR 0.046 0.003 TYR c 130 ARG 0.020 0.001 ARG c 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2144 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 2115 time to evaluate : 6.463 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 248 HIS cc_start: 0.5754 (p-80) cc_final: 0.5547 (p90) REVERT: Y 304 LYS cc_start: 0.6585 (pttt) cc_final: 0.4895 (mmtp) REVERT: X 7 PHE cc_start: 0.8969 (t80) cc_final: 0.8637 (t80) REVERT: X 57 ARG cc_start: 0.8338 (ptp-170) cc_final: 0.8024 (ptm-80) REVERT: X 109 CYS cc_start: 0.8142 (t) cc_final: 0.7826 (t) REVERT: X 225 GLN cc_start: 0.5010 (pt0) cc_final: 0.4683 (pm20) REVERT: W 136 VAL cc_start: 0.6920 (OUTLIER) cc_final: 0.6669 (m) REVERT: W 165 LYS cc_start: 0.8798 (mttt) cc_final: 0.8477 (mtmt) REVERT: W 187 VAL cc_start: 0.7639 (t) cc_final: 0.7263 (p) REVERT: W 199 ASP cc_start: 0.8126 (p0) cc_final: 0.7729 (p0) REVERT: W 205 VAL cc_start: 0.7594 (t) cc_final: 0.7346 (t) REVERT: W 320 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8587 (mttp) REVERT: W 381 ASP cc_start: 0.8352 (m-30) cc_final: 0.8092 (t0) REVERT: W 384 MET cc_start: 0.7094 (ttp) cc_final: 0.6732 (ttp) REVERT: W 385 LEU cc_start: 0.7707 (mt) cc_final: 0.7412 (pp) REVERT: W 493 ASN cc_start: 0.8361 (m-40) cc_final: 0.7968 (m-40) REVERT: V 113 ARG cc_start: 0.7511 (ttm110) cc_final: 0.7056 (mtp-110) REVERT: V 241 LYS cc_start: 0.8903 (ttpt) cc_final: 0.7356 (ttpp) REVERT: V 267 MET cc_start: 0.8735 (ptp) cc_final: 0.8470 (ptt) REVERT: V 370 MET cc_start: 0.7874 (mmm) cc_final: 0.7448 (mmt) REVERT: V 379 TYR cc_start: 0.8787 (m-80) cc_final: 0.8513 (m-10) REVERT: V 382 ASP cc_start: 0.7561 (m-30) cc_final: 0.7271 (m-30) REVERT: D 22 LEU cc_start: 0.9339 (mt) cc_final: 0.9112 (mt) REVERT: D 89 TYR cc_start: 0.8762 (m-80) cc_final: 0.8217 (m-10) REVERT: D 231 SER cc_start: 0.9189 (m) cc_final: 0.8910 (p) REVERT: E 108 GLU cc_start: 0.7636 (tt0) cc_final: 0.7178 (tt0) REVERT: E 109 HIS cc_start: 0.7699 (m-70) cc_final: 0.7326 (m-70) REVERT: E 274 SER cc_start: 0.9500 (m) cc_final: 0.9295 (p) REVERT: E 360 ASP cc_start: 0.8739 (t70) cc_final: 0.8513 (t0) REVERT: F 157 GLU cc_start: 0.7304 (pt0) cc_final: 0.6983 (pt0) REVERT: G 69 ILE cc_start: 0.9121 (pp) cc_final: 0.8682 (mt) REVERT: G 206 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7477 (tm-30) REVERT: G 272 TYR cc_start: 0.7743 (m-80) cc_final: 0.7458 (m-80) REVERT: H 92 SER cc_start: 0.9264 (t) cc_final: 0.7482 (t) REVERT: I 56 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7385 (mt-10) REVERT: I 59 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8000 (tm-30) REVERT: J 45 ASN cc_start: 0.8966 (t0) cc_final: 0.8736 (t0) REVERT: K 11 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7863 (tm-30) REVERT: K 59 ASN cc_start: 0.9020 (t0) cc_final: 0.8737 (t0) REVERT: K 62 ARG cc_start: 0.8590 (ttt180) cc_final: 0.8387 (ttt-90) REVERT: K 100 ASN cc_start: 0.8675 (t0) cc_final: 0.8403 (t0) REVERT: K 102 ASN cc_start: 0.8559 (t0) cc_final: 0.8309 (t0) REVERT: K 116 ASN cc_start: 0.9044 (t0) cc_final: 0.8801 (t0) REVERT: M 14 ILE cc_start: 0.8459 (mp) cc_final: 0.8192 (tt) REVERT: M 17 LEU cc_start: 0.9274 (tp) cc_final: 0.9072 (tp) REVERT: M 26 SER cc_start: 0.8780 (p) cc_final: 0.8267 (t) REVERT: M 60 ARG cc_start: 0.7289 (mtm110) cc_final: 0.6896 (ptm160) REVERT: M 71 VAL cc_start: 0.9558 (t) cc_final: 0.9339 (m) REVERT: M 101 ASN cc_start: 0.9029 (m-40) cc_final: 0.8588 (m-40) REVERT: M 144 CYS cc_start: 0.8677 (m) cc_final: 0.8369 (t) REVERT: M 168 ASP cc_start: 0.8100 (m-30) cc_final: 0.7683 (p0) REVERT: N 65 TYR cc_start: 0.8737 (m-10) cc_final: 0.8529 (m-80) REVERT: N 89 TYR cc_start: 0.9077 (t80) cc_final: 0.8861 (t80) REVERT: O 91 CYS cc_start: 0.7655 (m) cc_final: 0.7342 (m) REVERT: O 99 TRP cc_start: 0.8718 (t60) cc_final: 0.8112 (t60) REVERT: Q 47 GLN cc_start: 0.9093 (mm110) cc_final: 0.8771 (tp40) REVERT: Q 53 GLN cc_start: 0.9185 (tp40) cc_final: 0.8835 (tp40) REVERT: R 72 SER cc_start: 0.9340 (t) cc_final: 0.9073 (p) REVERT: a 54 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8551 (mmtm) REVERT: a 182 ASN cc_start: 0.7868 (m-40) cc_final: 0.7603 (m-40) REVERT: b 168 TYR cc_start: 0.9232 (t80) cc_final: 0.8943 (t80) REVERT: d 89 ASP cc_start: 0.8312 (t0) cc_final: 0.7955 (t0) REVERT: d 145 ASN cc_start: 0.8487 (m110) cc_final: 0.7671 (p0) REVERT: d 155 MET cc_start: 0.8504 (tpt) cc_final: 0.7922 (tpp) REVERT: d 158 HIS cc_start: 0.8067 (m-70) cc_final: 0.7810 (m90) REVERT: e 119 LEU cc_start: 0.9613 (tp) cc_final: 0.9327 (tp) REVERT: f 7 TYR cc_start: 0.9222 (m-80) cc_final: 0.8888 (m-80) REVERT: f 110 MET cc_start: 0.8410 (mmm) cc_final: 0.8074 (mmm) REVERT: f 124 LEU cc_start: 0.8977 (mt) cc_final: 0.8750 (mp) REVERT: f 138 GLN cc_start: 0.9044 (tp40) cc_final: 0.8811 (tp40) REVERT: g 45 ASN cc_start: 0.8872 (t0) cc_final: 0.8324 (t0) REVERT: g 48 ILE cc_start: 0.9546 (mm) cc_final: 0.9076 (tp) REVERT: g 61 THR cc_start: 0.9629 (m) cc_final: 0.9135 (p) REVERT: h 35 LYS cc_start: 0.9047 (tptp) cc_final: 0.8570 (tppt) REVERT: h 36 TYR cc_start: 0.9282 (t80) cc_final: 0.8765 (t80) REVERT: h 40 HIS cc_start: 0.7583 (m90) cc_final: 0.7001 (m170) REVERT: h 86 LYS cc_start: 0.8597 (tttt) cc_final: 0.8305 (tppt) REVERT: h 87 ASN cc_start: 0.8815 (m110) cc_final: 0.8547 (m-40) REVERT: i 29 SER cc_start: 0.9324 (p) cc_final: 0.8865 (t) REVERT: i 68 GLU cc_start: 0.8239 (mp0) cc_final: 0.7849 (mt-10) REVERT: j 26 SER cc_start: 0.9381 (m) cc_final: 0.9003 (p) REVERT: j 32 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8797 (tm-30) REVERT: j 35 LYS cc_start: 0.8836 (tttt) cc_final: 0.8533 (tttm) REVERT: k 75 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8671 (mttp) REVERT: k 80 ASN cc_start: 0.8738 (t0) cc_final: 0.8377 (t0) REVERT: k 96 LYS cc_start: 0.8903 (tppp) cc_final: 0.8627 (ttmm) REVERT: k 131 ASP cc_start: 0.7921 (t70) cc_final: 0.7397 (t0) REVERT: k 134 ASP cc_start: 0.6816 (m-30) cc_final: 0.6158 (m-30) REVERT: l 82 VAL cc_start: 0.9573 (t) cc_final: 0.9305 (m) REVERT: l 83 ASP cc_start: 0.7807 (t0) cc_final: 0.7586 (t0) REVERT: m 105 SER cc_start: 0.8990 (p) cc_final: 0.8346 (t) REVERT: n 44 ASN cc_start: 0.9266 (t0) cc_final: 0.8985 (t0) REVERT: n 90 TYR cc_start: 0.8599 (m-10) cc_final: 0.7517 (m-80) REVERT: n 125 VAL cc_start: 0.9545 (t) cc_final: 0.9276 (m) REVERT: o 48 HIS cc_start: 0.8504 (t-90) cc_final: 0.8152 (t70) REVERT: p 28 LYS cc_start: 0.9331 (mtpt) cc_final: 0.8982 (ttmt) REVERT: p 55 GLU cc_start: 0.6577 (tt0) cc_final: 0.6250 (tt0) REVERT: p 69 TYR cc_start: 0.8842 (m-10) cc_final: 0.8624 (m-80) REVERT: p 89 VAL cc_start: 0.9654 (p) cc_final: 0.9386 (m) REVERT: p 101 LEU cc_start: 0.9378 (mm) cc_final: 0.9157 (mp) REVERT: q 21 HIS cc_start: 0.8406 (t-90) cc_final: 0.8192 (t70) REVERT: q 62 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7639 (mtp85) REVERT: q 100 SER cc_start: 0.9088 (t) cc_final: 0.8767 (p) REVERT: r 78 ASN cc_start: 0.8622 (p0) cc_final: 0.8387 (p0) REVERT: r 99 ASN cc_start: 0.8884 (p0) cc_final: 0.8095 (p0) REVERT: r 121 ASN cc_start: 0.9593 (p0) cc_final: 0.9329 (p0) REVERT: t 86 LYS cc_start: 0.9244 (tmmm) cc_final: 0.8937 (tttp) REVERT: u 43 LYS cc_start: 0.7979 (mptp) cc_final: 0.7765 (mptt) REVERT: w 75 LYS cc_start: 0.8952 (tmmt) cc_final: 0.8728 (tttt) REVERT: x 19 ASP cc_start: 0.8902 (p0) cc_final: 0.8642 (p0) REVERT: x 63 LYS cc_start: 0.8428 (tttt) cc_final: 0.8201 (tmtt) REVERT: x 68 SER cc_start: 0.8626 (m) cc_final: 0.8331 (p) REVERT: y 12 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8838 (mttm) REVERT: z 83 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8168 (ttmt) REVERT: z 102 ARG cc_start: 0.8896 (ttm170) cc_final: 0.8661 (ttm170) outliers start: 29 outliers final: 12 residues processed: 2136 average time/residue: 1.3493 time to fit residues: 4907.4477 Evaluate side-chains 1236 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1223 time to evaluate : 6.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain V residue 92 LEU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain c residue 114 VAL 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 g residue 124 VAL Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain w residue 22 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 886 optimal weight: 0.9980 chunk 795 optimal weight: 0.9990 chunk 441 optimal weight: 30.0000 chunk 271 optimal weight: 10.0000 chunk 536 optimal weight: 10.0000 chunk 425 optimal weight: 0.0070 chunk 822 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 500 optimal weight: 1.9990 chunk 612 optimal weight: 6.9990 chunk 953 optimal weight: 5.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 296 GLN Y 318 ASN X 11 ASN X 106 ASN X 164 GLN W 170 GLN W 413 GLN W 458 GLN V 21 ASN V 119 GLN V 129 GLN V 181 HIS V 231 GLN V 358 HIS V 364 HIS V 380 ASN D 79 ASN D 97 ASN D 132 ASN D 140 ASN D 209 HIS D 217 GLN D 218 HIS E 173 GLN F 43 ASN F 48 GLN F 59 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN F 237 GLN F 320 ASN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN I 225 GLN I 237 ASN I 244 ASN J 24 ASN J 61 GLN K 8 GLN K 64 HIS ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN M 95 ASN M 150 ASN M 165 GLN N 19 GLN N 25 HIS N 37 ASN N 103 ASN N 137 GLN Q 22 GLN Q 82 GLN a 37 HIS a 57 GLN a 175 ASN b 26 GLN b 29 ASN b 55 HIS c 28 ASN c 97 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN d 45 ASN e 92 GLN f 63 GLN g 112 ASN g 146 ASN i 47 ASN i 98 ASN k 111 ASN l 42 GLN l 120 GLN m 127 ASN o 45 HIS p 47 ASN ** q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 GLN u 20 GLN u 62 GLN y 43 ASN y 50 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 141698 Z= 0.192 Angle : 0.650 16.407 208480 Z= 0.335 Chirality : 0.037 0.264 26218 Planarity : 0.005 0.067 13510 Dihedral : 23.114 179.649 62029 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.24 % Favored : 93.47 % Rotamer: Outliers : 3.28 % Allowed : 12.79 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.72 % Twisted General : 0.38 % 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: -2.49 (0.09), residues: 6987 helix: -1.53 (0.09), residues: 2117 sheet: -0.67 (0.16), residues: 983 loop : -2.01 (0.09), residues: 3887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP V 104 HIS 0.010 0.001 HIS V 358 PHE 0.023 0.002 PHE u 95 TYR 0.032 0.002 TYR m 49 ARG 0.017 0.001 ARG c 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1374 time to evaluate : 6.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 277 GLN cc_start: 0.8083 (mt0) cc_final: 0.7699 (mt0) REVERT: X 57 ARG cc_start: 0.8419 (ptp-170) cc_final: 0.8170 (mtm-85) REVERT: X 113 TYR cc_start: 0.7942 (m-80) cc_final: 0.7699 (m-80) REVERT: X 145 ASN cc_start: 0.7834 (m110) cc_final: 0.7330 (m-40) REVERT: X 157 GLN cc_start: 0.7915 (mt0) cc_final: 0.7714 (mt0) REVERT: X 162 HIS cc_start: 0.8936 (t70) cc_final: 0.8679 (t70) REVERT: W 320 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8684 (mttp) REVERT: W 379 LEU cc_start: 0.7646 (tp) cc_final: 0.7354 (tt) REVERT: W 381 ASP cc_start: 0.8510 (m-30) cc_final: 0.7962 (t0) REVERT: W 385 LEU cc_start: 0.7516 (mt) cc_final: 0.7239 (pp) REVERT: V 52 GLU cc_start: 0.6776 (pm20) cc_final: 0.6451 (pm20) REVERT: V 62 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6194 (pm20) REVERT: V 113 ARG cc_start: 0.7256 (ttm110) cc_final: 0.7023 (mtp-110) REVERT: V 296 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8621 (tt) REVERT: D 34 TYR cc_start: 0.9034 (t80) cc_final: 0.8718 (t80) REVERT: D 89 TYR cc_start: 0.8708 (m-80) cc_final: 0.8183 (m-10) REVERT: D 231 SER cc_start: 0.9087 (m) cc_final: 0.8792 (p) REVERT: E 109 HIS cc_start: 0.7815 (m-70) cc_final: 0.7492 (m-70) REVERT: E 274 SER cc_start: 0.9464 (m) cc_final: 0.9248 (p) REVERT: E 360 ASP cc_start: 0.8742 (t70) cc_final: 0.8500 (t0) REVERT: F 252 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7822 (tm-30) REVERT: G 38 THR cc_start: 0.9418 (t) cc_final: 0.9103 (p) REVERT: G 69 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8770 (mt) REVERT: G 117 GLU cc_start: 0.8492 (pm20) cc_final: 0.8220 (pm20) REVERT: G 272 TYR cc_start: 0.7584 (m-80) cc_final: 0.7105 (m-10) REVERT: H 148 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7538 (mm-30) REVERT: I 189 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.9006 (tp) REVERT: K 7 GLU cc_start: 0.8199 (pt0) cc_final: 0.7880 (pm20) REVERT: K 52 LEU cc_start: 0.8717 (tt) cc_final: 0.8447 (tt) REVERT: K 86 TYR cc_start: 0.8929 (m-80) cc_final: 0.7863 (m-10) REVERT: K 113 GLU cc_start: 0.7889 (tt0) cc_final: 0.7573 (tm-30) REVERT: K 118 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9185 (tt) REVERT: M 14 ILE cc_start: 0.8310 (mp) cc_final: 0.7946 (tt) REVERT: M 60 ARG cc_start: 0.7104 (mtm110) cc_final: 0.6735 (ptm160) REVERT: M 144 CYS cc_start: 0.8660 (m) cc_final: 0.8399 (t) REVERT: N 89 TYR cc_start: 0.9026 (t80) cc_final: 0.8784 (t80) REVERT: O 114 ASP cc_start: 0.8801 (t70) cc_final: 0.8526 (t70) REVERT: Q 47 GLN cc_start: 0.9092 (mm110) cc_final: 0.8774 (tp40) REVERT: Q 53 GLN cc_start: 0.9023 (tp40) cc_final: 0.8803 (tp40) REVERT: R 32 GLN cc_start: 0.8904 (mt0) cc_final: 0.8657 (mt0) REVERT: a 54 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8599 (mmtm) REVERT: b 168 TYR cc_start: 0.9422 (t80) cc_final: 0.8701 (t80) REVERT: d 23 ASN cc_start: 0.8812 (t0) cc_final: 0.8214 (t0) REVERT: d 145 ASN cc_start: 0.8518 (m110) cc_final: 0.7863 (p0) REVERT: d 155 MET cc_start: 0.8697 (tpt) cc_final: 0.8186 (tpp) REVERT: d 158 HIS cc_start: 0.8098 (m-70) cc_final: 0.7838 (m90) REVERT: e 29 THR cc_start: 0.9637 (t) cc_final: 0.9425 (m) REVERT: f 7 TYR cc_start: 0.9385 (m-80) cc_final: 0.9026 (m-80) REVERT: f 66 GLU cc_start: 0.7526 (tp30) cc_final: 0.6875 (tp30) REVERT: f 124 LEU cc_start: 0.9143 (mt) cc_final: 0.8875 (mp) REVERT: f 138 GLN cc_start: 0.8903 (tp40) cc_final: 0.8403 (tp40) REVERT: f 147 ASP cc_start: 0.8384 (t0) cc_final: 0.7967 (t0) REVERT: g 45 ASN cc_start: 0.9162 (t0) cc_final: 0.8863 (t0) REVERT: g 48 ILE cc_start: 0.9433 (mm) cc_final: 0.7920 (tp) REVERT: g 61 THR cc_start: 0.9587 (m) cc_final: 0.9199 (p) REVERT: g 82 ASN cc_start: 0.9194 (p0) cc_final: 0.8992 (p0) REVERT: h 35 LYS cc_start: 0.8991 (tptp) cc_final: 0.8521 (tppt) REVERT: h 36 TYR cc_start: 0.9168 (t80) cc_final: 0.8849 (t80) REVERT: h 40 HIS cc_start: 0.7522 (m90) cc_final: 0.7088 (m170) REVERT: h 87 ASN cc_start: 0.8630 (m110) cc_final: 0.8307 (m110) REVERT: h 88 GLN cc_start: 0.8387 (tp40) cc_final: 0.8125 (tp40) REVERT: i 29 SER cc_start: 0.9317 (p) cc_final: 0.8930 (t) REVERT: i 75 PRO cc_start: 0.9278 (Cg_endo) cc_final: 0.8833 (Cg_exo) REVERT: i 88 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7608 (mtt180) REVERT: j 26 SER cc_start: 0.9424 (m) cc_final: 0.9117 (p) REVERT: j 32 GLN cc_start: 0.9281 (tm-30) cc_final: 0.9019 (tm-30) REVERT: j 48 ARG cc_start: 0.7680 (ttm-80) cc_final: 0.7418 (ttm-80) REVERT: k 80 ASN cc_start: 0.8784 (t0) cc_final: 0.8440 (t0) REVERT: l 82 VAL cc_start: 0.9568 (t) cc_final: 0.9267 (m) REVERT: l 83 ASP cc_start: 0.7793 (t0) cc_final: 0.7583 (t0) REVERT: l 112 ASP cc_start: 0.6795 (t0) cc_final: 0.6559 (t0) REVERT: l 114 ASP cc_start: 0.8759 (m-30) cc_final: 0.8289 (m-30) REVERT: m 97 SER cc_start: 0.9088 (m) cc_final: 0.8681 (t) REVERT: m 109 GLU cc_start: 0.7527 (mp0) cc_final: 0.7141 (mp0) REVERT: n 44 ASN cc_start: 0.9273 (t0) cc_final: 0.8909 (t0) REVERT: n 52 TYR cc_start: 0.8950 (t80) cc_final: 0.8697 (t80) REVERT: n 135 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7712 (tm-30) REVERT: o 21 ILE cc_start: 0.8033 (mm) cc_final: 0.7612 (mm) REVERT: p 28 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8557 (ttmm) REVERT: p 63 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8278 (t) REVERT: q 21 HIS cc_start: 0.8443 (t-90) cc_final: 0.8198 (t70) REVERT: q 54 GLU cc_start: 0.8458 (mp0) cc_final: 0.8234 (mp0) REVERT: q 57 GLN cc_start: 0.7871 (mp10) cc_final: 0.7474 (mp10) REVERT: q 62 ARG cc_start: 0.7713 (mtt180) cc_final: 0.7505 (mtp85) REVERT: q 100 SER cc_start: 0.9099 (t) cc_final: 0.8704 (p) REVERT: r 69 SER cc_start: 0.9431 (p) cc_final: 0.9008 (t) REVERT: r 78 ASN cc_start: 0.8764 (p0) cc_final: 0.8429 (p0) REVERT: r 83 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7302 (mm-30) REVERT: r 99 ASN cc_start: 0.8881 (p0) cc_final: 0.8124 (p0) REVERT: r 121 ASN cc_start: 0.9616 (p0) cc_final: 0.9253 (p0) REVERT: u 8 GLU cc_start: 0.8440 (tt0) cc_final: 0.8093 (tp30) REVERT: u 28 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9261 (tp) REVERT: v 15 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7860 (ttpp) REVERT: v 62 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7282 (mtm-85) REVERT: w 75 LYS cc_start: 0.9129 (tmmt) cc_final: 0.8837 (tttt) REVERT: x 31 LEU cc_start: 0.8452 (pt) cc_final: 0.8169 (mp) REVERT: x 68 SER cc_start: 0.8642 (m) cc_final: 0.8440 (p) REVERT: y 19 GLN cc_start: 0.8468 (mt0) cc_final: 0.8081 (tp40) REVERT: z 102 ARG cc_start: 0.8900 (ttm170) cc_final: 0.8589 (ttm170) outliers start: 193 outliers final: 104 residues processed: 1481 average time/residue: 1.1221 time to fit residues: 2914.6931 Evaluate side-chains 1276 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1164 time to evaluate : 6.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 197 MET Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 242 THR Chi-restraints excluded: chain W residue 317 PHE Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 141 MET Chi-restraints excluded: chain V residue 184 HIS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 123 PHE Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 165 GLN Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 140 GLU Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain g residue 47 SER Chi-restraints excluded: chain g residue 79 MET Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 47 ASN Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 98 HIS Chi-restraints excluded: chain r residue 107 VAL Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain v residue 15 LYS Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain y residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 529 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 793 optimal weight: 10.0000 chunk 649 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 955 optimal weight: 10.0000 chunk 1031 optimal weight: 9.9990 chunk 850 optimal weight: 9.9990 chunk 947 optimal weight: 0.0470 chunk 325 optimal weight: 20.0000 chunk 766 optimal weight: 7.9990 overall best weight: 7.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 292 GLN Y 343 GLN X 11 ASN X 50 HIS W 375 GLN W 406 ASN W 500 ASN W 504 HIS V 130 GLN V 163 GLN ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS V 380 ASN D 38 HIS D 187 HIS D 217 GLN E 173 GLN F 115 HIS G 63 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN N 103 ASN R 33 GLN a 57 GLN a 175 ASN b 55 HIS ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN g 127 GLN i 47 ASN j 59 HIS l 42 GLN m 36 HIS ** m 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 127 ASN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 ASN p 47 ASN q 17 HIS q 57 GLN r 71 HIS s 5 HIS ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 18 ASN y 11 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 141698 Z= 0.394 Angle : 0.723 16.979 208480 Z= 0.368 Chirality : 0.041 0.292 26218 Planarity : 0.005 0.064 13510 Dihedral : 23.044 179.745 62023 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.87 % Favored : 91.81 % Rotamer: Outliers : 5.97 % Allowed : 13.59 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.38 % 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: -1.94 (0.09), residues: 6987 helix: -0.52 (0.11), residues: 2148 sheet: -0.66 (0.16), residues: 994 loop : -1.96 (0.09), residues: 3845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 255 HIS 0.009 0.002 HIS r 20 PHE 0.023 0.002 PHE E 67 TYR 0.029 0.002 TYR j 14 ARG 0.011 0.001 ARG c 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 351 poor density : 1181 time to evaluate : 6.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 277 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: Y 289 LYS cc_start: 0.5967 (tttp) cc_final: 0.5703 (tttm) REVERT: Y 346 LEU cc_start: 0.8017 (tt) cc_final: 0.7628 (mt) REVERT: X 157 GLN cc_start: 0.8110 (mt0) cc_final: 0.7827 (mt0) REVERT: X 162 HIS cc_start: 0.9007 (t70) cc_final: 0.8684 (t70) REVERT: W 379 LEU cc_start: 0.7645 (tp) cc_final: 0.7358 (tp) REVERT: W 381 ASP cc_start: 0.8591 (m-30) cc_final: 0.7976 (t0) REVERT: W 490 ASP cc_start: 0.7868 (m-30) cc_final: 0.7492 (m-30) REVERT: V 62 GLU cc_start: 0.7782 (tm-30) cc_final: 0.6720 (pm20) REVERT: V 129 GLN cc_start: 0.7333 (mm110) cc_final: 0.6882 (pm20) REVERT: V 374 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8118 (mt) REVERT: V 379 TYR cc_start: 0.8759 (m-80) cc_final: 0.8523 (m-10) REVERT: D 34 TYR cc_start: 0.8950 (t80) cc_final: 0.8736 (t80) REVERT: D 40 TYR cc_start: 0.9001 (p90) cc_final: 0.8763 (p90) REVERT: D 60 LYS cc_start: 0.9176 (mttt) cc_final: 0.8923 (mttp) REVERT: D 231 SER cc_start: 0.9211 (m) cc_final: 0.8872 (p) REVERT: E 109 HIS cc_start: 0.7837 (m-70) cc_final: 0.7630 (m-70) REVERT: E 274 SER cc_start: 0.9556 (m) cc_final: 0.9252 (p) REVERT: F 34 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9102 (tt) REVERT: F 115 HIS cc_start: 0.9164 (OUTLIER) cc_final: 0.8852 (t70) REVERT: F 252 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7915 (tm-30) REVERT: F 313 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8796 (tp) REVERT: G 69 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8740 (mt) REVERT: G 117 GLU cc_start: 0.8550 (pm20) cc_final: 0.8280 (pm20) REVERT: G 272 TYR cc_start: 0.7625 (m-80) cc_final: 0.7269 (m-10) REVERT: H 97 ASN cc_start: 0.8310 (t0) cc_final: 0.8021 (t0) REVERT: H 148 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7483 (mm-30) REVERT: I 180 SER cc_start: 0.7007 (p) cc_final: 0.6775 (p) REVERT: J 214 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8919 (tp) REVERT: K 52 LEU cc_start: 0.8873 (tt) cc_final: 0.8660 (mm) REVERT: K 86 TYR cc_start: 0.9088 (m-80) cc_final: 0.8062 (m-10) REVERT: K 118 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9307 (tt) REVERT: M 14 ILE cc_start: 0.8379 (mp) cc_final: 0.7838 (tt) REVERT: M 60 ARG cc_start: 0.7240 (mtm110) cc_final: 0.7037 (mtp180) REVERT: M 81 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8343 (mm-30) REVERT: N 89 TYR cc_start: 0.9013 (t80) cc_final: 0.8775 (t80) REVERT: O 114 ASP cc_start: 0.8891 (t70) cc_final: 0.8633 (t70) REVERT: Q 47 GLN cc_start: 0.9050 (mm110) cc_final: 0.8807 (tp40) REVERT: Q 53 GLN cc_start: 0.9173 (tp40) cc_final: 0.8862 (tp40) REVERT: Q 57 VAL cc_start: 0.9432 (t) cc_final: 0.9186 (p) REVERT: R 32 GLN cc_start: 0.8968 (mt0) cc_final: 0.8674 (mt0) REVERT: a 127 TYR cc_start: 0.8730 (m-80) cc_final: 0.8523 (m-80) REVERT: b 125 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8274 (ppt-90) REVERT: b 168 TYR cc_start: 0.9484 (t80) cc_final: 0.8800 (t80) REVERT: c 120 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8485 (p0) REVERT: c 168 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8786 (pp) REVERT: d 17 THR cc_start: 0.8360 (m) cc_final: 0.8134 (t) REVERT: d 23 ASN cc_start: 0.8976 (t0) cc_final: 0.8416 (t0) REVERT: d 89 ASP cc_start: 0.8313 (t0) cc_final: 0.8112 (t0) REVERT: d 155 MET cc_start: 0.8698 (tpt) cc_final: 0.8228 (tpp) REVERT: d 158 HIS cc_start: 0.8150 (m-70) cc_final: 0.7902 (m-70) REVERT: f 7 TYR cc_start: 0.9353 (m-80) cc_final: 0.8878 (m-80) REVERT: f 66 GLU cc_start: 0.7949 (tp30) cc_final: 0.7085 (tp30) REVERT: f 124 LEU cc_start: 0.9267 (mt) cc_final: 0.8990 (mp) REVERT: f 138 GLN cc_start: 0.9012 (tp40) cc_final: 0.8668 (tp40) REVERT: g 58 GLN cc_start: 0.9395 (tp-100) cc_final: 0.8973 (tp40) REVERT: g 61 THR cc_start: 0.9498 (m) cc_final: 0.9153 (p) REVERT: h 35 LYS cc_start: 0.9103 (tptp) cc_final: 0.8633 (tppt) REVERT: h 36 TYR cc_start: 0.9247 (t80) cc_final: 0.8875 (t80) REVERT: h 40 HIS cc_start: 0.7475 (m90) cc_final: 0.7027 (m170) REVERT: h 87 ASN cc_start: 0.8615 (m110) cc_final: 0.8362 (m110) REVERT: h 88 GLN cc_start: 0.8487 (tp40) cc_final: 0.8284 (tp40) REVERT: h 89 LEU cc_start: 0.9332 (mm) cc_final: 0.8808 (tp) REVERT: i 29 SER cc_start: 0.9393 (p) cc_final: 0.9164 (t) REVERT: i 74 MET cc_start: 0.8323 (pmm) cc_final: 0.8020 (pmm) REVERT: i 75 PRO cc_start: 0.9307 (Cg_endo) cc_final: 0.8913 (Cg_exo) REVERT: j 26 SER cc_start: 0.9365 (m) cc_final: 0.9035 (p) REVERT: j 32 GLN cc_start: 0.9395 (tm-30) cc_final: 0.9155 (tm-30) REVERT: k 80 ASN cc_start: 0.8971 (t0) cc_final: 0.8604 (t0) REVERT: m 97 SER cc_start: 0.9112 (m) cc_final: 0.8698 (t) REVERT: m 109 GLU cc_start: 0.7645 (mp0) cc_final: 0.7378 (mp0) REVERT: n 75 LEU cc_start: 0.9439 (mt) cc_final: 0.9219 (tp) REVERT: p 47 ASN cc_start: 0.8932 (p0) cc_final: 0.8670 (p0) REVERT: p 58 TYR cc_start: 0.9335 (t80) cc_final: 0.9092 (t80) REVERT: p 63 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8366 (t) REVERT: q 100 SER cc_start: 0.9147 (t) cc_final: 0.8764 (p) REVERT: r 69 SER cc_start: 0.9495 (p) cc_final: 0.9264 (t) REVERT: r 78 ASN cc_start: 0.8920 (p0) cc_final: 0.8508 (p0) REVERT: r 80 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8404 (mptt) REVERT: r 99 ASN cc_start: 0.9010 (p0) cc_final: 0.8260 (p0) REVERT: r 121 ASN cc_start: 0.9689 (p0) cc_final: 0.9330 (p0) REVERT: s 42 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8983 (mm-40) REVERT: t 18 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8067 (t160) REVERT: v 62 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7384 (mtm-85) REVERT: v 92 ASN cc_start: 0.7916 (m-40) cc_final: 0.7649 (m-40) REVERT: x 68 SER cc_start: 0.8689 (m) cc_final: 0.8481 (p) REVERT: y 19 GLN cc_start: 0.8478 (mt0) cc_final: 0.8102 (tp40) REVERT: z 88 LYS cc_start: 0.8449 (ttpt) cc_final: 0.7782 (mtmt) REVERT: z 102 ARG cc_start: 0.8869 (ttm170) cc_final: 0.8572 (ttm170) outliers start: 351 outliers final: 246 residues processed: 1389 average time/residue: 1.1070 time to fit residues: 2725.6042 Evaluate side-chains 1353 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1092 time to evaluate : 6.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 277 GLN Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 168 GLN Chi-restraints excluded: chain X residue 169 ASP Chi-restraints excluded: chain X residue 185 THR Chi-restraints excluded: chain X residue 197 MET Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 261 THR Chi-restraints excluded: chain W residue 317 PHE Chi-restraints excluded: chain W residue 380 SER Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 141 MET Chi-restraints excluded: chain V residue 184 HIS Chi-restraints excluded: chain V residue 212 ASP Chi-restraints excluded: chain V residue 252 CYS Chi-restraints excluded: chain V residue 255 ASP Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 115 HIS Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 319 LYS Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 229 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 160 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 224 ASP Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 62 ASN Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 4 SER Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 125 ARG Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 120 ASN Chi-restraints excluded: chain c residue 168 LEU Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 ARG Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 76 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain e residue 140 GLU Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 47 SER Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 151 LEU Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 43 VAL Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 22 ILE Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 107 THR Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 98 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 39 SER Chi-restraints excluded: chain p residue 44 ILE Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 22 SER Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 79 VAL Chi-restraints excluded: chain r residue 80 LYS Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 86 THR Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 98 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 18 ASN Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 57 LEU Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain t residue 105 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 15 GLU Chi-restraints excluded: chain u residue 33 VAL Chi-restraints excluded: chain u residue 44 ILE Chi-restraints excluded: chain u residue 58 ILE Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 81 THR Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain x residue 5 ILE Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 943 optimal weight: 7.9990 chunk 718 optimal weight: 3.9990 chunk 495 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 641 optimal weight: 10.0000 chunk 958 optimal weight: 0.5980 chunk 1014 optimal weight: 6.9990 chunk 500 optimal weight: 4.9990 chunk 908 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 11 ASN W 375 GLN V 21 ASN ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS V 380 ASN D 79 ASN D 233 GLN F 320 ASN G 39 GLN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN K 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 ASN N 102 GLN ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 GLN b 122 GLN c 97 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 HIS d 45 ASN ** g 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 47 ASN l 120 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 108 GLN ** w 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 141698 Z= 0.207 Angle : 0.600 15.897 208480 Z= 0.311 Chirality : 0.036 0.301 26218 Planarity : 0.004 0.064 13510 Dihedral : 22.963 179.429 62023 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.04 % Favored : 92.73 % Rotamer: Outliers : 4.66 % Allowed : 16.52 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.28 % 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: -1.50 (0.10), residues: 6987 helix: 0.10 (0.11), residues: 2126 sheet: -0.57 (0.16), residues: 984 loop : -1.80 (0.09), residues: 3877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 95 HIS 0.009 0.001 HIS F 115 PHE 0.019 0.001 PHE X 34 TYR 0.027 0.002 TYR j 14 ARG 0.011 0.000 ARG q 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1208 time to evaluate : 6.525 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 277 GLN cc_start: 0.8212 (mt0) cc_final: 0.7998 (mp10) REVERT: Y 283 PHE cc_start: 0.8344 (m-10) cc_final: 0.8112 (m-10) REVERT: Y 346 LEU cc_start: 0.8032 (tt) cc_final: 0.7669 (mt) REVERT: X 4 ARG cc_start: 0.8689 (ptp-170) cc_final: 0.8265 (ptp-170) REVERT: X 139 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8072 (ttm-80) REVERT: X 157 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7902 (mt0) REVERT: X 162 HIS cc_start: 0.8903 (t70) cc_final: 0.8583 (t70) REVERT: W 136 VAL cc_start: 0.6931 (OUTLIER) cc_final: 0.6715 (m) REVERT: W 379 LEU cc_start: 0.7402 (tp) cc_final: 0.7157 (tt) REVERT: W 381 ASP cc_start: 0.8505 (m-30) cc_final: 0.7936 (t0) REVERT: W 490 ASP cc_start: 0.7779 (m-30) cc_final: 0.7387 (m-30) REVERT: V 129 GLN cc_start: 0.7383 (mm110) cc_final: 0.6773 (pm20) REVERT: V 241 LYS cc_start: 0.8584 (ttpt) cc_final: 0.7800 (ttmm) REVERT: V 314 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: V 374 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8355 (mt) REVERT: D 34 TYR cc_start: 0.8991 (t80) cc_final: 0.8766 (t80) REVERT: D 60 LYS cc_start: 0.9134 (mttt) cc_final: 0.8836 (mttp) REVERT: D 231 SER cc_start: 0.9124 (m) cc_final: 0.8753 (p) REVERT: E 270 ARG cc_start: 0.8710 (ttp80) cc_final: 0.7933 (tmm-80) REVERT: E 274 SER cc_start: 0.9527 (m) cc_final: 0.9188 (p) REVERT: E 323 MET cc_start: 0.8756 (ttp) cc_final: 0.8555 (ttp) REVERT: F 34 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9037 (tt) REVERT: F 252 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7872 (tm-30) REVERT: F 339 LEU cc_start: 0.8903 (mt) cc_final: 0.7988 (tp) REVERT: G 69 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8800 (mt) REVERT: G 117 GLU cc_start: 0.8469 (pm20) cc_final: 0.8253 (pm20) REVERT: H 137 ASP cc_start: 0.8613 (m-30) cc_final: 0.7424 (m-30) REVERT: H 148 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7257 (mm-30) REVERT: I 189 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8922 (tp) REVERT: J 130 TYR cc_start: 0.8166 (m-80) cc_final: 0.7828 (m-80) REVERT: K 86 TYR cc_start: 0.9048 (m-80) cc_final: 0.7967 (m-10) REVERT: K 118 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9251 (tt) REVERT: M 43 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: N 89 TYR cc_start: 0.9021 (t80) cc_final: 0.8783 (t80) REVERT: O 114 ASP cc_start: 0.8860 (t70) cc_final: 0.8594 (t70) REVERT: Q 47 GLN cc_start: 0.9045 (mm110) cc_final: 0.8800 (tp40) REVERT: Q 53 GLN cc_start: 0.9071 (tp40) cc_final: 0.8781 (tp40) REVERT: Q 57 VAL cc_start: 0.9435 (t) cc_final: 0.9224 (p) REVERT: R 32 GLN cc_start: 0.8957 (mt0) cc_final: 0.8702 (mt0) REVERT: a 11 GLN cc_start: 0.8511 (tp40) cc_final: 0.8138 (tp40) REVERT: a 138 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: a 142 ILE cc_start: 0.9564 (mm) cc_final: 0.9349 (mm) REVERT: b 125 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8323 (ppt-90) REVERT: b 168 TYR cc_start: 0.9469 (t80) cc_final: 0.8845 (t80) REVERT: c 92 GLN cc_start: 0.8326 (pt0) cc_final: 0.7651 (tm-30) REVERT: d 23 ASN cc_start: 0.8906 (t0) cc_final: 0.8328 (t0) REVERT: d 89 ASP cc_start: 0.8323 (t0) cc_final: 0.8110 (t0) REVERT: d 96 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: d 155 MET cc_start: 0.8765 (tpt) cc_final: 0.8224 (tpp) REVERT: d 158 HIS cc_start: 0.8111 (m-70) cc_final: 0.7847 (m90) REVERT: f 7 TYR cc_start: 0.9384 (m-80) cc_final: 0.8818 (m-80) REVERT: f 14 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7816 (mp) REVERT: f 66 GLU cc_start: 0.7885 (tp30) cc_final: 0.7587 (tp30) REVERT: f 124 LEU cc_start: 0.9211 (mt) cc_final: 0.8925 (mp) REVERT: g 58 GLN cc_start: 0.9365 (tp-100) cc_final: 0.8943 (tp-100) REVERT: g 68 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8905 (p) REVERT: h 35 LYS cc_start: 0.9033 (tptp) cc_final: 0.8595 (tppt) REVERT: h 36 TYR cc_start: 0.9214 (t80) cc_final: 0.8845 (t80) REVERT: h 40 HIS cc_start: 0.7484 (m90) cc_final: 0.7010 (m170) REVERT: h 87 ASN cc_start: 0.8583 (m110) cc_final: 0.8328 (m110) REVERT: i 75 PRO cc_start: 0.9243 (Cg_endo) cc_final: 0.8958 (Cg_exo) REVERT: j 26 SER cc_start: 0.9279 (m) cc_final: 0.8926 (p) REVERT: k 54 TYR cc_start: 0.8521 (p90) cc_final: 0.8110 (p90) REVERT: k 80 ASN cc_start: 0.8936 (t0) cc_final: 0.8587 (t0) REVERT: l 38 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7622 (tm-30) REVERT: l 42 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: l 114 ASP cc_start: 0.8723 (m-30) cc_final: 0.8313 (m-30) REVERT: m 97 SER cc_start: 0.9043 (m) cc_final: 0.8693 (t) REVERT: n 135 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7791 (tm-30) REVERT: o 21 ILE cc_start: 0.8032 (mm) cc_final: 0.7616 (mm) REVERT: p 47 ASN cc_start: 0.8977 (p0) cc_final: 0.8686 (p0) REVERT: p 58 TYR cc_start: 0.9269 (t80) cc_final: 0.9053 (t80) REVERT: p 63 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8302 (t) REVERT: q 100 SER cc_start: 0.9141 (t) cc_final: 0.8734 (p) REVERT: r 66 LEU cc_start: 0.9401 (mm) cc_final: 0.9065 (mm) REVERT: r 69 SER cc_start: 0.9583 (p) cc_final: 0.9257 (t) REVERT: r 78 ASN cc_start: 0.8858 (p0) cc_final: 0.8462 (p0) REVERT: r 80 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8424 (mptt) REVERT: r 99 ASN cc_start: 0.8986 (p0) cc_final: 0.8221 (p0) REVERT: r 121 ASN cc_start: 0.9666 (p0) cc_final: 0.9304 (p0) REVERT: s 31 LYS cc_start: 0.9109 (tptt) cc_final: 0.8827 (ttmm) REVERT: t 98 GLN cc_start: 0.8824 (tp40) cc_final: 0.8516 (tp40) REVERT: u 43 LYS cc_start: 0.8385 (mptt) cc_final: 0.7769 (pttt) REVERT: u 96 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8496 (mp0) REVERT: v 58 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8325 (pp) REVERT: v 62 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7175 (mtm-85) REVERT: v 92 ASN cc_start: 0.7813 (m-40) cc_final: 0.7518 (m110) REVERT: x 31 LEU cc_start: 0.8493 (pt) cc_final: 0.8238 (mp) REVERT: x 68 SER cc_start: 0.8725 (m) cc_final: 0.8524 (p) REVERT: y 19 GLN cc_start: 0.8493 (mt0) cc_final: 0.8151 (tp40) REVERT: z 88 LYS cc_start: 0.8475 (ttpt) cc_final: 0.7792 (mtmt) REVERT: z 102 ARG cc_start: 0.8900 (ttm170) cc_final: 0.8573 (ttm170) outliers start: 274 outliers final: 171 residues processed: 1365 average time/residue: 1.1138 time to fit residues: 2685.1788 Evaluate side-chains 1331 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1142 time to evaluate : 6.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 279 ASN Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 136 VAL Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 484 SER Chi-restraints excluded: chain W residue 513 ARG Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 184 HIS Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 135 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 138 GLN Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 125 ARG Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 96 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 14 LEU Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 151 LEU Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 57 MET Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 56 VAL Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 63 SER Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 23 ASP Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 80 LYS Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 98 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 15 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 845 optimal weight: 3.9990 chunk 576 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 755 optimal weight: 7.9990 chunk 418 optimal weight: 0.4980 chunk 866 optimal weight: 7.9990 chunk 701 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 518 optimal weight: 1.9990 chunk 910 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 292 GLN X 145 ASN W 127 GLN W 190 GLN ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS V 380 ASN F 307 GLN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 63 GLN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 ASN O 59 ASN ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN ** g 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 ASN l 120 GLN ** m 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 GLN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 141698 Z= 0.197 Angle : 0.579 15.080 208480 Z= 0.299 Chirality : 0.035 0.372 26218 Planarity : 0.004 0.108 13510 Dihedral : 22.878 179.888 62020 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.64 % Favored : 92.14 % Rotamer: Outliers : 5.22 % Allowed : 17.01 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.24 % 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: -1.23 (0.10), residues: 6987 helix: 0.47 (0.11), residues: 2140 sheet: -0.45 (0.17), residues: 972 loop : -1.72 (0.09), residues: 3875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP V 104 HIS 0.007 0.001 HIS E 109 PHE 0.023 0.001 PHE X 34 TYR 0.026 0.001 TYR j 14 ARG 0.013 0.000 ARG b 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1218 time to evaluate : 6.752 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 253 LYS cc_start: 0.5509 (tptp) cc_final: 0.4545 (mtmm) REVERT: Y 277 GLN cc_start: 0.8101 (mt0) cc_final: 0.7868 (mp10) REVERT: Y 283 PHE cc_start: 0.8389 (m-10) cc_final: 0.8078 (m-10) REVERT: Y 346 LEU cc_start: 0.8098 (tt) cc_final: 0.7734 (mt) REVERT: X 4 ARG cc_start: 0.8641 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: X 139 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8108 (ttm-80) REVERT: X 157 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7947 (mt0) REVERT: X 162 HIS cc_start: 0.8905 (t70) cc_final: 0.8550 (t70) REVERT: W 206 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.6320 (t0) REVERT: W 233 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6078 (mt) REVERT: W 327 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.5923 (mt) REVERT: W 379 LEU cc_start: 0.7416 (tp) cc_final: 0.7130 (tt) REVERT: W 381 ASP cc_start: 0.8545 (m-30) cc_final: 0.7926 (t0) REVERT: W 490 ASP cc_start: 0.7774 (m-30) cc_final: 0.7430 (m-30) REVERT: V 36 TYR cc_start: 0.7434 (t80) cc_final: 0.7149 (t80) REVERT: V 62 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6960 (tm-30) REVERT: V 129 GLN cc_start: 0.7170 (mm110) cc_final: 0.6576 (pm20) REVERT: V 227 GLU cc_start: 0.8420 (pm20) cc_final: 0.7965 (pm20) REVERT: V 241 LYS cc_start: 0.8597 (ttpt) cc_final: 0.7688 (ttmm) REVERT: V 374 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8319 (mt) REVERT: V 380 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8811 (t0) REVERT: D 60 LYS cc_start: 0.9169 (mttt) cc_final: 0.8853 (mttp) REVERT: D 231 SER cc_start: 0.9151 (m) cc_final: 0.8765 (p) REVERT: E 67 PHE cc_start: 0.8575 (m-80) cc_final: 0.8323 (m-80) REVERT: E 74 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6925 (mt-10) REVERT: E 270 ARG cc_start: 0.8733 (ttp80) cc_final: 0.7884 (tmm-80) REVERT: E 274 SER cc_start: 0.9489 (m) cc_final: 0.9124 (p) REVERT: E 323 MET cc_start: 0.8826 (ttp) cc_final: 0.8615 (ttp) REVERT: F 252 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7982 (tm-30) REVERT: F 339 LEU cc_start: 0.8723 (mt) cc_final: 0.8462 (tp) REVERT: G 69 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8821 (mt) REVERT: H 133 GLU cc_start: 0.5843 (tm-30) cc_final: 0.5621 (tm-30) REVERT: H 137 ASP cc_start: 0.7921 (m-30) cc_final: 0.7454 (m-30) REVERT: H 148 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7205 (mm-30) REVERT: I 180 SER cc_start: 0.6472 (OUTLIER) cc_final: 0.6262 (p) REVERT: I 189 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8918 (tp) REVERT: J 130 TYR cc_start: 0.8066 (m-80) cc_final: 0.7767 (m-80) REVERT: K 86 TYR cc_start: 0.9042 (m-80) cc_final: 0.8022 (m-10) REVERT: K 118 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9226 (tt) REVERT: M 11 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7022 (p0) REVERT: M 25 GLU cc_start: 0.7316 (pm20) cc_final: 0.7056 (tp30) REVERT: M 43 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: O 114 ASP cc_start: 0.8851 (t70) cc_final: 0.8509 (t70) REVERT: Q 57 VAL cc_start: 0.9435 (t) cc_final: 0.9229 (p) REVERT: R 32 GLN cc_start: 0.8931 (mt0) cc_final: 0.8708 (mt0) REVERT: a 81 TYR cc_start: 0.8809 (m-10) cc_final: 0.8487 (m-10) REVERT: a 138 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: a 142 ILE cc_start: 0.9563 (mm) cc_final: 0.9339 (mm) REVERT: b 168 TYR cc_start: 0.9462 (t80) cc_final: 0.8939 (t80) REVERT: c 31 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7861 (mm-30) REVERT: c 92 GLN cc_start: 0.8358 (pt0) cc_final: 0.7625 (tm-30) REVERT: d 23 ASN cc_start: 0.8872 (t0) cc_final: 0.8204 (t0) REVERT: d 155 MET cc_start: 0.8738 (tpt) cc_final: 0.8492 (tpt) REVERT: d 158 HIS cc_start: 0.8137 (m-70) cc_final: 0.7932 (m90) REVERT: f 7 TYR cc_start: 0.9392 (m-80) cc_final: 0.8804 (m-80) REVERT: f 66 GLU cc_start: 0.7936 (tp30) cc_final: 0.7678 (tp30) REVERT: f 124 LEU cc_start: 0.9166 (mt) cc_final: 0.8833 (mp) REVERT: g 58 GLN cc_start: 0.9348 (tp-100) cc_final: 0.8998 (tp40) REVERT: g 68 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8863 (p) REVERT: h 35 LYS cc_start: 0.9014 (tptp) cc_final: 0.8518 (tppt) REVERT: h 40 HIS cc_start: 0.7496 (m90) cc_final: 0.7160 (m170) REVERT: h 87 ASN cc_start: 0.8599 (m110) cc_final: 0.8274 (m110) REVERT: i 11 PHE cc_start: 0.8395 (t80) cc_final: 0.8078 (t80) REVERT: i 75 PRO cc_start: 0.9121 (Cg_endo) cc_final: 0.8730 (Cg_exo) REVERT: j 4 GLU cc_start: 0.8583 (mp0) cc_final: 0.8351 (mp0) REVERT: j 26 SER cc_start: 0.9271 (m) cc_final: 0.8911 (p) REVERT: j 32 GLN cc_start: 0.9301 (tm-30) cc_final: 0.8932 (tm-30) REVERT: k 54 TYR cc_start: 0.8526 (p90) cc_final: 0.8150 (p90) REVERT: k 80 ASN cc_start: 0.8952 (t0) cc_final: 0.8590 (t0) REVERT: l 91 ASN cc_start: 0.9341 (p0) cc_final: 0.8835 (p0) REVERT: l 114 ASP cc_start: 0.8686 (m-30) cc_final: 0.8297 (m-30) REVERT: m 97 SER cc_start: 0.9036 (m) cc_final: 0.8667 (t) REVERT: m 109 GLU cc_start: 0.7772 (mp0) cc_final: 0.7421 (mp0) REVERT: m 120 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8237 (tm-30) REVERT: n 32 ARG cc_start: 0.9273 (mtt-85) cc_final: 0.8370 (mtt90) REVERT: n 73 LEU cc_start: 0.9231 (tp) cc_final: 0.8900 (tp) REVERT: o 21 ILE cc_start: 0.8007 (mm) cc_final: 0.7630 (mm) REVERT: p 47 ASN cc_start: 0.9008 (p0) cc_final: 0.8762 (p0) REVERT: r 69 SER cc_start: 0.9581 (p) cc_final: 0.9282 (t) REVERT: r 78 ASN cc_start: 0.8908 (p0) cc_final: 0.8488 (p0) REVERT: r 99 ASN cc_start: 0.8951 (p0) cc_final: 0.8160 (p0) REVERT: r 121 ASN cc_start: 0.9673 (p0) cc_final: 0.9286 (p0) REVERT: s 31 LYS cc_start: 0.9003 (tptt) cc_final: 0.8781 (ttmm) REVERT: t 98 GLN cc_start: 0.8789 (tp40) cc_final: 0.8505 (tp40) REVERT: u 43 LYS cc_start: 0.8343 (mptt) cc_final: 0.7866 (pttt) REVERT: u 96 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8507 (mp0) REVERT: v 58 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8343 (pp) REVERT: v 62 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7156 (mtm-85) REVERT: v 92 ASN cc_start: 0.7764 (m-40) cc_final: 0.7502 (m110) REVERT: y 19 GLN cc_start: 0.8478 (mt0) cc_final: 0.8174 (tp40) REVERT: z 88 LYS cc_start: 0.8606 (ttpt) cc_final: 0.7932 (mtmt) REVERT: z 102 ARG cc_start: 0.8959 (ttm170) cc_final: 0.8615 (ttm170) outliers start: 307 outliers final: 216 residues processed: 1392 average time/residue: 1.1729 time to fit residues: 2899.2479 Evaluate side-chains 1370 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1138 time to evaluate : 6.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 279 ASN Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 206 ASP Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 233 LEU Chi-restraints excluded: chain W residue 327 LEU Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 380 SER Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 484 SER Chi-restraints excluded: chain W residue 513 ARG Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 184 HIS Chi-restraints excluded: chain V residue 255 ASP Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 337 ASP Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 380 ASN Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 57 GLN Chi-restraints excluded: chain a residue 138 GLN Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain a residue 183 THR Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 76 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain g residue 14 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 151 LEU Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain i residue 22 ILE Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 107 THR Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 98 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain q residue 46 THR Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 86 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 341 optimal weight: 10.0000 chunk 913 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 595 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 1015 optimal weight: 10.0000 chunk 843 optimal weight: 0.0770 chunk 470 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 533 optimal weight: 0.7980 overall best weight: 6.1746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 292 GLN W 127 GLN W 375 GLN V 21 ASN V 130 GLN ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS E 293 ASN F 59 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN G 39 GLN G 63 GLN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN Q 22 GLN ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 55 GLN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 36 GLN r 49 ASN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 141698 Z= 0.337 Angle : 0.655 15.219 208480 Z= 0.334 Chirality : 0.038 0.337 26218 Planarity : 0.005 0.062 13510 Dihedral : 22.860 179.702 62020 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.39 % Favored : 91.44 % Rotamer: Outliers : 5.80 % Allowed : 17.72 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 6987 helix: 0.46 (0.11), residues: 2148 sheet: -0.51 (0.17), residues: 948 loop : -1.79 (0.09), residues: 3891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP V 104 HIS 0.008 0.001 HIS q 21 PHE 0.019 0.002 PHE I 229 TYR 0.026 0.002 TYR b 167 ARG 0.008 0.001 ARG R 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1138 time to evaluate : 6.595 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: Y 277 GLN cc_start: 0.8047 (mt0) cc_final: 0.7825 (mp10) REVERT: Y 283 PHE cc_start: 0.8433 (m-10) cc_final: 0.8134 (m-10) REVERT: Y 289 LYS cc_start: 0.5806 (tttm) cc_final: 0.5554 (tttm) REVERT: Y 346 LEU cc_start: 0.8085 (tt) cc_final: 0.7725 (mt) REVERT: X 139 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8075 (ttm-80) REVERT: X 157 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7945 (mm-40) REVERT: X 162 HIS cc_start: 0.8944 (t70) cc_final: 0.8635 (t70) REVERT: W 206 ASP cc_start: 0.7788 (m-30) cc_final: 0.6127 (t0) REVERT: W 233 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5988 (mt) REVERT: W 379 LEU cc_start: 0.7458 (tp) cc_final: 0.7109 (tt) REVERT: W 381 ASP cc_start: 0.8605 (m-30) cc_final: 0.7980 (t0) REVERT: W 490 ASP cc_start: 0.7890 (m-30) cc_final: 0.7549 (m-30) REVERT: V 36 TYR cc_start: 0.7402 (t80) cc_final: 0.7157 (t80) REVERT: V 129 GLN cc_start: 0.6994 (mm110) cc_final: 0.6436 (pm20) REVERT: V 227 GLU cc_start: 0.8425 (pm20) cc_final: 0.7672 (pm20) REVERT: V 241 LYS cc_start: 0.8610 (ttpt) cc_final: 0.7580 (ttpp) REVERT: V 314 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: V 374 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8055 (mt) REVERT: D 60 LYS cc_start: 0.9223 (mttt) cc_final: 0.8918 (mttp) REVERT: D 193 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8171 (pmm150) REVERT: D 231 SER cc_start: 0.9174 (m) cc_final: 0.8809 (p) REVERT: E 74 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: E 114 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8470 (t) REVERT: E 274 SER cc_start: 0.9506 (m) cc_final: 0.9135 (p) REVERT: E 323 MET cc_start: 0.8919 (ttp) cc_final: 0.8702 (ttp) REVERT: F 59 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8656 (mt0) REVERT: F 193 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8294 (mttp) REVERT: F 252 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8071 (tm-30) REVERT: G 69 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8798 (mt) REVERT: G 265 TYR cc_start: 0.7825 (m-80) cc_final: 0.5642 (m-80) REVERT: H 60 ASP cc_start: 0.7594 (t0) cc_final: 0.7339 (t0) REVERT: H 97 ASN cc_start: 0.8355 (t0) cc_final: 0.8101 (t0) REVERT: H 133 GLU cc_start: 0.5965 (tm-30) cc_final: 0.5549 (tm-30) REVERT: H 137 ASP cc_start: 0.7901 (m-30) cc_final: 0.7365 (m-30) REVERT: I 180 SER cc_start: 0.6656 (OUTLIER) cc_final: 0.6424 (p) REVERT: I 189 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8897 (tp) REVERT: J 130 TYR cc_start: 0.8059 (m-80) cc_final: 0.7833 (m-80) REVERT: K 86 TYR cc_start: 0.9133 (m-80) cc_final: 0.8477 (m-10) REVERT: K 118 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9297 (tt) REVERT: M 43 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: M 110 ILE cc_start: 0.7596 (mm) cc_final: 0.7049 (mm) REVERT: M 126 ASP cc_start: 0.7426 (m-30) cc_final: 0.6651 (t0) REVERT: O 93 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8833 (mttm) REVERT: O 114 ASP cc_start: 0.8961 (t70) cc_final: 0.8659 (t70) REVERT: R 32 GLN cc_start: 0.8993 (mt0) cc_final: 0.8773 (mt0) REVERT: a 11 GLN cc_start: 0.8651 (tp40) cc_final: 0.8049 (tp40) REVERT: a 138 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: b 168 TYR cc_start: 0.9463 (t80) cc_final: 0.8865 (t80) REVERT: c 92 GLN cc_start: 0.8375 (pt0) cc_final: 0.7800 (tm-30) REVERT: d 23 ASN cc_start: 0.8970 (t0) cc_final: 0.8350 (t0) REVERT: d 155 MET cc_start: 0.8768 (tpt) cc_final: 0.8271 (tpp) REVERT: d 158 HIS cc_start: 0.8152 (m-70) cc_final: 0.7925 (m90) REVERT: f 7 TYR cc_start: 0.9475 (m-80) cc_final: 0.9013 (m-80) REVERT: f 66 GLU cc_start: 0.8009 (tp30) cc_final: 0.7800 (tp30) REVERT: f 124 LEU cc_start: 0.9246 (mt) cc_final: 0.8941 (mp) REVERT: g 58 GLN cc_start: 0.9330 (tp-100) cc_final: 0.9010 (tp40) REVERT: g 68 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8886 (p) REVERT: h 32 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8737 (t) REVERT: h 35 LYS cc_start: 0.9025 (tptp) cc_final: 0.8573 (tppt) REVERT: h 40 HIS cc_start: 0.7661 (m90) cc_final: 0.7305 (m90) REVERT: h 87 ASN cc_start: 0.8682 (m110) cc_final: 0.8389 (m110) REVERT: h 88 GLN cc_start: 0.8376 (tp40) cc_final: 0.8174 (tp40) REVERT: i 11 PHE cc_start: 0.8347 (t80) cc_final: 0.8017 (t80) REVERT: i 75 PRO cc_start: 0.9309 (Cg_endo) cc_final: 0.9087 (Cg_exo) REVERT: j 4 GLU cc_start: 0.8729 (mp0) cc_final: 0.8496 (mp0) REVERT: j 26 SER cc_start: 0.9317 (m) cc_final: 0.9008 (p) REVERT: j 32 GLN cc_start: 0.9384 (tm-30) cc_final: 0.8883 (tm-30) REVERT: k 54 TYR cc_start: 0.8611 (p90) cc_final: 0.8237 (p90) REVERT: k 80 ASN cc_start: 0.8983 (t0) cc_final: 0.8551 (t0) REVERT: l 38 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7603 (tm-30) REVERT: l 42 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: l 91 ASN cc_start: 0.9384 (p0) cc_final: 0.8982 (p0) REVERT: l 114 ASP cc_start: 0.8754 (m-30) cc_final: 0.8152 (m-30) REVERT: m 97 SER cc_start: 0.9004 (m) cc_final: 0.8657 (t) REVERT: n 73 LEU cc_start: 0.9308 (tp) cc_final: 0.9031 (tp) REVERT: n 135 GLU cc_start: 0.8220 (tm-30) cc_final: 0.8012 (tm-30) REVERT: o 18 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8551 (tpp80) REVERT: o 41 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8594 (mtp85) REVERT: p 47 ASN cc_start: 0.9059 (p0) cc_final: 0.8816 (p0) REVERT: r 69 SER cc_start: 0.9573 (p) cc_final: 0.9285 (t) REVERT: r 78 ASN cc_start: 0.8965 (p0) cc_final: 0.8550 (p0) REVERT: r 99 ASN cc_start: 0.9032 (p0) cc_final: 0.8308 (p0) REVERT: r 121 ASN cc_start: 0.9689 (p0) cc_final: 0.9315 (p0) REVERT: s 31 LYS cc_start: 0.9044 (tptt) cc_final: 0.8690 (ttmm) REVERT: s 92 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8831 (ttmm) REVERT: t 98 GLN cc_start: 0.8872 (tp40) cc_final: 0.8524 (tp40) REVERT: u 43 LYS cc_start: 0.8403 (mptt) cc_final: 0.7798 (pttt) REVERT: u 96 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8534 (mt-10) REVERT: v 58 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8376 (pp) REVERT: v 62 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7162 (mtm-85) REVERT: v 92 ASN cc_start: 0.7758 (m-40) cc_final: 0.7494 (m110) REVERT: y 19 GLN cc_start: 0.8513 (mt0) cc_final: 0.8210 (tp40) REVERT: z 88 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8159 (mtmt) REVERT: z 102 ARG cc_start: 0.8962 (ttm170) cc_final: 0.8613 (ttm170) outliers start: 341 outliers final: 273 residues processed: 1339 average time/residue: 1.1947 time to fit residues: 2864.3693 Evaluate side-chains 1399 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1106 time to evaluate : 6.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 279 ASN Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 338 THR Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 169 ASP Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 233 LEU Chi-restraints excluded: chain W residue 364 VAL Chi-restraints excluded: chain W residue 380 SER Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 484 SER Chi-restraints excluded: chain W residue 509 THR Chi-restraints excluded: chain W residue 513 ARG Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 21 ASN Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 141 MET Chi-restraints excluded: chain V residue 184 HIS Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 ASP Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 299 SER Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 337 ASP Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 LYS Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 197 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 171 ASP Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 4 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain Q residue 29 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 79 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 57 GLN Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 138 GLN Chi-restraints excluded: chain a residue 165 THR 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 6 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain c residue 29 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 124 LYS Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 ARG Chi-restraints excluded: chain d residue 186 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 76 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain f residue 8 GLN Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 14 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 151 LEU Chi-restraints excluded: chain h residue 32 SER Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain i residue 22 ILE Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 107 THR Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 98 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 46 ASP Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 124 ILE Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 86 THR Chi-restraints excluded: chain r residue 98 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain t residue 105 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 15 GLU Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 58 ILE Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain x residue 73 LEU Chi-restraints excluded: chain y residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 979 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 741 optimal weight: 30.0000 chunk 574 optimal weight: 5.9990 chunk 855 optimal weight: 5.9990 chunk 567 optimal weight: 7.9990 chunk 1012 optimal weight: 3.9990 chunk 633 optimal weight: 6.9990 chunk 616 optimal weight: 10.0000 chunk 467 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 145 ASN W 127 GLN V 21 ASN V 184 HIS ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 87 GLN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN d 9 GLN ** g 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 120 GLN ** m 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 67 HIS ** q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 49 ASN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 141698 Z= 0.267 Angle : 0.617 15.156 208480 Z= 0.317 Chirality : 0.037 0.303 26218 Planarity : 0.004 0.062 13510 Dihedral : 22.860 179.933 62020 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.20 % Favored : 91.61 % Rotamer: Outliers : 5.68 % Allowed : 18.25 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: -1.22 (0.10), residues: 6987 helix: 0.57 (0.11), residues: 2136 sheet: -0.49 (0.17), residues: 961 loop : -1.75 (0.09), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP V 104 HIS 0.008 0.001 HIS H 172 PHE 0.019 0.002 PHE I 229 TYR 0.029 0.002 TYR b 167 ARG 0.009 0.000 ARG R 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1141 time to evaluate : 6.615 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 253 LYS cc_start: 0.5340 (tptp) cc_final: 0.4411 (mtmm) REVERT: Y 283 PHE cc_start: 0.8457 (m-10) cc_final: 0.8149 (m-10) REVERT: Y 346 LEU cc_start: 0.8029 (tt) cc_final: 0.7678 (mt) REVERT: X 4 ARG cc_start: 0.8672 (ptp-170) cc_final: 0.8361 (ptp-170) REVERT: X 157 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7965 (mm-40) REVERT: X 162 HIS cc_start: 0.8908 (t70) cc_final: 0.8572 (t70) REVERT: W 206 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.5975 (t0) REVERT: W 233 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5874 (mt) REVERT: W 327 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5842 (mp) REVERT: W 379 LEU cc_start: 0.7357 (tp) cc_final: 0.7039 (tt) REVERT: W 381 ASP cc_start: 0.8572 (m-30) cc_final: 0.7969 (t0) REVERT: W 490 ASP cc_start: 0.7855 (m-30) cc_final: 0.7515 (m-30) REVERT: V 36 TYR cc_start: 0.7382 (t80) cc_final: 0.6745 (t80) REVERT: V 227 GLU cc_start: 0.8401 (pm20) cc_final: 0.7568 (pm20) REVERT: V 241 LYS cc_start: 0.8617 (ttpt) cc_final: 0.7606 (ttpp) REVERT: V 314 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: V 374 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8238 (mt) REVERT: D 60 LYS cc_start: 0.9181 (mttt) cc_final: 0.8752 (mtpt) REVERT: D 180 LEU cc_start: 0.9383 (mt) cc_final: 0.9144 (mt) REVERT: D 193 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8147 (pmm150) REVERT: D 231 SER cc_start: 0.9146 (m) cc_final: 0.8805 (p) REVERT: E 74 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: E 114 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8430 (t) REVERT: E 270 ARG cc_start: 0.8771 (ttp80) cc_final: 0.7942 (tmm-80) REVERT: E 274 SER cc_start: 0.9512 (m) cc_final: 0.9118 (p) REVERT: E 323 MET cc_start: 0.8899 (ttp) cc_final: 0.8678 (ttp) REVERT: F 193 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8296 (mtmm) REVERT: F 252 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8076 (tm-30) REVERT: G 69 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8798 (mt) REVERT: G 117 GLU cc_start: 0.8626 (pm20) cc_final: 0.8237 (pm20) REVERT: H 97 ASN cc_start: 0.8429 (t0) cc_final: 0.8181 (t0) REVERT: H 133 GLU cc_start: 0.5976 (tm-30) cc_final: 0.5673 (tm-30) REVERT: H 137 ASP cc_start: 0.7826 (m-30) cc_final: 0.7161 (m-30) REVERT: I 180 SER cc_start: 0.6714 (OUTLIER) cc_final: 0.6461 (p) REVERT: I 189 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8873 (tp) REVERT: J 69 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8471 (mp) REVERT: J 130 TYR cc_start: 0.8153 (m-80) cc_final: 0.7913 (m-80) REVERT: J 214 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8879 (tp) REVERT: K 86 TYR cc_start: 0.9138 (m-80) cc_final: 0.8367 (m-10) REVERT: K 118 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9279 (tt) REVERT: M 11 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7118 (p0) REVERT: M 25 GLU cc_start: 0.7454 (pm20) cc_final: 0.7053 (tp30) REVERT: M 43 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: M 126 ASP cc_start: 0.7507 (m-30) cc_final: 0.6681 (t0) REVERT: O 93 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8699 (mttm) REVERT: O 114 ASP cc_start: 0.8998 (t70) cc_final: 0.8717 (t70) REVERT: R 32 GLN cc_start: 0.8962 (mt0) cc_final: 0.8740 (mt0) REVERT: a 11 GLN cc_start: 0.8595 (tp40) cc_final: 0.7941 (tp40) REVERT: a 138 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: a 142 ILE cc_start: 0.9571 (mm) cc_final: 0.9357 (mm) REVERT: b 168 TYR cc_start: 0.9448 (t80) cc_final: 0.8952 (t80) REVERT: c 92 GLN cc_start: 0.8357 (pt0) cc_final: 0.7747 (tm-30) REVERT: c 152 GLU cc_start: 0.8713 (pm20) cc_final: 0.8419 (pm20) REVERT: d 23 ASN cc_start: 0.8979 (t0) cc_final: 0.8534 (t0) REVERT: d 155 MET cc_start: 0.8746 (tpt) cc_final: 0.8265 (tpp) REVERT: f 7 TYR cc_start: 0.9490 (m-80) cc_final: 0.8818 (m-80) REVERT: f 66 GLU cc_start: 0.8000 (tp30) cc_final: 0.7787 (tp30) REVERT: f 124 LEU cc_start: 0.9232 (mt) cc_final: 0.8936 (mp) REVERT: g 58 GLN cc_start: 0.9321 (tp-100) cc_final: 0.9034 (tp40) REVERT: g 68 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8882 (p) REVERT: h 32 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8681 (t) REVERT: h 35 LYS cc_start: 0.9014 (tptp) cc_final: 0.8571 (tppt) REVERT: h 40 HIS cc_start: 0.7717 (m90) cc_final: 0.7360 (m90) REVERT: h 87 ASN cc_start: 0.8639 (m110) cc_final: 0.8357 (m110) REVERT: h 88 GLN cc_start: 0.8419 (tp40) cc_final: 0.8192 (tp40) REVERT: i 11 PHE cc_start: 0.8371 (t80) cc_final: 0.8065 (t80) REVERT: i 87 ARG cc_start: 0.8076 (mmt90) cc_final: 0.7839 (mtm-85) REVERT: j 4 GLU cc_start: 0.8564 (mp0) cc_final: 0.8346 (mp0) REVERT: j 23 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8351 (ttp80) REVERT: j 26 SER cc_start: 0.9297 (m) cc_final: 0.8942 (p) REVERT: j 32 GLN cc_start: 0.9378 (tm-30) cc_final: 0.8881 (tm-30) REVERT: k 54 TYR cc_start: 0.8573 (p90) cc_final: 0.8175 (p90) REVERT: k 80 ASN cc_start: 0.8958 (t0) cc_final: 0.8524 (t0) REVERT: l 38 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7692 (tm-30) REVERT: l 42 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: l 91 ASN cc_start: 0.9350 (p0) cc_final: 0.9000 (p0) REVERT: l 114 ASP cc_start: 0.8746 (m-30) cc_final: 0.8134 (m-30) REVERT: m 97 SER cc_start: 0.8942 (m) cc_final: 0.8604 (t) REVERT: m 109 GLU cc_start: 0.7712 (mp0) cc_final: 0.7428 (mp0) REVERT: n 73 LEU cc_start: 0.9306 (tp) cc_final: 0.9043 (tp) REVERT: n 135 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7875 (tm-30) REVERT: o 18 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8527 (tpp80) REVERT: o 41 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8550 (mtm-85) REVERT: p 47 ASN cc_start: 0.9081 (p0) cc_final: 0.8833 (p0) REVERT: q 35 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7722 (mm-30) REVERT: r 69 SER cc_start: 0.9572 (p) cc_final: 0.9285 (t) REVERT: r 78 ASN cc_start: 0.8985 (p0) cc_final: 0.8562 (p0) REVERT: r 99 ASN cc_start: 0.9029 (p0) cc_final: 0.8285 (p0) REVERT: r 121 ASN cc_start: 0.9672 (p0) cc_final: 0.9281 (p0) REVERT: s 31 LYS cc_start: 0.9007 (tttt) cc_final: 0.8794 (ttmm) REVERT: s 92 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8833 (ttmm) REVERT: t 98 GLN cc_start: 0.8851 (tp40) cc_final: 0.8543 (tp40) REVERT: u 96 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8490 (mp0) REVERT: v 72 VAL cc_start: 0.9046 (t) cc_final: 0.8841 (p) REVERT: v 92 ASN cc_start: 0.7776 (m-40) cc_final: 0.7502 (m110) REVERT: y 13 MET cc_start: 0.8502 (mtt) cc_final: 0.8279 (mtt) REVERT: y 19 GLN cc_start: 0.8526 (mt0) cc_final: 0.8238 (tp40) REVERT: z 88 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8110 (mtmt) REVERT: z 102 ARG cc_start: 0.9044 (ttm170) cc_final: 0.8675 (ttm170) outliers start: 334 outliers final: 264 residues processed: 1334 average time/residue: 1.0861 time to fit residues: 2572.6378 Evaluate side-chains 1391 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1105 time to evaluate : 6.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 279 ASN Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 338 THR Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 164 GLN Chi-restraints excluded: chain X residue 197 MET Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 206 ASP Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 233 LEU Chi-restraints excluded: chain W residue 327 LEU Chi-restraints excluded: chain W residue 380 SER Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 484 SER Chi-restraints excluded: chain W residue 509 THR Chi-restraints excluded: chain W residue 513 ARG Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 141 MET Chi-restraints excluded: chain V residue 184 HIS Chi-restraints excluded: chain V residue 255 ASP Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 337 ASP Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 LYS Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 4 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 138 GLN Chi-restraints excluded: chain a residue 165 THR 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 3 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 124 LYS Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 180 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 76 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 8 GLN Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 14 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 137 GLU Chi-restraints excluded: chain g residue 151 LEU Chi-restraints excluded: chain h residue 32 SER Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain i residue 22 ILE Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 107 THR Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 98 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 124 ILE Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain p residue 84 LEU Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 91 SER Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 86 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain t residue 105 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 626 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 604 optimal weight: 7.9990 chunk 304 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 643 optimal weight: 5.9990 chunk 689 optimal weight: 7.9990 chunk 500 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 795 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 127 GLN ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN M 39 GLN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 ASN m 57 HIS ** q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 49 ASN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 141698 Z= 0.282 Angle : 0.628 15.136 208480 Z= 0.322 Chirality : 0.037 0.479 26218 Planarity : 0.004 0.059 13510 Dihedral : 22.850 179.951 62020 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.30 % Favored : 91.54 % Rotamer: Outliers : 5.82 % Allowed : 18.51 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.21 % 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: -1.22 (0.10), residues: 6987 helix: 0.59 (0.11), residues: 2134 sheet: -0.59 (0.17), residues: 981 loop : -1.74 (0.09), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 95 HIS 0.008 0.001 HIS H 172 PHE 0.026 0.002 PHE X 34 TYR 0.031 0.002 TYR b 167 ARG 0.010 0.000 ARG R 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1121 time to evaluate : 6.917 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 253 LYS cc_start: 0.5287 (tptp) cc_final: 0.4366 (mtmm) REVERT: Y 283 PHE cc_start: 0.8495 (m-10) cc_final: 0.8185 (m-10) REVERT: Y 346 LEU cc_start: 0.8022 (tt) cc_final: 0.7668 (mt) REVERT: X 4 ARG cc_start: 0.8673 (ptp-170) cc_final: 0.8377 (ptp-170) REVERT: X 157 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7974 (mm-40) REVERT: X 162 HIS cc_start: 0.8931 (t70) cc_final: 0.8617 (t70) REVERT: W 206 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.5989 (t0) REVERT: W 327 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5760 (mp) REVERT: W 379 LEU cc_start: 0.7326 (tp) cc_final: 0.7003 (tt) REVERT: W 381 ASP cc_start: 0.8582 (m-30) cc_final: 0.7970 (t0) REVERT: W 490 ASP cc_start: 0.7852 (m-30) cc_final: 0.7512 (m-30) REVERT: V 36 TYR cc_start: 0.7265 (t80) cc_final: 0.6767 (t80) REVERT: V 129 GLN cc_start: 0.6944 (mm110) cc_final: 0.6527 (pm20) REVERT: V 142 GLN cc_start: 0.8155 (mm-40) cc_final: 0.6232 (pm20) REVERT: V 241 LYS cc_start: 0.8599 (ttpt) cc_final: 0.7834 (ttmm) REVERT: V 314 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7240 (mp10) REVERT: V 374 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8124 (mt) REVERT: V 379 TYR cc_start: 0.8929 (m-10) cc_final: 0.8636 (m-10) REVERT: D 60 LYS cc_start: 0.9221 (mttt) cc_final: 0.8798 (mtpt) REVERT: D 193 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8147 (pmm150) REVERT: D 231 SER cc_start: 0.9156 (m) cc_final: 0.8826 (p) REVERT: E 74 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6902 (mt-10) REVERT: E 114 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8447 (t) REVERT: E 274 SER cc_start: 0.9477 (m) cc_final: 0.9114 (p) REVERT: E 323 MET cc_start: 0.8934 (ttp) cc_final: 0.8730 (ttp) REVERT: F 193 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8304 (mtmm) REVERT: F 252 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8079 (tm-30) REVERT: G 69 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8802 (mt) REVERT: G 117 GLU cc_start: 0.8621 (pm20) cc_final: 0.8263 (pm20) REVERT: H 97 ASN cc_start: 0.8472 (t0) cc_final: 0.8233 (t0) REVERT: I 180 SER cc_start: 0.6846 (OUTLIER) cc_final: 0.6613 (p) REVERT: I 189 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8870 (tp) REVERT: J 61 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: J 69 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8383 (mp) REVERT: J 130 TYR cc_start: 0.8141 (m-80) cc_final: 0.7914 (m-80) REVERT: J 214 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8868 (tp) REVERT: K 86 TYR cc_start: 0.9137 (m-80) cc_final: 0.8711 (m-80) REVERT: K 113 GLU cc_start: 0.8110 (tt0) cc_final: 0.7617 (tm-30) REVERT: K 118 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9306 (tp) REVERT: M 25 GLU cc_start: 0.7609 (pm20) cc_final: 0.7275 (tp30) REVERT: M 43 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: M 126 ASP cc_start: 0.7546 (m-30) cc_final: 0.6765 (t0) REVERT: O 93 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8738 (mttm) REVERT: O 114 ASP cc_start: 0.9059 (t70) cc_final: 0.8794 (t70) REVERT: R 32 GLN cc_start: 0.8958 (mt0) cc_final: 0.8740 (mt0) REVERT: a 11 GLN cc_start: 0.8598 (tp40) cc_final: 0.7935 (tp40) REVERT: a 138 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: a 142 ILE cc_start: 0.9577 (mm) cc_final: 0.9355 (mm) REVERT: b 168 TYR cc_start: 0.9446 (t80) cc_final: 0.8937 (t80) REVERT: c 92 GLN cc_start: 0.8362 (pt0) cc_final: 0.7793 (tm-30) REVERT: d 23 ASN cc_start: 0.8977 (t0) cc_final: 0.8525 (t0) REVERT: d 155 MET cc_start: 0.8744 (tpt) cc_final: 0.8262 (tpp) REVERT: f 7 TYR cc_start: 0.9481 (m-80) cc_final: 0.8836 (m-80) REVERT: f 66 GLU cc_start: 0.8032 (tp30) cc_final: 0.7801 (tp30) REVERT: f 124 LEU cc_start: 0.9252 (mt) cc_final: 0.8961 (mp) REVERT: g 58 GLN cc_start: 0.9313 (tp-100) cc_final: 0.9029 (tp40) REVERT: g 68 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8893 (p) REVERT: h 32 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8697 (t) REVERT: h 35 LYS cc_start: 0.9022 (tptp) cc_final: 0.8583 (tppt) REVERT: h 40 HIS cc_start: 0.7733 (m90) cc_final: 0.7371 (m90) REVERT: h 87 ASN cc_start: 0.8603 (m110) cc_final: 0.8302 (m110) REVERT: i 11 PHE cc_start: 0.8369 (t80) cc_final: 0.8047 (t80) REVERT: j 23 ARG cc_start: 0.8619 (ttp80) cc_final: 0.8380 (ttp80) REVERT: j 26 SER cc_start: 0.9292 (m) cc_final: 0.8982 (p) REVERT: j 32 GLN cc_start: 0.9378 (tm-30) cc_final: 0.8927 (tm-30) REVERT: k 54 TYR cc_start: 0.8587 (p90) cc_final: 0.8204 (p90) REVERT: k 73 MET cc_start: 0.8916 (mmm) cc_final: 0.8682 (mmm) REVERT: k 80 ASN cc_start: 0.8920 (t0) cc_final: 0.8526 (t0) REVERT: l 38 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7718 (tm-30) REVERT: l 42 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: l 91 ASN cc_start: 0.9345 (p0) cc_final: 0.9023 (p0) REVERT: l 114 ASP cc_start: 0.8749 (m-30) cc_final: 0.8123 (m-30) REVERT: m 97 SER cc_start: 0.8902 (m) cc_final: 0.8579 (t) REVERT: m 109 GLU cc_start: 0.7694 (mp0) cc_final: 0.7398 (mp0) REVERT: n 73 LEU cc_start: 0.9324 (tp) cc_final: 0.9076 (tp) REVERT: o 18 ARG cc_start: 0.8736 (mmm-85) cc_final: 0.8521 (tpp80) REVERT: o 41 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8544 (mtm-85) REVERT: q 35 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7743 (mm-30) REVERT: q 55 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8924 (tt) REVERT: r 69 SER cc_start: 0.9573 (p) cc_final: 0.9296 (t) REVERT: r 78 ASN cc_start: 0.9018 (p0) cc_final: 0.8599 (p0) REVERT: r 99 ASN cc_start: 0.9058 (p0) cc_final: 0.8355 (p0) REVERT: r 121 ASN cc_start: 0.9674 (p0) cc_final: 0.9275 (p0) REVERT: s 31 LYS cc_start: 0.9017 (tttt) cc_final: 0.8761 (ttmm) REVERT: s 92 LYS cc_start: 0.9044 (ttpp) cc_final: 0.8831 (ttmm) REVERT: t 98 GLN cc_start: 0.8855 (tp40) cc_final: 0.8564 (tp40) REVERT: u 43 LYS cc_start: 0.8269 (mptt) cc_final: 0.7783 (pttt) REVERT: u 96 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8469 (mp0) REVERT: y 13 MET cc_start: 0.8590 (mtt) cc_final: 0.8359 (mtt) REVERT: y 19 GLN cc_start: 0.8542 (mt0) cc_final: 0.8250 (tp40) REVERT: z 88 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8146 (mtmt) outliers start: 342 outliers final: 283 residues processed: 1315 average time/residue: 1.1160 time to fit residues: 2597.7670 Evaluate side-chains 1410 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1105 time to evaluate : 6.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 279 ASN Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 338 THR Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 197 MET Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 206 ASP Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 327 LEU Chi-restraints excluded: chain W residue 380 SER Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 484 SER Chi-restraints excluded: chain W residue 509 THR Chi-restraints excluded: chain W residue 513 ARG Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 114 ILE Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 141 MET Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 ASP Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 299 SER Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 337 ASP Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 193 LYS Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 61 GLN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain N residue 4 SER Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 93 ILE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 46 THR Chi-restraints excluded: chain R residue 60 CYS Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 19 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 138 GLN Chi-restraints excluded: chain a residue 165 THR 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 3 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 124 LYS Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 105 ARG Chi-restraints excluded: chain d residue 180 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 76 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 14 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 137 GLU Chi-restraints excluded: chain g residue 151 LEU Chi-restraints excluded: chain h residue 32 SER Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain i residue 22 ILE Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain j residue 19 THR Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain k residue 63 ILE Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 107 THR Chi-restraints excluded: chain m residue 33 SER Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 98 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 64 GLN Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 124 ILE Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain p residue 84 LEU Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 65 LYS Chi-restraints excluded: chain q residue 87 ASN Chi-restraints excluded: chain q residue 91 SER Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 86 THR Chi-restraints excluded: chain r residue 98 HIS Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 52 GLN Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain t residue 105 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 81 THR Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 26 SER Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain y residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 920 optimal weight: 4.9990 chunk 969 optimal weight: 6.9990 chunk 884 optimal weight: 9.9990 chunk 943 optimal weight: 3.9990 chunk 567 optimal weight: 10.0000 chunk 410 optimal weight: 7.9990 chunk 740 optimal weight: 40.0000 chunk 289 optimal weight: 10.0000 chunk 852 optimal weight: 0.0970 chunk 891 optimal weight: 10.0000 chunk 939 optimal weight: 3.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 21 ASN ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 31 GLN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 GLN h 49 ASN r 49 ASN r 88 HIS ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 141698 Z= 0.238 Angle : 0.602 14.989 208480 Z= 0.309 Chirality : 0.036 0.455 26218 Planarity : 0.004 0.078 13510 Dihedral : 22.815 179.732 62020 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.90 % Favored : 91.94 % Rotamer: Outliers : 5.36 % Allowed : 18.98 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.19 % 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: 6987 helix: 0.68 (0.12), residues: 2137 sheet: -0.53 (0.17), residues: 977 loop : -1.71 (0.09), residues: 3873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 95 HIS 0.010 0.001 HIS H 172 PHE 0.023 0.001 PHE X 34 TYR 0.026 0.001 TYR b 167 ARG 0.010 0.000 ARG R 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1456 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1141 time to evaluate : 6.570 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 253 LYS cc_start: 0.5225 (tptp) cc_final: 0.4346 (mtmm) REVERT: Y 283 PHE cc_start: 0.8511 (m-10) cc_final: 0.8231 (m-10) REVERT: Y 289 LYS cc_start: 0.5781 (tttm) cc_final: 0.4771 (tppt) REVERT: Y 346 LEU cc_start: 0.8084 (tt) cc_final: 0.7710 (mt) REVERT: X 4 ARG cc_start: 0.8731 (ptp-170) cc_final: 0.8474 (ptp-170) REVERT: X 61 ARG cc_start: 0.8814 (mmp80) cc_final: 0.8009 (tpp80) REVERT: X 157 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7944 (mm-40) REVERT: X 162 HIS cc_start: 0.8905 (t70) cc_final: 0.8589 (t70) REVERT: W 206 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.5734 (t0) REVERT: W 327 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.5754 (mp) REVERT: W 379 LEU cc_start: 0.7264 (tp) cc_final: 0.6938 (tt) REVERT: W 381 ASP cc_start: 0.8538 (m-30) cc_final: 0.7864 (t0) REVERT: W 384 MET cc_start: 0.7401 (ttp) cc_final: 0.6912 (ttm) REVERT: W 490 ASP cc_start: 0.7858 (m-30) cc_final: 0.7513 (m-30) REVERT: V 36 TYR cc_start: 0.7116 (t80) cc_final: 0.6603 (t80) REVERT: V 129 GLN cc_start: 0.7072 (mm110) cc_final: 0.6684 (pm20) REVERT: V 142 GLN cc_start: 0.8108 (mm-40) cc_final: 0.6210 (pm20) REVERT: V 222 HIS cc_start: 0.9113 (p-80) cc_final: 0.8782 (p90) REVERT: V 227 GLU cc_start: 0.8384 (pm20) cc_final: 0.7369 (pm20) REVERT: V 241 LYS cc_start: 0.8610 (ttpt) cc_final: 0.7579 (ttpp) REVERT: V 314 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: V 374 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8212 (mt) REVERT: V 379 TYR cc_start: 0.8930 (m-10) cc_final: 0.8622 (m-10) REVERT: D 60 LYS cc_start: 0.9188 (mttt) cc_final: 0.8745 (mtpt) REVERT: D 180 LEU cc_start: 0.9375 (mt) cc_final: 0.9146 (mt) REVERT: D 193 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8222 (pmm150) REVERT: D 231 SER cc_start: 0.9153 (m) cc_final: 0.8844 (p) REVERT: E 74 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: E 114 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8448 (t) REVERT: E 270 ARG cc_start: 0.8740 (ttp80) cc_final: 0.7816 (tmm-80) REVERT: E 274 SER cc_start: 0.9452 (m) cc_final: 0.9071 (p) REVERT: E 323 MET cc_start: 0.8920 (ttp) cc_final: 0.8707 (ttp) REVERT: F 252 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 69 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8821 (mt) REVERT: G 117 GLU cc_start: 0.8589 (pm20) cc_final: 0.8243 (pm20) REVERT: H 48 ARG cc_start: 0.8577 (mtm110) cc_final: 0.8354 (mtm110) REVERT: H 97 ASN cc_start: 0.8550 (t0) cc_final: 0.8335 (t0) REVERT: H 137 ASP cc_start: 0.8275 (m-30) cc_final: 0.7891 (m-30) REVERT: I 180 SER cc_start: 0.6998 (OUTLIER) cc_final: 0.6744 (p) REVERT: I 189 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8857 (tp) REVERT: J 61 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: J 69 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8393 (mp) REVERT: J 214 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8836 (tp) REVERT: K 52 LEU cc_start: 0.8869 (mm) cc_final: 0.8586 (mm) REVERT: K 86 TYR cc_start: 0.9118 (m-80) cc_final: 0.8671 (m-80) REVERT: K 113 GLU cc_start: 0.8094 (tt0) cc_final: 0.7576 (tm-30) REVERT: K 118 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9294 (tt) REVERT: M 11 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7351 (p0) REVERT: M 43 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: M 126 ASP cc_start: 0.7605 (m-30) cc_final: 0.6839 (t0) REVERT: N 140 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.9057 (t) REVERT: O 24 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8726 (ttpp) REVERT: O 93 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8715 (mttm) REVERT: O 114 ASP cc_start: 0.8975 (t70) cc_final: 0.8678 (t70) REVERT: R 32 GLN cc_start: 0.8919 (mt0) cc_final: 0.8702 (mt0) REVERT: a 11 GLN cc_start: 0.8566 (tp40) cc_final: 0.7899 (tp40) REVERT: a 138 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8300 (mp10) REVERT: a 142 ILE cc_start: 0.9574 (mm) cc_final: 0.9354 (mm) REVERT: b 168 TYR cc_start: 0.9429 (t80) cc_final: 0.9074 (t80) REVERT: c 92 GLN cc_start: 0.8305 (pt0) cc_final: 0.7729 (tm-30) REVERT: d 23 ASN cc_start: 0.8933 (t0) cc_final: 0.8505 (t0) REVERT: d 155 MET cc_start: 0.8709 (tpt) cc_final: 0.8199 (tpp) REVERT: f 7 TYR cc_start: 0.9486 (m-80) cc_final: 0.8851 (m-80) REVERT: f 66 GLU cc_start: 0.7990 (tp30) cc_final: 0.7744 (tp30) REVERT: f 85 SER cc_start: 0.8923 (m) cc_final: 0.8637 (t) REVERT: f 124 LEU cc_start: 0.9236 (mt) cc_final: 0.8938 (mp) REVERT: g 58 GLN cc_start: 0.9291 (tp-100) cc_final: 0.9040 (tp40) REVERT: g 68 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8932 (p) REVERT: g 136 ARG cc_start: 0.8674 (pmm-80) cc_final: 0.8360 (ptp90) REVERT: g 138 SER cc_start: 0.9043 (p) cc_final: 0.8731 (m) REVERT: h 32 SER cc_start: 0.8942 (t) cc_final: 0.8724 (t) REVERT: h 35 LYS cc_start: 0.9017 (tptp) cc_final: 0.8590 (tppt) REVERT: h 36 TYR cc_start: 0.9036 (t80) cc_final: 0.8396 (t80) REVERT: h 40 HIS cc_start: 0.7813 (m90) cc_final: 0.7453 (m90) REVERT: h 87 ASN cc_start: 0.8615 (m110) cc_final: 0.8315 (m110) REVERT: i 11 PHE cc_start: 0.8380 (t80) cc_final: 0.8064 (t80) REVERT: j 23 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8340 (ttp80) REVERT: j 26 SER cc_start: 0.9362 (m) cc_final: 0.8942 (p) REVERT: j 32 GLN cc_start: 0.9375 (tm-30) cc_final: 0.8928 (tm-30) REVERT: k 54 TYR cc_start: 0.8543 (p90) cc_final: 0.8132 (p90) REVERT: k 73 MET cc_start: 0.8889 (mmm) cc_final: 0.8675 (mmm) REVERT: k 80 ASN cc_start: 0.8943 (t0) cc_final: 0.8495 (t0) REVERT: l 38 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7576 (tm-30) REVERT: l 42 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: l 91 ASN cc_start: 0.9328 (p0) cc_final: 0.9062 (p0) REVERT: l 114 ASP cc_start: 0.8701 (m-30) cc_final: 0.8066 (m-30) REVERT: m 109 GLU cc_start: 0.7730 (mp0) cc_final: 0.7403 (mp0) REVERT: n 32 ARG cc_start: 0.9274 (mtt-85) cc_final: 0.8409 (mtt90) REVERT: n 73 LEU cc_start: 0.9308 (tp) cc_final: 0.9052 (tp) REVERT: o 21 ILE cc_start: 0.8541 (mm) cc_final: 0.7842 (mm) REVERT: o 41 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8577 (mtm-85) REVERT: p 47 ASN cc_start: 0.9096 (p0) cc_final: 0.8855 (p0) REVERT: q 35 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7790 (mm-30) REVERT: q 55 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9054 (tt) REVERT: r 69 SER cc_start: 0.9568 (p) cc_final: 0.9301 (t) REVERT: r 78 ASN cc_start: 0.8984 (p0) cc_final: 0.8574 (p0) REVERT: r 99 ASN cc_start: 0.9022 (p0) cc_final: 0.8269 (p0) REVERT: r 121 ASN cc_start: 0.9663 (p0) cc_final: 0.9257 (p0) REVERT: u 43 LYS cc_start: 0.8325 (mptt) cc_final: 0.7826 (pttt) REVERT: u 96 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8532 (mp0) REVERT: v 62 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7334 (mtm-85) REVERT: y 19 GLN cc_start: 0.8525 (mt0) cc_final: 0.8253 (tp40) REVERT: z 88 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8101 (mtmt) outliers start: 315 outliers final: 265 residues processed: 1320 average time/residue: 1.1059 time to fit residues: 2590.6268 Evaluate side-chains 1390 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1102 time to evaluate : 6.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 279 ASN Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 112 ASP Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 164 GLN Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 135 ILE Chi-restraints excluded: chain W residue 206 ASP Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 327 LEU Chi-restraints excluded: chain W residue 380 SER Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 484 SER Chi-restraints excluded: chain W residue 509 THR Chi-restraints excluded: chain W residue 513 ARG Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 114 ILE Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 249 VAL Chi-restraints excluded: chain V residue 255 ASP Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 299 SER Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 337 ASP Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU 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 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 61 GLN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain Q residue 29 LYS Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 42 CYS Chi-restraints excluded: chain R residue 46 THR 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 19 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 138 GLN Chi-restraints excluded: chain a residue 165 THR 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 3 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 124 LYS Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 94 PHE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 30 SER Chi-restraints excluded: chain e residue 76 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 8 GLN Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 100 VAL Chi-restraints excluded: chain f residue 105 THR Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 14 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 151 LEU Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain h residue 38 ILE Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 84 LEU Chi-restraints excluded: chain i residue 22 ILE Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 107 THR Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 98 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 125 VAL Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 65 LYS Chi-restraints excluded: chain q residue 91 SER Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 86 THR Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 52 GLN Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 62 ARG Chi-restraints excluded: chain v residue 81 THR Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 619 optimal weight: 3.9990 chunk 997 optimal weight: 0.7980 chunk 608 optimal weight: 10.0000 chunk 473 optimal weight: 9.9990 chunk 693 optimal weight: 2.9990 chunk 1046 optimal weight: 9.9990 chunk 962 optimal weight: 5.9990 chunk 832 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 643 optimal weight: 6.9990 chunk 510 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS ** E 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 ASN q 57 GLN r 49 ASN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 141698 Z= 0.225 Angle : 0.600 15.155 208480 Z= 0.308 Chirality : 0.036 0.452 26218 Planarity : 0.004 0.078 13510 Dihedral : 22.798 179.708 62020 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 4.98 % Allowed : 19.63 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.18 % 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: 6987 helix: 0.74 (0.12), residues: 2130 sheet: -0.52 (0.17), residues: 965 loop : -1.69 (0.09), residues: 3892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 95 HIS 0.010 0.001 HIS H 172 PHE 0.025 0.001 PHE X 34 TYR 0.035 0.002 TYR b 167 ARG 0.013 0.000 ARG R 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1143 time to evaluate : 6.679 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: Y 283 PHE cc_start: 0.8530 (m-10) cc_final: 0.8261 (m-10) REVERT: Y 289 LYS cc_start: 0.5799 (tttm) cc_final: 0.4888 (tptp) REVERT: Y 298 LYS cc_start: 0.8820 (pttp) cc_final: 0.8558 (pptt) REVERT: Y 346 LEU cc_start: 0.8087 (tt) cc_final: 0.7723 (mt) REVERT: X 4 ARG cc_start: 0.8738 (ptp-170) cc_final: 0.8486 (ptp-170) REVERT: X 57 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8413 (mtm-85) REVERT: X 61 ARG cc_start: 0.8778 (mmp80) cc_final: 0.8033 (tpp80) REVERT: X 157 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7983 (mm-40) REVERT: X 162 HIS cc_start: 0.8900 (t70) cc_final: 0.8559 (t70) REVERT: X 218 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8235 (mt) REVERT: W 206 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.5642 (t0) REVERT: W 327 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.5743 (mp) REVERT: W 379 LEU cc_start: 0.7253 (tp) cc_final: 0.6938 (tt) REVERT: W 381 ASP cc_start: 0.8531 (m-30) cc_final: 0.7829 (t0) REVERT: W 490 ASP cc_start: 0.7860 (m-30) cc_final: 0.7511 (m-30) REVERT: V 36 TYR cc_start: 0.7052 (t80) cc_final: 0.6561 (t80) REVERT: V 129 GLN cc_start: 0.7106 (mm110) cc_final: 0.6726 (pm20) REVERT: V 222 HIS cc_start: 0.9107 (p-80) cc_final: 0.8774 (p90) REVERT: V 241 LYS cc_start: 0.8598 (ttpt) cc_final: 0.7996 (ttmm) REVERT: V 314 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: V 374 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8219 (mt) REVERT: V 379 TYR cc_start: 0.8917 (m-10) cc_final: 0.8609 (m-10) REVERT: D 60 LYS cc_start: 0.9218 (mttt) cc_final: 0.8789 (mtpt) REVERT: D 193 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8220 (pmm150) REVERT: D 231 SER cc_start: 0.9148 (m) cc_final: 0.8831 (p) REVERT: E 67 PHE cc_start: 0.8596 (m-80) cc_final: 0.8252 (m-80) REVERT: E 74 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: E 114 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8441 (t) REVERT: E 274 SER cc_start: 0.9455 (m) cc_final: 0.9068 (p) REVERT: E 323 MET cc_start: 0.8890 (ttp) cc_final: 0.8678 (ttp) REVERT: F 252 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8062 (tm-30) REVERT: G 69 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8824 (mt) REVERT: G 117 GLU cc_start: 0.8588 (pm20) cc_final: 0.8241 (pm20) REVERT: H 48 ARG cc_start: 0.8562 (mtm110) cc_final: 0.8347 (mtm110) REVERT: H 97 ASN cc_start: 0.8481 (t0) cc_final: 0.8279 (t0) REVERT: I 189 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8858 (tp) REVERT: J 61 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: J 69 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8386 (mp) REVERT: J 214 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8818 (tp) REVERT: K 52 LEU cc_start: 0.8939 (mm) cc_final: 0.8642 (mm) REVERT: K 86 TYR cc_start: 0.9113 (m-80) cc_final: 0.8682 (m-80) REVERT: K 113 GLU cc_start: 0.8078 (tt0) cc_final: 0.7547 (tm-30) REVERT: K 118 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9290 (tt) REVERT: M 11 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7350 (p0) REVERT: M 43 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: M 126 ASP cc_start: 0.7590 (m-30) cc_final: 0.6823 (t0) REVERT: N 140 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.9050 (t) REVERT: O 24 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8719 (ttpp) REVERT: O 93 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8744 (mttm) REVERT: O 114 ASP cc_start: 0.8967 (t70) cc_final: 0.8658 (t70) REVERT: R 32 GLN cc_start: 0.8905 (mt0) cc_final: 0.8701 (mt0) REVERT: a 11 GLN cc_start: 0.8572 (tp40) cc_final: 0.7909 (tp40) REVERT: a 138 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8308 (mp10) REVERT: a 142 ILE cc_start: 0.9572 (mm) cc_final: 0.9361 (mm) REVERT: b 49 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7681 (ttm-80) REVERT: b 168 TYR cc_start: 0.9441 (t80) cc_final: 0.9015 (t80) REVERT: c 31 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7635 (mm-30) REVERT: c 92 GLN cc_start: 0.8289 (pt0) cc_final: 0.7701 (tm-30) REVERT: d 23 ASN cc_start: 0.8940 (t0) cc_final: 0.8498 (t0) REVERT: d 155 MET cc_start: 0.8694 (tpt) cc_final: 0.8200 (tpp) REVERT: f 7 TYR cc_start: 0.9474 (m-80) cc_final: 0.8866 (m-80) REVERT: f 66 GLU cc_start: 0.7911 (tp30) cc_final: 0.7673 (tp30) REVERT: f 124 LEU cc_start: 0.9241 (mt) cc_final: 0.8938 (mp) REVERT: g 58 GLN cc_start: 0.9277 (tp-100) cc_final: 0.9004 (tp40) REVERT: g 68 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8973 (p) REVERT: g 136 ARG cc_start: 0.8660 (pmm-80) cc_final: 0.8356 (ptp90) REVERT: g 138 SER cc_start: 0.9044 (p) cc_final: 0.8742 (m) REVERT: h 32 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8760 (t) REVERT: h 35 LYS cc_start: 0.9022 (tptp) cc_final: 0.8586 (tppt) REVERT: h 87 ASN cc_start: 0.8576 (m110) cc_final: 0.8300 (m110) REVERT: i 11 PHE cc_start: 0.8372 (t80) cc_final: 0.8052 (t80) REVERT: i 27 ASP cc_start: 0.8671 (p0) cc_final: 0.8324 (p0) REVERT: j 23 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8328 (ttp80) REVERT: j 26 SER cc_start: 0.9350 (m) cc_final: 0.8940 (p) REVERT: k 39 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7948 (ptpp) REVERT: k 54 TYR cc_start: 0.8565 (p90) cc_final: 0.8178 (p90) REVERT: k 73 MET cc_start: 0.8919 (mmm) cc_final: 0.8687 (mmm) REVERT: k 80 ASN cc_start: 0.8943 (t0) cc_final: 0.8507 (t0) REVERT: l 38 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7542 (tm-30) REVERT: l 42 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: l 91 ASN cc_start: 0.9323 (p0) cc_final: 0.9080 (p0) REVERT: l 114 ASP cc_start: 0.8810 (m-30) cc_final: 0.8317 (m-30) REVERT: m 97 SER cc_start: 0.9039 (m) cc_final: 0.8762 (t) REVERT: m 99 GLU cc_start: 0.8682 (pm20) cc_final: 0.8185 (pm20) REVERT: m 109 GLU cc_start: 0.7724 (mp0) cc_final: 0.7417 (mp0) REVERT: n 32 ARG cc_start: 0.9258 (mtt-85) cc_final: 0.8366 (mtt90) REVERT: n 64 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: n 73 LEU cc_start: 0.9307 (tp) cc_final: 0.9055 (tp) REVERT: o 21 ILE cc_start: 0.8574 (mm) cc_final: 0.7905 (mm) REVERT: o 41 ARG cc_start: 0.8885 (ttm110) cc_final: 0.8549 (mtm-85) REVERT: p 47 ASN cc_start: 0.9087 (p0) cc_final: 0.8852 (p0) REVERT: q 6 ASP cc_start: 0.7003 (m-30) cc_final: 0.6761 (m-30) REVERT: q 35 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7788 (mm-30) REVERT: q 55 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9052 (tt) REVERT: r 69 SER cc_start: 0.9551 (p) cc_final: 0.9285 (t) REVERT: r 78 ASN cc_start: 0.9005 (p0) cc_final: 0.8606 (p0) REVERT: r 99 ASN cc_start: 0.9012 (p0) cc_final: 0.8260 (p0) REVERT: r 121 ASN cc_start: 0.9661 (p0) cc_final: 0.9254 (p0) REVERT: u 43 LYS cc_start: 0.8320 (mptt) cc_final: 0.7823 (pttt) REVERT: u 96 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8531 (mp0) REVERT: y 19 GLN cc_start: 0.8516 (mt0) cc_final: 0.8249 (tp40) REVERT: z 88 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8142 (mttt) outliers start: 293 outliers final: 253 residues processed: 1317 average time/residue: 1.1059 time to fit residues: 2592.5023 Evaluate side-chains 1399 residues out of total 5966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1121 time to evaluate : 6.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 235 CYS Chi-restraints excluded: chain Y residue 279 ASN Chi-restraints excluded: chain Y residue 307 CYS Chi-restraints excluded: chain Y residue 338 THR Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 114 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 164 GLN Chi-restraints excluded: chain X residue 211 THR Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain W residue 133 ASP Chi-restraints excluded: chain W residue 206 ASP Chi-restraints excluded: chain W residue 218 LEU Chi-restraints excluded: chain W residue 327 LEU Chi-restraints excluded: chain W residue 380 SER Chi-restraints excluded: chain W residue 383 VAL Chi-restraints excluded: chain W residue 392 VAL Chi-restraints excluded: chain W residue 428 ILE Chi-restraints excluded: chain W residue 484 SER Chi-restraints excluded: chain W residue 509 THR Chi-restraints excluded: chain W residue 513 ARG Chi-restraints excluded: chain W residue 524 TYR Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 89 LEU Chi-restraints excluded: chain V residue 114 ILE Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 255 ASP Chi-restraints excluded: chain V residue 279 ILE Chi-restraints excluded: chain V residue 299 SER Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 314 GLN Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 337 ASP Chi-restraints excluded: chain V residue 340 VAL Chi-restraints excluded: chain V residue 352 VAL Chi-restraints excluded: chain V residue 363 CYS Chi-restraints excluded: chain V residue 374 ILE Chi-restraints excluded: chain V residue 396 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 212 ASN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 289 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 194 TYR Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 226 GLU Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 178 ASN Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 260 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain I residue 113 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 182 ASP Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain J residue 36 ILE Chi-restraints excluded: chain J residue 61 GLN Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 126 SER Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 160 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 219 ASP Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 102 ASN Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 11 ASP Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 43 GLN Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 128 TYR Chi-restraints excluded: chain M residue 167 TYR Chi-restraints excluded: chain M residue 171 VAL Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain N residue 5 LYS Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 155 GLU Chi-restraints excluded: chain N residue 169 THR Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 80 THR Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 105 GLN Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain R residue 10 ILE Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 31 ILE 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 19 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 115 VAL Chi-restraints excluded: chain a residue 138 GLN Chi-restraints excluded: chain a residue 165 THR 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 3 VAL Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 118 VAL Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain b residue 144 SER Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 36 ILE Chi-restraints excluded: chain c residue 42 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 119 VAL Chi-restraints excluded: chain c residue 124 LYS Chi-restraints excluded: chain c residue 148 LEU Chi-restraints excluded: chain c residue 169 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 93 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 180 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 76 SER Chi-restraints excluded: chain e residue 84 THR Chi-restraints excluded: chain e residue 127 SER Chi-restraints excluded: chain f residue 8 GLN Chi-restraints excluded: chain f residue 16 THR Chi-restraints excluded: chain f residue 24 LEU Chi-restraints excluded: chain f residue 48 LEU Chi-restraints excluded: chain f residue 58 ILE Chi-restraints excluded: chain f residue 61 ILE Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 74 ASN Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 135 VAL Chi-restraints excluded: chain f residue 160 THR Chi-restraints excluded: chain g residue 14 MET Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 84 TYR Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 137 GLU Chi-restraints excluded: chain h residue 32 SER Chi-restraints excluded: chain h residue 37 LEU Chi-restraints excluded: chain h residue 50 LEU Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain i residue 73 VAL Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain k residue 39 LYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain k residue 135 ILE Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 107 THR Chi-restraints excluded: chain m residue 46 ILE Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 THR Chi-restraints excluded: chain m residue 134 LEU Chi-restraints excluded: chain n residue 22 ILE Chi-restraints excluded: chain n residue 58 MET Chi-restraints excluded: chain n residue 64 GLN Chi-restraints excluded: chain n residue 72 VAL Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 88 ASP Chi-restraints excluded: chain n residue 125 VAL Chi-restraints excluded: chain o residue 27 TYR Chi-restraints excluded: chain o residue 35 VAL Chi-restraints excluded: chain p residue 10 ILE Chi-restraints excluded: chain p residue 11 ASN Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 16 LEU Chi-restraints excluded: chain p residue 74 ASN Chi-restraints excluded: chain q residue 55 LEU Chi-restraints excluded: chain q residue 65 LYS Chi-restraints excluded: chain q residue 91 SER Chi-restraints excluded: chain q residue 96 VAL Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 14 THR Chi-restraints excluded: chain r residue 59 SER Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain r residue 84 THR Chi-restraints excluded: chain r residue 86 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 37 THR Chi-restraints excluded: chain s residue 71 VAL Chi-restraints excluded: chain s residue 84 THR Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 98 VAL Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 40 THR Chi-restraints excluded: chain t residue 47 CYS Chi-restraints excluded: chain t residue 51 LEU Chi-restraints excluded: chain t residue 52 GLN Chi-restraints excluded: chain t residue 83 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain t residue 104 VAL Chi-restraints excluded: chain u residue 11 THR Chi-restraints excluded: chain u residue 15 GLU Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 51 SER Chi-restraints excluded: chain v residue 88 GLU Chi-restraints excluded: chain w residue 5 THR Chi-restraints excluded: chain w residue 22 CYS Chi-restraints excluded: chain w residue 58 THR Chi-restraints excluded: chain w residue 59 THR Chi-restraints excluded: chain w residue 72 ARG Chi-restraints excluded: chain x residue 24 THR Chi-restraints excluded: chain x residue 45 VAL Chi-restraints excluded: chain x residue 56 ILE Chi-restraints excluded: chain x residue 68 SER Chi-restraints excluded: chain y residue 6 SER Chi-restraints excluded: chain y residue 27 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1050 random chunks: chunk 661 optimal weight: 9.9990 chunk 887 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 768 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 231 optimal weight: 30.0000 chunk 834 optimal weight: 3.9990 chunk 349 optimal weight: 0.0030 chunk 856 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 6.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 364 HIS F 234 ASN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** I 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 ASN ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN ** a 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 97 ASN ** c 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 ASN r 49 ASN ** s 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.078158 restraints weight = 300571.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.080288 restraints weight = 116727.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 73)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.081623 restraints weight = 67726.357| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 141698 Z= 0.353 Angle : 0.670 14.921 208480 Z= 0.339 Chirality : 0.039 0.455 26218 Planarity : 0.005 0.091 13510 Dihedral : 22.792 179.868 62020 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.89 % Favored : 90.95 % Rotamer: Outliers : 5.22 % Allowed : 19.66 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.36 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.10), residues: 6987 helix: 0.60 (0.11), residues: 2144 sheet: -0.65 (0.17), residues: 968 loop : -1.78 (0.09), residues: 3875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 95 HIS 0.015 0.001 HIS H 172 PHE 0.023 0.002 PHE X 34 TYR 0.034 0.002 TYR c 139 ARG 0.014 0.001 ARG R 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37613.42 seconds wall clock time: 654 minutes 11.03 seconds (39251.03 seconds total)