Starting phenix.real_space_refine on Tue Apr 16 22:36:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu7_42566/04_2024/8uu7_42566_updated.pdb" } resolution = 3.2 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= -0.003 sd= 1.092 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4616 5.49 5 Mg 392 5.21 5 S 137 5.16 5 C 72922 2.51 5 N 26842 2.21 5 O 40338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 187": "OE1" <-> "OE2" Residue "d TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 168": "OD1" <-> "OD2" Residue "e GLU 14": "OE1" <-> "OE2" Residue "e ASP 143": "OD1" <-> "OD2" Residue "f GLU 19": "OE1" <-> "OE2" Residue "f ASP 28": "OD1" <-> "OD2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "g ASP 11": "OD1" <-> "OD2" Residue "g ASP 48": "OD1" <-> "OD2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ASP 140": "OD1" <-> "OD2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h GLU 126": "OE1" <-> "OE2" Residue "i ASP 37": "OD1" <-> "OD2" Residue "i GLU 46": "OE1" <-> "OE2" Residue "i TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 23": "OE1" <-> "OE2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 99": "OE1" <-> "OE2" Residue "n GLU 25": "OE1" <-> "OE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "q ASP 17": "OD1" <-> "OD2" Residue "v GLU 22": "OE1" <-> "OE2" Residue "v PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L GLU 132": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 105": "OE1" <-> "OE2" Residue "P ASP 101": "OD1" <-> "OD2" Residue "Q ASP 46": "OD1" <-> "OD2" Residue "R ASP 6": "OD1" <-> "OD2" Residue "R PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 102": "OD1" <-> "OD2" Residue "U ASP 68": "OD1" <-> "OD2" Residue "U ASP 70": "OD1" <-> "OD2" Residue "U ASP 82": "OD1" <-> "OD2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "W ASP 72": "OD1" <-> "OD2" Residue "2 ASP 39": "OD1" <-> "OD2" Residue "3 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 8": "OE1" <-> "OE2" Residue "5 GLU 25": "OE1" <-> "OE2" Residue "5 GLU 31": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 145251 Number of models: 1 Model: "" Number of chains: 70 Chain: "a" Number of atoms: 32515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1516, 32515 Classifications: {'RNA': 1516} Modifications used: {'rna2p_pur': 109, 'rna2p_pyr': 77, 'rna3p_pur': 751, 'rna3p_pyr': 579} Link IDs: {'rna2p': 186, 'rna3p': 1329} Chain breaks: 3 Chain: "b" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1624 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain: "d" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1592 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "e" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1154 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "f" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 781 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "g" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1186 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 144} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1022 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "j" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "k" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 837 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "l" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1049 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 126} Chain: "m" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "n" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 490 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 727 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 711 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "q" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "s" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 655 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "t" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 619 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "y" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1585 Classifications: {'RNA': 74} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 6, 'rna3p_pur': 32, 'rna3p_pyr': 26} Link IDs: {'rna2p': 9, 'rna3p': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'MIA%rna3p:plan-2': 1, 'MIA%rna3p:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "v" Number of atoms: 3254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3254 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 405} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "w" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 828 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "A" Number of atoms: 62493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2909, 62493 Classifications: {'RNA': 2909} Modifications used: {'rna2p_pur': 309, 'rna2p_pyr': 151, 'rna3p_pur': 1399, 'rna3p_pyr': 1050} Link IDs: {'rna2p': 460, 'rna3p': 2448} Chain breaks: 3 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2428 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 13, 'rna3p_pur': 54, 'rna3p_pyr': 45} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "C" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2108 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "D" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1583 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1579 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain: "F" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1356 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1128 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1104 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "O" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1063 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "P" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 982 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "Q" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain: "R" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 909 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "S" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 944 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "T" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 785 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "U" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 855 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "V" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 751 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "W" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 775 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "Y" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 585 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "Z" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 462 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "2" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "3" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 511 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "4" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 425 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "5" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 408 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "6" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 365 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "7" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 520 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "8" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "a" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 169 Unusual residues: {' MG': 169} Classifications: {'undetermined': 169} Link IDs: {None: 168} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 212 Unusual residues: {' MG': 212} Classifications: {'undetermined': 212} Link IDs: {None: 211} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 46417 SG CYS n 24 116.239 72.171 51.737 1.00 42.70 S ATOM 46443 SG CYS n 27 117.108 75.397 53.576 1.00 45.69 S ATOM 46550 SG CYS n 40 113.743 73.691 54.258 1.00 41.52 S ATOM 46575 SG CYS n 43 114.288 75.366 50.965 1.00 41.21 S ATOM A0X7H SG CYS 4 30 145.204 200.820 198.768 1.00103.45 S ATOM A0X81 SG CYS 4 33 141.857 200.220 200.436 1.00109.75 S ATOM A0XAC SG CYS 4 43 142.089 200.417 196.507 1.00104.43 S ATOM A0XAY SG CYS 4 46 142.158 203.358 198.700 1.00112.96 S ATOM A0XEN SG CYS 5 9 88.552 57.316 179.721 1.00 90.50 S ATOM A0XF9 SG CYS 5 12 87.170 57.761 183.355 1.00 94.60 S ATOM A0XL0 SG CYS 5 36 90.967 58.198 182.648 1.00 90.75 S ATOM A0YEX SG CYS 8 11 182.298 112.806 133.450 1.00 98.53 S ATOM A0YFL SG CYS 8 14 181.080 114.089 136.874 1.00 99.12 S ATOM A0YIH SG CYS 8 27 183.350 116.273 134.740 1.00 99.31 S Time building chain proxies: 53.80, per 1000 atoms: 0.37 Number of scatterers: 145251 At special positions: 0 Unit cell: (232.05, 252.45, 280.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 137 16.00 P 4616 15.00 Mg 392 11.99 O 40338 8.00 N 26842 7.00 C 72922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 56.01 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 32 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb=" ZN n 102 " pdb="ZN ZN n 102 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 102 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 102 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 102 " - pdb=" SG CYS n 40 " Number of angles added : 15 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10724 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 172 helices and 71 sheets defined 38.0% alpha, 18.3% beta 1574 base pairs and 2406 stacking pairs defined. Time for finding SS restraints: 72.84 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.510A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TYR b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 32' Processing helix chain 'b' and resid 42 through 62 removed outlier: 3.512A pdb=" N ASP b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG b 58 " --> pdb=" O PHE b 54 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU b 59 " --> pdb=" O ASN b 55 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL b 60 " --> pdb=" O PHE b 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA b 61 " --> pdb=" O MET b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 4.256A pdb=" N GLU b 83 " --> pdb=" O SER b 79 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE b 85 " --> pdb=" O ARG b 81 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG b 86 " --> pdb=" O ASP b 82 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER b 87 " --> pdb=" O GLU b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 3.552A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU b 121 " --> pdb=" O ILE b 117 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP b 123 " --> pdb=" O LYS b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 149 removed outlier: 3.529A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 4.377A pdb=" N ARG b 170 " --> pdb=" O PRO b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 removed outlier: 3.655A pdb=" N LYS b 178 " --> pdb=" O ALA b 174 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU b 179 " --> pdb=" O GLU b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.115A pdb=" N ILE b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 225 removed outlier: 3.717A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS b 216 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE b 221 " --> pdb=" O MET b 217 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLU b 223 " --> pdb=" O ASP b 219 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN b 225 " --> pdb=" O ILE b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.358A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.693A pdb=" N ARG c 45 " --> pdb=" O TYR c 41 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER c 47 " --> pdb=" O ALA c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.735A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.710A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.261A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY c 144 " --> pdb=" O THR c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.705A pdb=" N VAL d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER d 12 " --> pdb=" O SER d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 4.095A pdb=" N LEU d 57 " --> pdb=" O GLU d 53 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 4.008A pdb=" N LYS d 77 " --> pdb=" O ASN d 73 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU d 78 " --> pdb=" O LYS d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 3.820A pdb=" N GLU d 91 " --> pdb=" O MET d 87 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 removed outlier: 3.545A pdb=" N GLY d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.644A pdb=" N GLY d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 147 removed outlier: 6.300A pdb=" N ALA d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS d 147 " --> pdb=" O GLU d 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 142 through 147' Processing helix chain 'd' and resid 148 through 158 removed outlier: 3.960A pdb=" N LEU d 155 " --> pdb=" O ILE d 151 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU d 156 " --> pdb=" O ALA d 152 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 6.501A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ALA d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 181 through 186' Processing helix chain 'd' and resid 190 through 200 removed outlier: 3.717A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 4.194A pdb=" N LYS e 70 " --> pdb=" O GLU e 66 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN e 71 " --> pdb=" O ASP e 67 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 120 removed outlier: 3.766A pdb=" N ALA e 114 " --> pdb=" O GLY e 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 148 removed outlier: 3.943A pdb=" N LEU e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 159 Processing helix chain 'e' and resid 161 through 166 removed outlier: 3.587A pdb=" N LEU e 166 " --> pdb=" O VAL e 162 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 35 removed outlier: 3.933A pdb=" N PHE f 27 " --> pdb=" O VAL f 23 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP f 28 " --> pdb=" O VAL f 24 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN f 34 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLY f 35 " --> pdb=" O LEU f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 85 removed outlier: 3.888A pdb=" N ASN f 75 " --> pdb=" O ALA f 71 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER f 84 " --> pdb=" O LEU f 80 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP f 85 " --> pdb=" O ALA f 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.710A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.773A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA g 46 " --> pdb=" O ILE g 42 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 4.602A pdb=" N ASN g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.691A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER g 97 " --> pdb=" O ALA g 93 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR g 98 " --> pdb=" O ASP g 94 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU g 110 " --> pdb=" O ASN g 106 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.614A pdb=" N ARG g 119 " --> pdb=" O THR g 115 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN g 129 " --> pdb=" O MET g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 4.764A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.546A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.891A pdb=" N GLU h 35 " --> pdb=" O LYS h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.613A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA h 120 " --> pdb=" O LYS h 116 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 40 removed outlier: 3.895A pdb=" N ILE i 39 " --> pdb=" O TRP i 35 " (cutoff:3.500A) Proline residue: i 40 - end of helix Processing helix chain 'i' and resid 44 through 53 removed outlier: 5.528A pdb=" N ILE i 48 " --> pdb=" O LEU i 44 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.548A pdb=" N ALA i 76 " --> pdb=" O TYR i 72 " (cutoff:3.500A) Proline residue: i 92 - end of helix Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.543A pdb=" N LEU i 98 " --> pdb=" O TYR i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.757A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER j 21 " --> pdb=" O ILE j 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.681A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.836A pdb=" N GLU k 76 " --> pdb=" O LYS k 72 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N HIS k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY k 78 " --> pdb=" O ALA k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 4.102A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 27 removed outlier: 4.000A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLY l 27 " --> pdb=" O ALA l 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 27' Processing helix chain 'l' and resid 126 through 131 removed outlier: 5.229A pdb=" N TYR l 130 " --> pdb=" O SER l 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.428A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.716A pdb=" N LYS m 31 " --> pdb=" O LYS m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.817A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.970A pdb=" N GLU m 58 " --> pdb=" O GLY m 54 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE m 59 " --> pdb=" O LYS m 55 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE m 63 " --> pdb=" O ILE m 59 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS m 64 " --> pdb=" O LEU m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 84 removed outlier: 3.513A pdb=" N LEU m 69 " --> pdb=" O VAL m 65 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'n' and resid 2 through 13 removed outlier: 5.044A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 removed outlier: 3.523A pdb=" N PHE n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU n 47 " --> pdb=" O CYS n 43 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY n 51 " --> pdb=" O LEU n 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.636A pdb=" N ILE o 11 " --> pdb=" O ARG o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.683A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS o 42 " --> pdb=" O SER o 38 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS o 47 " --> pdb=" O VAL o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.639A pdb=" N TYR o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.546A pdb=" N LYS o 83 " --> pdb=" O ARG o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 5.180A pdb=" N THR p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN p 62 " --> pdb=" O LYS p 58 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLY p 63 " --> pdb=" O TRP p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 89 Processing helix chain 'r' and resid 15 through 21 removed outlier: 3.619A pdb=" N SER r 19 " --> pdb=" O CYS r 15 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 38 removed outlier: 3.559A pdb=" N LEU r 33 " --> pdb=" O ASP r 29 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS r 35 " --> pdb=" O GLU r 31 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE r 36 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER r 38 " --> pdb=" O LYS r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 50 Processing helix chain 'r' and resid 52 through 70 removed outlier: 3.682A pdb=" N LYS r 58 " --> pdb=" O LYS r 54 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET r 69 " --> pdb=" O ARG r 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA r 70 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 24 removed outlier: 4.283A pdb=" N LYS s 18 " --> pdb=" O HIS s 14 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.439A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.512A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU t 15 " --> pdb=" O VAL t 11 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET t 28 " --> pdb=" O GLN t 24 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA t 38 " --> pdb=" O LYS t 34 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 removed outlier: 5.083A pdb=" N LYS t 47 " --> pdb=" O ALA t 43 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP t 48 " --> pdb=" O ASP t 44 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL t 51 " --> pdb=" O LYS t 47 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER t 59 " --> pdb=" O LYS t 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA t 60 " --> pdb=" O LYS t 56 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL t 61 " --> pdb=" O LEU t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 Processing helix chain 'v' and resid 16 through 32 removed outlier: 4.707A pdb=" N SER v 20 " --> pdb=" O ASP v 16 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 68 removed outlier: 4.129A pdb=" N VAL v 57 " --> pdb=" O GLY v 53 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP v 58 " --> pdb=" O LYS v 54 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU v 59 " --> pdb=" O GLY v 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 79 through 91 Processing helix chain 'v' and resid 96 through 109 Processing helix chain 'v' and resid 111 through 130 Proline residue: v 128 - end of helix Processing helix chain 'v' and resid 134 through 140 removed outlier: 4.498A pdb=" N ASP v 138 " --> pdb=" O GLY v 134 " (cutoff:3.500A) Processing helix chain 'v' and resid 154 through 192 removed outlier: 3.645A pdb=" N ILE v 163 " --> pdb=" O ASP v 159 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU v 182 " --> pdb=" O VAL v 178 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL v 183 " --> pdb=" O ASP v 179 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ARG v 184 " --> pdb=" O ASP v 180 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG v 185 " --> pdb=" O ARG v 181 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS v 187 " --> pdb=" O VAL v 183 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG v 188 " --> pdb=" O ARG v 184 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS v 189 " --> pdb=" O ARG v 185 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU v 192 " --> pdb=" O ARG v 188 " (cutoff:3.500A) Processing helix chain 'v' and resid 205 through 217 Processing helix chain 'v' and resid 263 through 275 removed outlier: 3.993A pdb=" N SER v 272 " --> pdb=" O LYS v 268 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR v 273 " --> pdb=" O ALA v 269 " (cutoff:3.500A) Processing helix chain 'v' and resid 293 through 309 Processing helix chain 'v' and resid 321 through 326 removed outlier: 3.849A pdb=" N LEU v 325 " --> pdb=" O LYS v 321 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLU v 326 " --> pdb=" O ALA v 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 321 through 326' Processing helix chain 'v' and resid 344 through 359 removed outlier: 4.101A pdb=" N LEU v 348 " --> pdb=" O GLU v 344 " (cutoff:3.500A) Processing helix chain 'v' and resid 375 through 385 removed outlier: 6.400A pdb=" N ALA v 379 " --> pdb=" O GLY v 375 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR v 380 " --> pdb=" O GLN v 376 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA v 385 " --> pdb=" O LEU v 381 " (cutoff:3.500A) Processing helix chain 'v' and resid 404 through 412 Processing helix chain 'w' and resid 14 through 29 removed outlier: 4.317A pdb=" N LEU w 28 " --> pdb=" O LYS w 24 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU w 29 " --> pdb=" O ILE w 25 " (cutoff:3.500A) Processing helix chain 'w' and resid 73 through 100 removed outlier: 3.570A pdb=" N PHE w 100 " --> pdb=" O VAL w 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.949A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.596A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.031A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.626A pdb=" N HIS C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.125A pdb=" N ASN D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 4.064A pdb=" N HIS D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.532A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.516A pdb=" N VAL D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA D 103 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.566A pdb=" N GLY D 45 " --> pdb=" O THR D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'E' and resid 29 through 45 removed outlier: 4.121A pdb=" N ASP E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.721A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS E 117 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.580A pdb=" N LYS E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 168 removed outlier: 3.849A pdb=" N SER E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.616A pdb=" N HIS E 189 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ASP E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.642A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 12 through 21 removed outlier: 3.788A pdb=" N MET F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN F 21 " --> pdb=" O MET F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 62 removed outlier: 4.291A pdb=" N ASP F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.891A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 111 removed outlier: 4.534A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 111' Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.518A pdb=" N THR F 171 " --> pdb=" O HIS F 167 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 4.019A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA F 45 " --> pdb=" O ASP F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.782A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 3 through 8 removed outlier: 5.886A pdb=" N THR G 8 " --> pdb=" O ILE G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 6.239A pdb=" N ARG G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY G 78 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.966A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'L' and resid 25 through 39 removed outlier: 4.216A pdb=" N GLU L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER L 35 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG L 38 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 97 Processing helix chain 'L' and resid 98 through 111 removed outlier: 3.643A pdb=" N LEU L 102 " --> pdb=" O PRO L 98 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Proline residue: L 111 - end of helix Processing helix chain 'L' and resid 113 through 124 removed outlier: 3.749A pdb=" N PHE L 120 " --> pdb=" O GLY L 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.150A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 110' Processing helix chain 'M' and resid 111 through 118 removed outlier: 3.655A pdb=" N LEU M 117 " --> pdb=" O LYS M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.728A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Proline residue: N 62 - end of helix No H-bonds generated for 'chain 'N' and resid 56 through 62' Processing helix chain 'N' and resid 78 through 85 removed outlier: 4.019A pdb=" N LEU N 82 " --> pdb=" O ASN N 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE N 85 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 85' Processing helix chain 'N' and resid 92 through 100 removed outlier: 3.847A pdb=" N GLU N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY N 100 " --> pdb=" O LEU N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 140 removed outlier: 3.645A pdb=" N GLU N 134 " --> pdb=" O ALA N 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA N 139 " --> pdb=" O ALA N 135 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY N 140 " --> pdb=" O ILE N 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 3.657A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.656A pdb=" N HIS O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 9 through 28 removed outlier: 3.528A pdb=" N ASP P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 54 removed outlier: 4.008A pdb=" N GLU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS P 42 " --> pdb=" O LYS P 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 66 removed outlier: 3.787A pdb=" N ARG P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 100 Processing helix chain 'P' and resid 101 through 108 removed outlier: 4.030A pdb=" N ARG P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR P 106 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU P 108 " --> pdb=" O PRO P 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 101 through 108' Processing helix chain 'Q' and resid 6 through 21 removed outlier: 4.857A pdb=" N LYS Q 21 " --> pdb=" O ARG Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 88 removed outlier: 3.591A pdb=" N SER Q 74 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS Q 75 " --> pdb=" O ASP Q 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL Q 76 " --> pdb=" O ALA Q 72 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY Q 77 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU Q 78 " --> pdb=" O SER Q 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU Q 79 " --> pdb=" O LYS Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.674A pdb=" N ASN Q 115 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 10 removed outlier: 3.621A pdb=" N GLU R 7 " --> pdb=" O LYS R 3 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS R 10 " --> pdb=" O ASP R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 104 removed outlier: 4.888A pdb=" N ARG R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 97 through 104' Processing helix chain 'S' and resid 8 through 22 removed outlier: 3.792A pdb=" N LYS S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.769A pdb=" N GLN S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 4.158A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP S 73 " --> pdb=" O ALA S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 removed outlier: 3.521A pdb=" N HIS S 81 " --> pdb=" O SER S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 102 removed outlier: 3.937A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN S 101 " --> pdb=" O ASP S 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 118 removed outlier: 3.619A pdb=" N THR S 108 " --> pdb=" O ALA S 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 30 removed outlier: 4.126A pdb=" N ILE U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL U 25 " --> pdb=" O LYS U 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP U 27 " --> pdb=" O ARG U 23 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG U 30 " --> pdb=" O ILE U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 45 removed outlier: 3.854A pdb=" N ALA U 39 " --> pdb=" O GLY U 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR U 44 " --> pdb=" O ILE U 40 " (cutoff:3.500A) Proline residue: U 45 - end of helix Processing helix chain 'U' and resid 46 through 66 Proline residue: U 50 - end of helix removed outlier: 3.669A pdb=" N VAL U 55 " --> pdb=" O ILE U 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU U 64 " --> pdb=" O ILE U 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 8 removed outlier: 3.719A pdb=" N ILE V 7 " --> pdb=" O ALA V 3 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS V 8 " --> pdb=" O ARG V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 21 removed outlier: 3.896A pdb=" N ILE V 19 " --> pdb=" O GLU V 15 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU V 20 " --> pdb=" O SER V 16 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP V 21 " --> pdb=" O THR V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.737A pdb=" N LYS V 39 " --> pdb=" O LYS V 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 69 removed outlier: 4.379A pdb=" N VAL W 68 " --> pdb=" O HIS W 64 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N MET W 69 " --> pdb=" O VAL W 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 64 through 69' Processing helix chain 'Z' and resid 50 through 56 removed outlier: 4.673A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 8 removed outlier: 3.857A pdb=" N ARG 1 7 " --> pdb=" O ALA 1 3 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 3 through 8' Processing helix chain '1' and resid 10 through 35 removed outlier: 6.202A pdb=" N ILE 1 14 " --> pdb=" O SER 1 10 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN 1 15 " --> pdb=" O THR 1 11 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP 1 16 " --> pdb=" O THR 1 12 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 62 removed outlier: 3.992A pdb=" N GLU 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU 1 61 " --> pdb=" O VAL 1 57 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.501A pdb=" N GLN 2 24 " --> pdb=" O ARG 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.640A pdb=" N LYS 2 49 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 79 removed outlier: 5.963A pdb=" N PHE 3 74 " --> pdb=" O ARG 3 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS 3 76 " --> pdb=" O ASP 3 72 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 3.503A pdb=" N ARG 4 17 " --> pdb=" O LYS 4 13 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 4 18 " --> pdb=" O ARG 4 14 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 27 Proline residue: 5 27 - end of helix No H-bonds generated for 'chain '5' and resid 22 through 27' Processing helix chain '6' and resid 8 through 16 removed outlier: 3.559A pdb=" N VAL 6 15 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 25 removed outlier: 3.805A pdb=" N SER 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR 6 24 " --> pdb=" O THR 6 20 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 removed outlier: 3.685A pdb=" N LYS 6 37 " --> pdb=" O SER 6 33 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 4.390A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.122A pdb=" N LYS 7 36 " --> pdb=" O MET 7 32 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 47 removed outlier: 3.851A pdb=" N LYS 7 43 " --> pdb=" O LYS 7 39 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU 7 44 " --> pdb=" O GLN 7 40 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG 7 45 " --> pdb=" O LYS 7 41 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER 7 47 " --> pdb=" O LYS 7 43 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 3.703A pdb=" N ARG 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N MET 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA 7 63 " --> pdb=" O ARG 7 59 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 89 through 92 removed outlier: 3.550A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.829A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 163 through 169 Processing sheet with id= 4, first strand: chain 'd' and resid 164 through 169 removed outlier: 7.714A pdb=" N TYR d 164 " --> pdb=" O ASN d 177 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 13 through 17 removed outlier: 6.876A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 84 through 89 removed outlier: 7.983A pdb=" N HIS e 84 " --> pdb=" O PRO e 99 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU e 94 " --> pdb=" O LEU e 129 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA e 100 " --> pdb=" O ASP e 123 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP e 123 " --> pdb=" O ALA e 100 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 34 through 41 Processing sheet with id= 8, first strand: chain 'f' and resid 45 through 49 removed outlier: 6.902A pdb=" N ARG f 57 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASP f 58 " --> pdb=" O PRO f 13 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU f 66 " --> pdb=" O TYR f 5 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS f 4 " --> pdb=" O GLU f 95 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU f 95 " --> pdb=" O LYS f 4 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG f 89 " --> pdb=" O ILE f 10 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'g' and resid 73 through 77 Processing sheet with id= 10, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.810A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY h 58 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.937A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU h 126 " --> pdb=" O SER h 107 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 13, first strand: chain 'j' and resid 39 through 42 removed outlier: 3.629A pdb=" N LEU j 73 " --> pdb=" O ILE j 40 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU j 10 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG j 7 " --> pdb=" O LYS j 101 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 15, first strand: chain 'k' and resid 30 through 35 removed outlier: 7.741A pdb=" N VAL k 84 " --> pdb=" O THR k 108 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'k' and resid 83 through 86 removed outlier: 3.605A pdb=" N VAL k 84 " --> pdb=" O ALA k 109 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 42 through 45 removed outlier: 5.011A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 49 through 54 removed outlier: 3.671A pdb=" N GLY l 51 " --> pdb=" O TYR l 65 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'p' and resid 6 through 11 Processing sheet with id= 20, first strand: chain 'q' and resid 8 through 13 removed outlier: 5.794A pdb=" N LYS q 8 " --> pdb=" O GLU q 65 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG q 62 " --> pdb=" O LEU q 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'q' and resid 21 through 33 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 's' and resid 30 through 33 Processing sheet with id= 23, first strand: chain 'v' and resid 37 through 42 removed outlier: 4.489A pdb=" N GLY v 37 " --> pdb=" O VAL v 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY v 9 " --> pdb=" O ILE v 39 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU v 71 " --> pdb=" O LYS v 4 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'v' and resid 237 through 244 removed outlier: 4.009A pdb=" N LYS v 248 " --> pdb=" O LEU v 244 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU v 282 " --> pdb=" O VAL v 195 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL v 199 " --> pdb=" O ILE v 284 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR v 201 " --> pdb=" O VAL v 286 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP v 288 " --> pdb=" O TYR v 201 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASN v 336 " --> pdb=" O VAL v 315 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR v 317 " --> pdb=" O ASN v 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR v 337 " --> pdb=" O THR v 334 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'v' and resid 365 through 371 Processing sheet with id= 26, first strand: chain 'w' and resid 1 through 8 removed outlier: 4.365A pdb=" N ALA w 38 " --> pdb=" O MET w 1 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS w 3 " --> pdb=" O ALA w 38 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN w 39 " --> pdb=" O PRO w 59 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN w 51 " --> pdb=" O TYR w 47 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.673A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 91 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 165 through 168 removed outlier: 3.512A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.249A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.134A pdb=" N LYS D 3 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.908A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 28 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.818A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE D 79 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 2 through 8 removed outlier: 4.518A pdb=" N THR E 18 " --> pdb=" O PRO E 2 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU E 4 " --> pdb=" O GLU E 16 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU E 16 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 6 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.506A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'F' and resid 65 through 69 removed outlier: 6.623A pdb=" N ALA F 87 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR F 38 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE F 34 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.640A pdb=" N ASN F 72 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU F 81 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 39, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.650A pdb=" N ARG G 95 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN G 106 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 105 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 121 through 125 removed outlier: 6.249A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL G 131 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE G 90 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'L' and resid 15 through 20 Processing sheet with id= 42, first strand: chain 'L' and resid 75 through 79 removed outlier: 3.797A pdb=" N SER L 79 " --> pdb=" O GLY L 84 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY L 84 " --> pdb=" O SER L 79 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 17 through 21 removed outlier: 6.101A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER M 6 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'M' and resid 37 through 41 removed outlier: 4.711A pdb=" N ASP M 37 " --> pdb=" O ILE M 62 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 66 through 71 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'N' and resid 87 through 90 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'O' and resid 31 through 37 removed outlier: 8.248A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LYS O 128 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'O' and resid 38 through 41 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'O' and resid 63 through 66 Processing sheet with id= 50, first strand: chain 'P' and resid 29 through 33 removed outlier: 6.711A pdb=" N MET P 129 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR P 113 " --> pdb=" O VAL P 135 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'P' and resid 72 through 76 removed outlier: 3.647A pdb=" N GLU P 72 " --> pdb=" O VAL P 92 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS P 88 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Q' and resid 54 through 57 removed outlier: 4.052A pdb=" N ALA Q 54 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 95 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 38 through 45 removed outlier: 4.214A pdb=" N LYS R 83 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 49 through 52 removed outlier: 4.061A pdb=" N LYS R 49 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU R 57 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.614A pdb=" N PHE T 40 " --> pdb=" O ILE T 4 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T' and resid 17 through 21 removed outlier: 4.138A pdb=" N GLN T 18 " --> pdb=" O ILE T 97 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS T 94 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR T 59 " --> pdb=" O ASP T 98 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP T 31 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 64 through 68 removed outlier: 3.618A pdb=" N LYS T 64 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN T 90 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'U' and resid 7 through 13 removed outlier: 6.967A pdb=" N VAL U 111 " --> pdb=" O GLU U 77 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'U' and resid 78 through 84 removed outlier: 3.724A pdb=" N GLU U 78 " --> pdb=" O VAL U 111 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR U 105 " --> pdb=" O GLY U 84 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 86 through 93 removed outlier: 4.086A pdb=" N ARG U 97 " --> pdb=" O ARG U 93 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'V' and resid 24 through 29 removed outlier: 4.487A pdb=" N ARG V 76 " --> pdb=" O VAL V 29 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN V 73 " --> pdb=" O GLY V 60 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY V 60 " --> pdb=" O ASN V 73 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS V 61 " --> pdb=" O THR V 72 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.519A pdb=" N ASN W 39 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'W' and resid 80 through 83 removed outlier: 7.069A pdb=" N ARG W 80 " --> pdb=" O LYS W 95 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ARG W 92 " --> pdb=" O ILE W 101 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU W 99 " --> pdb=" O ALA W 94 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Y' and resid 37 through 40 removed outlier: 4.625A pdb=" N GLN Y 37 " --> pdb=" O VAL Y 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL Y 75 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Z' and resid 11 through 19 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain '2' and resid 32 through 38 removed outlier: 4.039A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '3' and resid 12 through 16 removed outlier: 4.495A pdb=" N PHE 3 21 " --> pdb=" O ASP 3 16 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '4' and resid 28 through 31 removed outlier: 4.073A pdb=" N GLU 4 35 " --> pdb=" O CYS 4 30 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '5' and resid 3 through 7 removed outlier: 3.515A pdb=" N TYR 5 17 " --> pdb=" O LEU 5 7 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '5' and resid 31 through 34 Processing sheet with id= 71, first strand: chain '8' and resid 14 through 19 1682 hydrogen bonds defined for protein. 4953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3951 hydrogen bonds 6278 hydrogen bond angles 0 basepair planarities 1574 basepair parallelities 2406 stacking parallelities Total time for adding SS restraints: 231.11 Time building geometry restraints manager: 61.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 26355 1.33 - 1.46: 65027 1.46 - 1.58: 56507 1.58 - 1.70: 9222 1.70 - 1.83: 252 Bond restraints: 157363 Sorted by residual: bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.484 0.318 2.00e-02 2.50e+03 2.53e+02 bond pdb=" N1 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.635 1.338 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C2' GCP v 501 " pdb=" C3' GCP v 501 " ideal model delta sigma weight residual 1.241 1.510 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C5 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.155 1.387 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C2 4SU y 8 " pdb=" N3 4SU y 8 " ideal model delta sigma weight residual 1.499 1.338 0.161 2.00e-02 2.50e+03 6.50e+01 ... (remaining 157358 not shown) Histogram of bond angle deviations from ideal: 96.49 - 105.07: 21334 105.07 - 113.65: 102551 113.65 - 122.22: 79154 122.22 - 130.80: 30784 130.80 - 139.38: 1497 Bond angle restraints: 235320 Sorted by residual: angle pdb=" C1' GCP v 501 " pdb=" N9 GCP v 501 " pdb=" C4 GCP v 501 " ideal model delta sigma weight residual 108.44 126.62 -18.18 3.00e+00 1.11e-01 3.67e+01 angle pdb=" C GLY b 150 " pdb=" N ILE b 151 " pdb=" CA ILE b 151 " ideal model delta sigma weight residual 121.97 131.92 -9.95 1.80e+00 3.09e-01 3.06e+01 angle pdb=" C6 5MU y 54 " pdb=" C5 5MU y 54 " pdb=" C5M 5MU y 54 " ideal model delta sigma weight residual 106.09 120.48 -14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N ILE f 39 " pdb=" CA ILE f 39 " pdb=" C ILE f 39 " ideal model delta sigma weight residual 113.53 108.94 4.59 9.80e-01 1.04e+00 2.20e+01 angle pdb=" C8 7MG y 46 " pdb=" N7 7MG y 46 " pdb=" CM7 7MG y 46 " ideal model delta sigma weight residual 126.72 112.99 13.73 3.00e+00 1.11e-01 2.10e+01 ... (remaining 235315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 89788 35.83 - 71.66: 9572 71.66 - 107.48: 1180 107.48 - 143.31: 21 143.31 - 179.14: 36 Dihedral angle restraints: 100597 sinusoidal: 83934 harmonic: 16663 Sorted by residual: dihedral pdb=" O4' C A1904 " pdb=" C1' C A1904 " pdb=" N1 C A1904 " pdb=" C2 C A1904 " ideal model delta sinusoidal sigma weight residual 200.00 32.16 167.84 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' U A2339 " pdb=" C1' U A2339 " pdb=" N1 U A2339 " pdb=" C2 U A2339 " ideal model delta sinusoidal sigma weight residual 200.00 43.72 156.28 1 1.50e+01 4.44e-03 8.17e+01 dihedral pdb=" O4' C a1166 " pdb=" C1' C a1166 " pdb=" N1 C a1166 " pdb=" C2 C a1166 " ideal model delta sinusoidal sigma weight residual 200.00 54.73 145.27 1 1.50e+01 4.44e-03 7.77e+01 ... (remaining 100594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 27451 0.059 - 0.118: 2267 0.118 - 0.177: 280 0.177 - 0.236: 32 0.236 - 0.295: 9 Chirality restraints: 30039 Sorted by residual: chirality pdb=" C3' A A2472 " pdb=" C4' A A2472 " pdb=" O3' A A2472 " pdb=" C2' A A2472 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' A a 756 " pdb=" C4' A a 756 " pdb=" O3' A a 756 " pdb=" C2' A a 756 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C1' U a 602 " pdb=" O4' U a 602 " pdb=" C2' U a 602 " pdb=" N1 U a 602 " both_signs ideal model delta sigma weight residual False 2.47 2.19 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 30036 not shown) Planarity restraints: 12626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG y 46 " -0.830 2.00e-02 2.50e+03 5.60e-01 7.05e+03 pdb=" C4' 7MG y 46 " 0.227 2.00e-02 2.50e+03 pdb=" O4' 7MG y 46 " 0.677 2.00e-02 2.50e+03 pdb=" C3' 7MG y 46 " -0.231 2.00e-02 2.50e+03 pdb=" O3' 7MG y 46 " 0.858 2.00e-02 2.50e+03 pdb=" C2' 7MG y 46 " -0.600 2.00e-02 2.50e+03 pdb=" O2' 7MG y 46 " -0.532 2.00e-02 2.50e+03 pdb=" C1' 7MG y 46 " 0.434 2.00e-02 2.50e+03 pdb=" N9 7MG y 46 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU y 54 " -0.052 2.00e-02 2.50e+03 5.00e-01 5.63e+03 pdb=" C4' 5MU y 54 " 0.424 2.00e-02 2.50e+03 pdb=" O4' 5MU y 54 " 0.613 2.00e-02 2.50e+03 pdb=" C3' 5MU y 54 " -0.554 2.00e-02 2.50e+03 pdb=" O3' 5MU y 54 " -0.393 2.00e-02 2.50e+03 pdb=" C2' 5MU y 54 " -0.284 2.00e-02 2.50e+03 pdb=" O2' 5MU y 54 " 0.743 2.00e-02 2.50e+03 pdb=" C1' 5MU y 54 " 0.238 2.00e-02 2.50e+03 pdb=" N1 5MU y 54 " -0.735 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GCP v 501 " -0.365 2.00e-02 2.50e+03 4.51e-01 4.58e+03 pdb=" C2' GCP v 501 " 0.457 2.00e-02 2.50e+03 pdb=" C3' GCP v 501 " 0.461 2.00e-02 2.50e+03 pdb=" C4' GCP v 501 " -0.375 2.00e-02 2.50e+03 pdb=" C5' GCP v 501 " 0.458 2.00e-02 2.50e+03 pdb=" N9 GCP v 501 " 0.480 2.00e-02 2.50e+03 pdb=" O2' GCP v 501 " -0.169 2.00e-02 2.50e+03 pdb=" O3' GCP v 501 " -0.142 2.00e-02 2.50e+03 pdb=" O4' GCP v 501 " -0.804 2.00e-02 2.50e+03 ... (remaining 12623 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 742 2.47 - 3.08: 87276 3.08 - 3.68: 255307 3.68 - 4.29: 387466 4.29 - 4.90: 544437 Nonbonded interactions: 1275228 Sorted by model distance: nonbonded pdb=" N GLU j 63 " pdb="MG MG j 201 " model vdw 1.860 2.250 nonbonded pdb=" N4 C A 786 " pdb="MG MG A3210 " model vdw 1.894 2.250 nonbonded pdb=" OP2 C a1063 " pdb="MG MG a3133 " model vdw 1.932 2.170 nonbonded pdb=" OP2 A A1386 " pdb="MG MG A3110 " model vdw 1.971 2.170 nonbonded pdb=" OP2 G A2875 " pdb="MG MG A3178 " model vdw 1.978 2.170 ... (remaining 1275223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 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: 0.120 Extract box with map and model: 28.680 Check model and map are aligned: 1.400 Set scattering table: 0.870 Process input model: 534.790 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.330 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 577.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.004 0.318 157363 Z= 0.255 Angle : 0.547 18.184 235320 Z= 0.286 Chirality : 0.035 0.295 30039 Planarity : 0.009 0.560 12626 Dihedral : 22.364 179.139 89873 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.11), residues: 5727 helix: -0.55 (0.12), residues: 1761 sheet: -0.42 (0.16), residues: 1109 loop : -1.14 (0.11), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP c 18 HIS 0.008 0.001 HIS p 84 PHE 0.035 0.001 PHE v 270 TYR 0.021 0.001 TYR d 47 ARG 0.011 0.000 ARG g 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1108 time to evaluate : 6.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 6 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7931 (tm-30) REVERT: g 92 ARG cc_start: 0.8360 (mpp-170) cc_final: 0.7478 (mtm180) REVERT: g 94 ASP cc_start: 0.8952 (p0) cc_final: 0.8681 (p0) REVERT: i 31 ASN cc_start: 0.8608 (t0) cc_final: 0.8262 (t0) REVERT: i 94 TYR cc_start: 0.7523 (m-80) cc_final: 0.7241 (m-80) REVERT: j 86 SER cc_start: 0.7924 (t) cc_final: 0.7690 (p) REVERT: l 107 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7647 (ttm170) REVERT: n 38 LYS cc_start: 0.8686 (mttt) cc_final: 0.8451 (mttm) REVERT: p 15 LYS cc_start: 0.8559 (mttp) cc_final: 0.8327 (mtmm) REVERT: v 41 GLN cc_start: 0.7108 (tm-30) cc_final: 0.6733 (tm-30) REVERT: v 156 ILE cc_start: 0.7957 (pt) cc_final: 0.7663 (tp) REVERT: w 86 GLU cc_start: 0.7945 (pt0) cc_final: 0.7742 (pt0) REVERT: C 3 ILE cc_start: 0.8836 (mm) cc_final: 0.8607 (mm) REVERT: P 28 GLU cc_start: 0.7852 (mp0) cc_final: 0.7371 (mp0) REVERT: R 2 ASN cc_start: 0.8692 (t0) cc_final: 0.8412 (t0) REVERT: V 22 ASP cc_start: 0.8110 (m-30) cc_final: 0.7864 (t0) REVERT: W 16 ASP cc_start: 0.8295 (t0) cc_final: 0.7997 (t0) REVERT: W 51 ASN cc_start: 0.8565 (t0) cc_final: 0.8328 (t0) REVERT: 1 61 GLU cc_start: 0.8048 (pp20) cc_final: 0.7745 (pp20) outliers start: 0 outliers final: 0 residues processed: 1108 average time/residue: 1.3821 time to fit residues: 2662.0102 Evaluate side-chains 920 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 920 time to evaluate : 6.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 862 optimal weight: 10.0000 chunk 774 optimal weight: 9.9990 chunk 429 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 522 optimal weight: 30.0000 chunk 413 optimal weight: 3.9990 chunk 801 optimal weight: 8.9990 chunk 309 optimal weight: 0.0470 chunk 487 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 chunk 928 optimal weight: 7.9990 overall best weight: 6.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 77 GLN b 113 HIS b 203 ASN c 133 GLN c 175 HIS d 85 ASN d 116 HIS d 118 HIS d 137 GLN e 44 ASN f 14 ASN f 90 HIS g 129 ASN ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 29 ASN l 59 ASN l 86 ASN l 122 ASN m 91 HIS m 104 ASN o 18 HIS o 28 GLN o 40 ASN o 51 HIS p 61 HIS v 12 GLN v 31 ASN v 67 GLN v 115 GLN v 139 GLN v 165 HIS v 247 ASN v 398 GLN w 41 HIS w 92 HIS w 97 ASN C 153 GLN C 163 GLN D 68 HIS E 162 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN G 38 ASN L 41 ASN M 110 ASN N 83 ASN P 61 GLN P 89 ASN Q 49 ASN T 65 GLN T 90 GLN U 107 HIS Z 16 ASN 3 6 HIS 3 75 ASN 7 35 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 157363 Z= 0.355 Angle : 0.645 18.771 235320 Z= 0.333 Chirality : 0.039 0.361 30039 Planarity : 0.005 0.125 12626 Dihedral : 22.802 179.384 78173 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.33 % Rotamer: Outliers : 2.05 % Allowed : 12.08 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5727 helix: -0.24 (0.12), residues: 1822 sheet: -0.43 (0.15), residues: 1149 loop : -1.20 (0.12), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP f 44 HIS 0.009 0.001 HIS G 65 PHE 0.023 0.002 PHE Q 34 TYR 0.031 0.002 TYR l 65 ARG 0.010 0.001 ARG b 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 984 time to evaluate : 6.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 169 GLU cc_start: 0.8061 (mp0) cc_final: 0.7831 (mp0) REVERT: g 92 ARG cc_start: 0.8374 (mpp-170) cc_final: 0.7467 (mtm180) REVERT: i 31 ASN cc_start: 0.8652 (t0) cc_final: 0.8302 (t0) REVERT: j 27 GLU cc_start: 0.8179 (mp0) cc_final: 0.7591 (mp0) REVERT: j 86 SER cc_start: 0.7957 (t) cc_final: 0.7683 (p) REVERT: l 99 ARG cc_start: 0.7523 (ttm110) cc_final: 0.7317 (ttm110) REVERT: l 102 ASP cc_start: 0.8658 (m-30) cc_final: 0.8335 (m-30) REVERT: v 19 TYR cc_start: 0.7587 (t80) cc_final: 0.7379 (t80) REVERT: v 41 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7107 (tm-30) REVERT: w 86 GLU cc_start: 0.8007 (pt0) cc_final: 0.7783 (pt0) REVERT: F 96 MET cc_start: 0.7938 (tpt) cc_final: 0.7589 (mmt) REVERT: G 37 PHE cc_start: 0.8446 (m-80) cc_final: 0.7755 (m-80) REVERT: P 23 ASP cc_start: 0.7833 (m-30) cc_final: 0.7553 (m-30) REVERT: P 72 GLU cc_start: 0.8296 (pp20) cc_final: 0.7920 (pp20) REVERT: S 102 ASP cc_start: 0.8315 (t0) cc_final: 0.8023 (t0) REVERT: V 22 ASP cc_start: 0.8193 (m-30) cc_final: 0.7828 (t0) REVERT: W 16 ASP cc_start: 0.8303 (t0) cc_final: 0.8016 (t0) REVERT: W 39 ASN cc_start: 0.8935 (t0) cc_final: 0.8532 (t0) REVERT: W 51 ASN cc_start: 0.8619 (t0) cc_final: 0.8302 (t0) REVERT: 1 54 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8583 (mtmt) REVERT: 1 61 GLU cc_start: 0.8069 (pp20) cc_final: 0.7845 (pp20) REVERT: 6 2 LYS cc_start: 0.8946 (ttpt) cc_final: 0.8543 (tttt) outliers start: 100 outliers final: 82 residues processed: 1025 average time/residue: 1.2443 time to fit residues: 2211.5998 Evaluate side-chains 1017 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 935 time to evaluate : 7.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 39 ILE Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 163 ILE Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 214 VAL Chi-restraints excluded: chain v residue 259 VAL Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 307 VAL Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 48 THR Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 515 optimal weight: 10.0000 chunk 288 optimal weight: 8.9990 chunk 772 optimal weight: 6.9990 chunk 631 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 929 optimal weight: 5.9990 chunk 1004 optimal weight: 5.9990 chunk 828 optimal weight: 10.0000 chunk 922 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 chunk 745 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 133 GLN f 34 ASN g 64 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 ASN r 24 HIS ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 ASN P 61 GLN Q 49 ASN Z 16 ASN 4 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 157363 Z= 0.255 Angle : 0.581 17.721 235320 Z= 0.303 Chirality : 0.036 0.325 30039 Planarity : 0.005 0.117 12626 Dihedral : 22.746 179.011 78173 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.25 % Rotamer: Outliers : 3.22 % Allowed : 15.16 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.11), residues: 5727 helix: 0.01 (0.12), residues: 1835 sheet: -0.42 (0.15), residues: 1146 loop : -1.14 (0.12), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP c 200 HIS 0.007 0.001 HIS p 84 PHE 0.029 0.002 PHE Q 34 TYR 0.032 0.002 TYR l 65 ARG 0.008 0.000 ARG 1 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 963 time to evaluate : 6.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 196 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7437 (mp) REVERT: g 50 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7080 (tp) REVERT: g 92 ARG cc_start: 0.8293 (mpp-170) cc_final: 0.7408 (mtm180) REVERT: i 31 ASN cc_start: 0.8646 (t0) cc_final: 0.8283 (t0) REVERT: i 94 TYR cc_start: 0.7597 (m-80) cc_final: 0.7310 (m-80) REVERT: j 75 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6940 (t0) REVERT: j 86 SER cc_start: 0.7978 (t) cc_final: 0.7763 (p) REVERT: k 33 MET cc_start: 0.7803 (tpt) cc_final: 0.7516 (tpt) REVERT: t 52 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8220 (tm-30) REVERT: v 66 MET cc_start: 0.8238 (ppp) cc_final: 0.7880 (tmm) REVERT: w 86 GLU cc_start: 0.7986 (pt0) cc_final: 0.7755 (pt0) REVERT: F 56 GLU cc_start: 0.8847 (pp20) cc_final: 0.8610 (pp20) REVERT: F 96 MET cc_start: 0.7914 (tpt) cc_final: 0.7593 (mmt) REVERT: O 32 TYR cc_start: 0.7734 (m-10) cc_final: 0.7346 (m-10) REVERT: O 111 GLU cc_start: 0.8161 (tp30) cc_final: 0.7794 (tp30) REVERT: P 23 ASP cc_start: 0.7844 (m-30) cc_final: 0.7579 (m-30) REVERT: P 72 GLU cc_start: 0.8257 (pp20) cc_final: 0.8027 (pp20) REVERT: P 90 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7569 (mmm-85) REVERT: V 22 ASP cc_start: 0.8249 (m-30) cc_final: 0.7729 (t0) REVERT: W 16 ASP cc_start: 0.8277 (t0) cc_final: 0.7715 (t0) REVERT: W 39 ASN cc_start: 0.8887 (t0) cc_final: 0.8162 (t0) REVERT: W 51 ASN cc_start: 0.8638 (t0) cc_final: 0.8297 (t0) REVERT: 4 29 GLU cc_start: 0.8004 (tt0) cc_final: 0.7800 (mt-10) REVERT: 5 11 GLU cc_start: 0.7577 (mp0) cc_final: 0.7369 (mp0) REVERT: 6 2 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8463 (ttpt) outliers start: 157 outliers final: 117 residues processed: 1040 average time/residue: 1.2032 time to fit residues: 2169.4915 Evaluate side-chains 1052 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 932 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 17 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 163 ILE Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 94 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 48 THR Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 918 optimal weight: 9.9990 chunk 699 optimal weight: 10.0000 chunk 482 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 443 optimal weight: 20.0000 chunk 624 optimal weight: 10.0000 chunk 933 optimal weight: 8.9990 chunk 987 optimal weight: 9.9990 chunk 487 optimal weight: 10.0000 chunk 884 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 ASN g 64 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN P 61 GLN Q 49 ASN Z 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 157363 Z= 0.476 Angle : 0.723 17.508 235320 Z= 0.369 Chirality : 0.043 0.406 30039 Planarity : 0.006 0.115 12626 Dihedral : 22.790 178.532 78173 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.67 % Favored : 93.23 % Rotamer: Outliers : 5.17 % Allowed : 16.67 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5727 helix: -0.19 (0.12), residues: 1831 sheet: -0.49 (0.15), residues: 1156 loop : -1.39 (0.11), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c 200 HIS 0.010 0.001 HIS l 85 PHE 0.034 0.002 PHE i 41 TYR 0.028 0.002 TYR l 65 ARG 0.007 0.001 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 949 time to evaluate : 8.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 196 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7418 (mp) REVERT: g 92 ARG cc_start: 0.8342 (mpp-170) cc_final: 0.7452 (mtm180) REVERT: i 31 ASN cc_start: 0.8746 (t0) cc_final: 0.8304 (t0) REVERT: j 27 GLU cc_start: 0.8326 (mp0) cc_final: 0.8083 (mp0) REVERT: j 74 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8212 (mm) REVERT: j 97 ASP cc_start: 0.7679 (t70) cc_final: 0.7459 (t0) REVERT: q 83 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7234 (tm-30) REVERT: t 42 ASN cc_start: 0.7696 (t0) cc_final: 0.7474 (t0) REVERT: v 19 TYR cc_start: 0.7695 (t80) cc_final: 0.7465 (t80) REVERT: v 41 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: v 66 MET cc_start: 0.8250 (ppp) cc_final: 0.7632 (tmm) REVERT: v 143 LYS cc_start: 0.7463 (mmtp) cc_final: 0.6780 (mmtp) REVERT: w 88 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: F 56 GLU cc_start: 0.8869 (pp20) cc_final: 0.8627 (pp20) REVERT: F 96 MET cc_start: 0.7864 (tpt) cc_final: 0.7444 (mmt) REVERT: O 32 TYR cc_start: 0.8016 (m-10) cc_final: 0.7361 (m-10) REVERT: O 111 GLU cc_start: 0.8152 (tp30) cc_final: 0.7681 (tp30) REVERT: P 23 ASP cc_start: 0.7883 (m-30) cc_final: 0.7653 (m-30) REVERT: Q 46 ASP cc_start: 0.7701 (t0) cc_final: 0.6422 (p0) REVERT: Q 102 HIS cc_start: 0.7882 (t-90) cc_final: 0.7660 (t-90) REVERT: R 7 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: R 100 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8855 (mp) REVERT: U 68 ASP cc_start: 0.8445 (t0) cc_final: 0.8183 (t0) REVERT: V 22 ASP cc_start: 0.8335 (m-30) cc_final: 0.7703 (t0) REVERT: W 16 ASP cc_start: 0.8195 (t0) cc_final: 0.7740 (t0) REVERT: W 39 ASN cc_start: 0.8871 (t0) cc_final: 0.8029 (t0) REVERT: 5 11 GLU cc_start: 0.7655 (mp0) cc_final: 0.7409 (mp0) REVERT: 6 2 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8466 (ttpt) outliers start: 252 outliers final: 196 residues processed: 1103 average time/residue: 1.2905 time to fit residues: 2497.7833 Evaluate side-chains 1137 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 935 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 200 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 166 LEU Chi-restraints excluded: chain f residue 19 GLU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 34 ASN Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 44 LEU Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain p residue 60 MET Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 39 ILE Chi-restraints excluded: chain v residue 41 GLN Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 163 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 214 VAL Chi-restraints excluded: chain v residue 234 THR Chi-restraints excluded: chain v residue 259 VAL Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 274 LEU Chi-restraints excluded: chain v residue 378 VAL Chi-restraints excluded: chain w residue 70 THR Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 88 GLN Chi-restraints excluded: chain w residue 94 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 56 ARG Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 7 GLU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 92 PHE Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 48 THR Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 822 optimal weight: 5.9990 chunk 560 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 735 optimal weight: 5.9990 chunk 407 optimal weight: 0.7980 chunk 842 optimal weight: 0.9980 chunk 682 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 504 optimal weight: 10.0000 chunk 886 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 133 GLN ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 ASN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN Q 49 ASN Z 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 157363 Z= 0.200 Angle : 0.567 16.966 235320 Z= 0.296 Chirality : 0.035 0.308 30039 Planarity : 0.004 0.114 12626 Dihedral : 22.730 179.835 78173 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 3.75 % Allowed : 19.44 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.11), residues: 5727 helix: 0.23 (0.12), residues: 1819 sheet: -0.41 (0.15), residues: 1159 loop : -1.20 (0.12), residues: 2749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 200 HIS 0.007 0.001 HIS p 84 PHE 0.015 0.001 PHE G 37 TYR 0.035 0.001 TYR l 65 ARG 0.008 0.000 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 981 time to evaluate : 6.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 196 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7425 (mp) REVERT: d 112 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: e 118 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9033 (mm) REVERT: g 92 ARG cc_start: 0.8322 (mpp-170) cc_final: 0.7348 (mtm180) REVERT: i 31 ASN cc_start: 0.8666 (t0) cc_final: 0.8232 (t0) REVERT: j 74 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8087 (mm) REVERT: k 33 MET cc_start: 0.7677 (tpt) cc_final: 0.7416 (tpt) REVERT: k 50 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8629 (mm) REVERT: m 62 ARG cc_start: 0.7223 (ttp-110) cc_final: 0.6874 (ttm170) REVERT: r 69 MET cc_start: 0.8339 (mmm) cc_final: 0.7918 (mmt) REVERT: t 10 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7334 (mmt180) REVERT: t 49 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8088 (mp) REVERT: v 66 MET cc_start: 0.8157 (ppp) cc_final: 0.7600 (tmm) REVERT: v 78 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8509 (mm) REVERT: v 102 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8279 (mp) REVERT: w 88 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: F 96 MET cc_start: 0.7783 (tpt) cc_final: 0.7519 (mmt) REVERT: F 114 PHE cc_start: 0.7768 (t80) cc_final: 0.7378 (t80) REVERT: O 32 TYR cc_start: 0.7886 (m-10) cc_final: 0.7617 (m-10) REVERT: P 90 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7781 (mtp-110) REVERT: Q 46 ASP cc_start: 0.7512 (t0) cc_final: 0.7194 (t0) REVERT: R 7 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: R 49 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8803 (ptmt) REVERT: V 22 ASP cc_start: 0.8327 (m-30) cc_final: 0.7633 (t0) REVERT: W 16 ASP cc_start: 0.8168 (t0) cc_final: 0.7794 (t0) REVERT: W 39 ASN cc_start: 0.8809 (t0) cc_final: 0.7954 (t0) REVERT: 5 11 GLU cc_start: 0.7576 (mp0) cc_final: 0.7327 (mp0) REVERT: 6 2 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8442 (ttpt) outliers start: 183 outliers final: 144 residues processed: 1086 average time/residue: 1.2493 time to fit residues: 2363.4413 Evaluate side-chains 1105 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 950 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain e residue 11 ASP Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 166 LEU Chi-restraints excluded: chain f residue 19 GLU Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain f residue 34 ASN Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 64 GLN Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 10 ARG Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 39 ILE Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 102 LEU Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain v residue 163 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 274 LEU Chi-restraints excluded: chain v residue 378 VAL Chi-restraints excluded: chain v residue 381 LEU Chi-restraints excluded: chain w residue 70 THR Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 88 GLN Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain R residue 7 GLU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 14 ASP Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 332 optimal weight: 10.0000 chunk 889 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 579 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 988 optimal weight: 6.9990 chunk 820 optimal weight: 9.9990 chunk 457 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 519 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 133 GLN d 59 HIS ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 46 HIS f 34 ASN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 65 ASN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN Q 49 ASN Z 16 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 157363 Z= 0.420 Angle : 0.686 17.017 235320 Z= 0.352 Chirality : 0.041 0.388 30039 Planarity : 0.005 0.115 12626 Dihedral : 22.753 178.811 78173 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.58 % Favored : 93.31 % Rotamer: Outliers : 5.39 % Allowed : 19.81 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5727 helix: 0.01 (0.12), residues: 1833 sheet: -0.51 (0.15), residues: 1167 loop : -1.34 (0.11), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 200 HIS 0.010 0.001 HIS l 85 PHE 0.028 0.002 PHE i 41 TYR 0.033 0.002 TYR l 65 ARG 0.012 0.001 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 952 time to evaluate : 6.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 169 GLU cc_start: 0.7907 (mp0) cc_final: 0.7685 (mp0) REVERT: b 196 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7419 (mp) REVERT: d 112 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: e 118 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9058 (mm) REVERT: g 92 ARG cc_start: 0.8340 (mpp-170) cc_final: 0.7384 (mtm180) REVERT: i 31 ASN cc_start: 0.8717 (t0) cc_final: 0.8317 (t0) REVERT: j 74 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8216 (mm) REVERT: k 33 MET cc_start: 0.7750 (tpt) cc_final: 0.7425 (tpt) REVERT: k 50 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8687 (mm) REVERT: q 83 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7229 (tm-30) REVERT: r 69 MET cc_start: 0.8367 (mmm) cc_final: 0.8048 (mmt) REVERT: t 3 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8168 (p0) REVERT: t 10 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7521 (mmt180) REVERT: t 49 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8077 (mp) REVERT: v 19 TYR cc_start: 0.7708 (t80) cc_final: 0.7453 (t80) REVERT: v 66 MET cc_start: 0.8181 (ppp) cc_final: 0.7591 (tmm) REVERT: v 78 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8638 (mm) REVERT: v 143 LYS cc_start: 0.7422 (mmtp) cc_final: 0.6716 (mmtp) REVERT: w 88 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7138 (mt0) REVERT: F 96 MET cc_start: 0.7775 (tpt) cc_final: 0.7432 (mmt) REVERT: O 32 TYR cc_start: 0.8113 (m-10) cc_final: 0.7827 (m-10) REVERT: O 111 GLU cc_start: 0.8127 (tp30) cc_final: 0.7856 (tp30) REVERT: P 8 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7881 (mtp85) REVERT: P 23 ASP cc_start: 0.7822 (m-30) cc_final: 0.7611 (m-30) REVERT: P 90 ARG cc_start: 0.8138 (mmt-90) cc_final: 0.7786 (mtp-110) REVERT: Q 1 MET cc_start: 0.6853 (tmm) cc_final: 0.6500 (tmm) REVERT: Q 46 ASP cc_start: 0.7735 (t0) cc_final: 0.6342 (p0) REVERT: R 7 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: R 100 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8836 (mp) REVERT: S 102 ASP cc_start: 0.8421 (t0) cc_final: 0.8161 (t0) REVERT: V 22 ASP cc_start: 0.8364 (m-30) cc_final: 0.7686 (t0) REVERT: W 39 ASN cc_start: 0.8882 (t0) cc_final: 0.7995 (t0) REVERT: Y 48 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: 6 2 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8464 (ttpt) outliers start: 263 outliers final: 203 residues processed: 1122 average time/residue: 1.2421 time to fit residues: 2438.6699 Evaluate side-chains 1144 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 927 time to evaluate : 6.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain e residue 11 ASP Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 166 LEU Chi-restraints excluded: chain f residue 19 GLU Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 44 LEU Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 61 TRP Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain p residue 60 MET Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 10 ARG Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 39 ILE Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 65 GLU Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 163 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 214 VAL Chi-restraints excluded: chain v residue 234 THR Chi-restraints excluded: chain v residue 259 VAL Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 274 LEU Chi-restraints excluded: chain v residue 378 VAL Chi-restraints excluded: chain w residue 70 THR Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 88 GLN Chi-restraints excluded: chain w residue 94 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 7 GLU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 48 GLN Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 2 residue 4 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 953 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 563 optimal weight: 10.0000 chunk 722 optimal weight: 30.0000 chunk 559 optimal weight: 8.9990 chunk 832 optimal weight: 5.9990 chunk 552 optimal weight: 10.0000 chunk 985 optimal weight: 20.0000 chunk 616 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 133 GLN ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 74 HIS v 249 GLN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN ** Q 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Z 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 157363 Z= 0.459 Angle : 0.723 17.118 235320 Z= 0.369 Chirality : 0.043 0.403 30039 Planarity : 0.006 0.115 12626 Dihedral : 22.803 178.521 78173 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 5.82 % Allowed : 20.41 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 5727 helix: -0.14 (0.12), residues: 1837 sheet: -0.60 (0.15), residues: 1162 loop : -1.49 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 200 HIS 0.011 0.001 HIS l 85 PHE 0.028 0.002 PHE i 41 TYR 0.043 0.002 TYR l 65 ARG 0.012 0.001 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 937 time to evaluate : 6.201 Fit side-chains REVERT: b 196 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7417 (mp) REVERT: c 178 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.6649 (ptp90) REVERT: d 112 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: d 194 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8978 (mm) REVERT: e 118 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9048 (mm) REVERT: e 143 ASP cc_start: 0.8677 (t0) cc_final: 0.8465 (t0) REVERT: g 92 ARG cc_start: 0.8350 (mpp-170) cc_final: 0.7426 (mtm180) REVERT: i 31 ASN cc_start: 0.8782 (t0) cc_final: 0.8395 (t0) REVERT: j 57 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7553 (ttmt) REVERT: j 74 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8276 (mm) REVERT: k 33 MET cc_start: 0.7726 (tpt) cc_final: 0.7472 (tpt) REVERT: k 50 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8705 (mm) REVERT: r 69 MET cc_start: 0.8348 (mmm) cc_final: 0.8040 (mmt) REVERT: t 10 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7530 (mmt180) REVERT: t 49 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8078 (mp) REVERT: v 66 MET cc_start: 0.8135 (ppp) cc_final: 0.7563 (tmm) REVERT: v 78 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8643 (mm) REVERT: v 155 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7004 (tmmt) REVERT: w 88 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: F 96 MET cc_start: 0.7801 (tpt) cc_final: 0.7428 (mmt) REVERT: F 165 GLU cc_start: 0.7320 (pm20) cc_final: 0.7087 (pm20) REVERT: G 62 ARG cc_start: 0.8258 (ppt170) cc_final: 0.8028 (ptt90) REVERT: P 8 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7912 (mtp85) REVERT: P 23 ASP cc_start: 0.7828 (m-30) cc_final: 0.7227 (m-30) REVERT: P 90 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7764 (mtp-110) REVERT: Q 1 MET cc_start: 0.6683 (tmm) cc_final: 0.6450 (tmm) REVERT: Q 46 ASP cc_start: 0.7813 (t0) cc_final: 0.6726 (p0) REVERT: R 3 LYS cc_start: 0.8436 (mtpt) cc_final: 0.6941 (mtmt) REVERT: R 7 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: R 100 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8825 (mp) REVERT: S 102 ASP cc_start: 0.8442 (t0) cc_final: 0.8188 (t0) REVERT: V 22 ASP cc_start: 0.8412 (m-30) cc_final: 0.7712 (t0) REVERT: W 16 ASP cc_start: 0.8098 (t0) cc_final: 0.7548 (t0) REVERT: W 39 ASN cc_start: 0.8811 (t0) cc_final: 0.7963 (t0) REVERT: Y 48 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: Z 45 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7649 (ptmt) REVERT: 1 42 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7575 (tpt-90) REVERT: 6 2 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8488 (ttpt) outliers start: 284 outliers final: 228 residues processed: 1122 average time/residue: 1.2623 time to fit residues: 2470.3341 Evaluate side-chains 1176 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 929 time to evaluate : 6.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 43 LYS Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 11 ASP Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 147 GLN Chi-restraints excluded: chain e residue 166 LEU Chi-restraints excluded: chain f residue 4 LYS Chi-restraints excluded: chain f residue 19 GLU Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 44 LEU Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain p residue 60 MET Chi-restraints excluded: chain p residue 69 THR Chi-restraints excluded: chain q residue 11 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 10 ARG Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 65 GLU Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain v residue 155 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 163 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 214 VAL Chi-restraints excluded: chain v residue 234 THR Chi-restraints excluded: chain v residue 249 GLN Chi-restraints excluded: chain v residue 259 VAL Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 274 LEU Chi-restraints excluded: chain v residue 308 VAL Chi-restraints excluded: chain v residue 312 ASP Chi-restraints excluded: chain v residue 315 VAL Chi-restraints excluded: chain v residue 378 VAL Chi-restraints excluded: chain w residue 70 THR Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 88 GLN Chi-restraints excluded: chain w residue 94 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain P residue 135 VAL Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 7 GLU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 48 GLN Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Z residue 45 LYS Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 34 THR Chi-restraints excluded: chain 1 residue 42 ARG Chi-restraints excluded: chain 1 residue 56 ILE Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 2 residue 4 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 27 MET Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 14 ASP Chi-restraints excluded: chain 5 residue 48 THR Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 8 residue 7 VAL Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 609 optimal weight: 10.0000 chunk 393 optimal weight: 9.9990 chunk 588 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 626 optimal weight: 10.0000 chunk 671 optimal weight: 10.0000 chunk 487 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 774 optimal weight: 4.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 64 ASN c 133 GLN ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 ASN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 32 ASN v 249 GLN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN Q 49 ASN Z 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 157363 Z= 0.300 Angle : 0.628 16.914 235320 Z= 0.326 Chirality : 0.038 0.353 30039 Planarity : 0.005 0.115 12626 Dihedral : 22.765 179.757 78173 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 4.86 % Allowed : 21.90 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5727 helix: 0.07 (0.12), residues: 1831 sheet: -0.54 (0.15), residues: 1163 loop : -1.37 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 200 HIS 0.030 0.001 HIS q 74 PHE 0.021 0.002 PHE F 77 TYR 0.040 0.002 TYR l 65 ARG 0.013 0.000 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 952 time to evaluate : 6.246 Fit side-chains revert: symmetry clash REVERT: b 27 MET cc_start: 0.8853 (mmm) cc_final: 0.8642 (mmm) REVERT: b 163 ILE cc_start: 0.8666 (mt) cc_final: 0.8252 (mm) REVERT: b 169 GLU cc_start: 0.7657 (mp0) cc_final: 0.7414 (mp0) REVERT: b 196 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7443 (mp) REVERT: c 178 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6603 (ptp90) REVERT: d 112 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: d 194 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8892 (mm) REVERT: e 118 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9061 (mm) REVERT: e 143 ASP cc_start: 0.8677 (t0) cc_final: 0.8463 (t0) REVERT: g 92 ARG cc_start: 0.8333 (mpp-170) cc_final: 0.7383 (mtm180) REVERT: i 31 ASN cc_start: 0.8770 (t0) cc_final: 0.8369 (t0) REVERT: j 57 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7497 (mtmt) REVERT: j 74 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8189 (mm) REVERT: k 33 MET cc_start: 0.7686 (tpt) cc_final: 0.7478 (tpt) REVERT: k 50 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8632 (mm) REVERT: m 62 ARG cc_start: 0.7314 (ttp-110) cc_final: 0.6965 (ttm170) REVERT: n 52 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: r 69 MET cc_start: 0.8311 (mmm) cc_final: 0.8071 (mmt) REVERT: t 3 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8087 (p0) REVERT: t 10 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7388 (mmt180) REVERT: t 49 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8081 (mp) REVERT: v 66 MET cc_start: 0.8099 (ppp) cc_final: 0.7546 (tmm) REVERT: v 78 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8594 (mm) REVERT: v 155 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6920 (tmmt) REVERT: w 88 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: F 96 MET cc_start: 0.7820 (tpt) cc_final: 0.7523 (mmt) REVERT: G 62 ARG cc_start: 0.8194 (ppt170) cc_final: 0.7955 (ptt90) REVERT: P 8 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.7781 (mtp85) REVERT: P 23 ASP cc_start: 0.7821 (m-30) cc_final: 0.7591 (m-30) REVERT: P 72 GLU cc_start: 0.8233 (pp20) cc_final: 0.7932 (pp20) REVERT: P 90 ARG cc_start: 0.8094 (mmt-90) cc_final: 0.7756 (mtp-110) REVERT: Q 46 ASP cc_start: 0.7714 (t0) cc_final: 0.6555 (p0) REVERT: R 3 LYS cc_start: 0.8526 (mtpt) cc_final: 0.7078 (mtmt) REVERT: R 7 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: R 100 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8849 (mp) REVERT: V 22 ASP cc_start: 0.8396 (m-30) cc_final: 0.7660 (t0) REVERT: W 39 ASN cc_start: 0.8803 (t0) cc_final: 0.7941 (t0) REVERT: Y 48 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: Z 45 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7628 (ptmt) outliers start: 237 outliers final: 200 residues processed: 1103 average time/residue: 1.2867 time to fit residues: 2506.1485 Evaluate side-chains 1155 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 936 time to evaluate : 5.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 ARG Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 18 TRP Chi-restraints excluded: chain c residue 40 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 100 ILE Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 151 GLN Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 43 LYS Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain d residue 153 GLU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 11 ASP Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 78 VAL Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 166 LEU Chi-restraints excluded: chain f residue 4 LYS Chi-restraints excluded: chain f residue 19 GLU Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 60 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 15 SER Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 47 SER Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 101 GLN Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 72 ASN Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 117 THR Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain m residue 114 LYS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 46 GLU Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain o residue 20 THR Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain p residue 60 MET Chi-restraints excluded: chain p residue 69 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 10 ARG Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 54 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 65 GLU Chi-restraints excluded: chain v residue 78 LEU Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain v residue 155 LYS Chi-restraints excluded: chain v residue 156 ILE Chi-restraints excluded: chain v residue 163 ILE Chi-restraints excluded: chain v residue 170 LEU Chi-restraints excluded: chain v residue 259 VAL Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 274 LEU Chi-restraints excluded: chain v residue 308 VAL Chi-restraints excluded: chain v residue 312 ASP Chi-restraints excluded: chain v residue 378 VAL Chi-restraints excluded: chain w residue 70 THR Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 88 GLN Chi-restraints excluded: chain w residue 94 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 152 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 MET Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 7 GLU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain S residue 34 VAL Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 6 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 48 GLN Chi-restraints excluded: chain Y residue 53 ILE Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 2 residue 4 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 48 THR Chi-restraints excluded: chain 7 residue 30 SER Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 896 optimal weight: 0.8980 chunk 943 optimal weight: 0.9990 chunk 860 optimal weight: 6.9990 chunk 917 optimal weight: 0.7980 chunk 552 optimal weight: 10.0000 chunk 399 optimal weight: 6.9990 chunk 720 optimal weight: 20.0000 chunk 281 optimal weight: 0.9990 chunk 829 optimal weight: 5.9990 chunk 868 optimal weight: 0.9990 chunk 914 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 64 ASN c 133 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS k 28 ASN k 40 ASN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 HIS q 74 HIS t 74 ASN ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN Q 49 ASN R 41 GLN Z 16 ASN Z 23 ASN 7 31 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 157363 Z= 0.116 Angle : 0.536 16.769 235320 Z= 0.280 Chirality : 0.032 0.278 30039 Planarity : 0.004 0.114 12626 Dihedral : 22.714 179.084 78173 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.83 % Rotamer: Outliers : 3.08 % Allowed : 23.85 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 5727 helix: 0.49 (0.13), residues: 1827 sheet: -0.44 (0.15), residues: 1170 loop : -1.08 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP k 44 HIS 0.011 0.001 HIS q 74 PHE 0.019 0.001 PHE b 56 TYR 0.032 0.001 TYR l 65 ARG 0.014 0.000 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1015 time to evaluate : 6.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 56 PHE cc_start: 0.8938 (t80) cc_final: 0.8728 (t80) REVERT: b 155 LYS cc_start: 0.7318 (mmmm) cc_final: 0.6778 (mtpp) REVERT: b 163 ILE cc_start: 0.8584 (mt) cc_final: 0.8274 (mm) REVERT: b 169 GLU cc_start: 0.7519 (mp0) cc_final: 0.7306 (mp0) REVERT: c 178 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6602 (ptp90) REVERT: d 44 ILE cc_start: 0.7385 (tt) cc_final: 0.7092 (mm) REVERT: d 112 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: e 143 ASP cc_start: 0.8662 (t0) cc_final: 0.8453 (t0) REVERT: g 18 TYR cc_start: 0.7448 (m-80) cc_final: 0.7199 (m-80) REVERT: g 92 ARG cc_start: 0.8263 (mpp-170) cc_final: 0.7278 (mtm180) REVERT: i 31 ASN cc_start: 0.8659 (t0) cc_final: 0.8291 (t0) REVERT: k 50 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8522 (mm) REVERT: m 62 ARG cc_start: 0.7193 (ttp-110) cc_final: 0.6898 (ttm170) REVERT: n 52 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: r 69 MET cc_start: 0.8246 (mmm) cc_final: 0.8043 (mmt) REVERT: t 25 ARG cc_start: 0.8891 (ttm170) cc_final: 0.8662 (ttm110) REVERT: v 66 MET cc_start: 0.8016 (ppp) cc_final: 0.7445 (tmm) REVERT: w 88 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7415 (mt0) REVERT: F 96 MET cc_start: 0.7851 (tpt) cc_final: 0.7597 (mmt) REVERT: G 3 ARG cc_start: 0.5497 (ptt-90) cc_final: 0.5279 (ptt-90) REVERT: G 62 ARG cc_start: 0.8152 (ppt170) cc_final: 0.7591 (ptt90) REVERT: P 8 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7763 (mtp85) REVERT: P 23 ASP cc_start: 0.7638 (m-30) cc_final: 0.6922 (m-30) REVERT: P 72 GLU cc_start: 0.8184 (pp20) cc_final: 0.7878 (pp20) REVERT: P 90 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.7759 (mtp-110) REVERT: Q 46 ASP cc_start: 0.7562 (t0) cc_final: 0.6031 (p0) REVERT: Q 49 ASN cc_start: 0.8901 (m-40) cc_final: 0.8651 (m110) REVERT: R 3 LYS cc_start: 0.8507 (mtpt) cc_final: 0.7087 (mtmt) REVERT: R 7 GLU cc_start: 0.8161 (mp0) cc_final: 0.7506 (mp0) REVERT: R 49 LYS cc_start: 0.9007 (ptpt) cc_final: 0.8788 (ptmt) REVERT: U 68 ASP cc_start: 0.8350 (t0) cc_final: 0.8116 (t0) REVERT: V 22 ASP cc_start: 0.8337 (m-30) cc_final: 0.7607 (t0) REVERT: W 16 ASP cc_start: 0.7999 (t70) cc_final: 0.7592 (t0) REVERT: Y 40 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8371 (p) REVERT: Z 45 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7595 (ptmt) REVERT: 4 50 ASP cc_start: 0.8007 (t0) cc_final: 0.7799 (t0) outliers start: 150 outliers final: 112 residues processed: 1104 average time/residue: 1.2591 time to fit residues: 2417.2171 Evaluate side-chains 1084 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 965 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 34 GLU Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 43 LYS Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 19 GLU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 56 ASN Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 44 LEU Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain t residue 32 ILE Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 234 THR Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 274 LEU Chi-restraints excluded: chain v residue 308 VAL Chi-restraints excluded: chain v residue 312 ASP Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 88 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 2 residue 4 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 602 optimal weight: 10.0000 chunk 970 optimal weight: 9.9990 chunk 592 optimal weight: 10.0000 chunk 460 optimal weight: 20.0000 chunk 674 optimal weight: 10.0000 chunk 1018 optimal weight: 5.9990 chunk 937 optimal weight: 0.2980 chunk 810 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 overall best weight: 6.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN k 40 ASN l 5 ASN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 ASN v 12 GLN v 169 HIS ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN W 39 ASN Z 16 ASN 8 34 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 157363 Z= 0.407 Angle : 0.672 16.806 235320 Z= 0.343 Chirality : 0.041 0.373 30039 Planarity : 0.005 0.115 12626 Dihedral : 22.693 179.216 78173 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.95 % Allowed : 24.16 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 5727 helix: 0.22 (0.12), residues: 1840 sheet: -0.42 (0.16), residues: 1161 loop : -1.29 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP k 44 HIS 0.010 0.001 HIS l 85 PHE 0.038 0.002 PHE b 32 TYR 0.030 0.002 TYR l 65 ARG 0.015 0.001 ARG F 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11454 Ramachandran restraints generated. 5727 Oldfield, 0 Emsley, 5727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 952 time to evaluate : 6.150 Fit side-chains REVERT: b 163 ILE cc_start: 0.8643 (mt) cc_final: 0.8236 (mm) REVERT: b 169 GLU cc_start: 0.7722 (mp0) cc_final: 0.7421 (mp0) REVERT: b 196 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7488 (mp) REVERT: c 178 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6567 (ptp90) REVERT: d 112 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: e 143 ASP cc_start: 0.8658 (t0) cc_final: 0.8456 (t0) REVERT: g 18 TYR cc_start: 0.7494 (m-80) cc_final: 0.7248 (m-80) REVERT: g 92 ARG cc_start: 0.8343 (mpp-170) cc_final: 0.7584 (mpp80) REVERT: i 31 ASN cc_start: 0.8798 (t0) cc_final: 0.8426 (t0) REVERT: k 50 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8646 (mm) REVERT: n 52 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: r 69 MET cc_start: 0.8318 (mmm) cc_final: 0.8068 (mmt) REVERT: v 66 MET cc_start: 0.8111 (ppp) cc_final: 0.7477 (tmm) REVERT: v 155 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6824 (tmmt) REVERT: w 88 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7194 (mt0) REVERT: C 201 GLU cc_start: 0.8308 (pt0) cc_final: 0.8023 (mt-10) REVERT: F 96 MET cc_start: 0.7933 (tpt) cc_final: 0.7608 (mmt) REVERT: G 37 PHE cc_start: 0.8416 (m-80) cc_final: 0.7701 (m-10) REVERT: G 62 ARG cc_start: 0.8209 (ppt170) cc_final: 0.7930 (ptt90) REVERT: P 8 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.7871 (mtp85) REVERT: P 72 GLU cc_start: 0.8209 (pp20) cc_final: 0.7903 (pp20) REVERT: P 90 ARG cc_start: 0.8116 (mmt-90) cc_final: 0.7761 (mtp-110) REVERT: Q 46 ASP cc_start: 0.7750 (t0) cc_final: 0.6635 (p0) REVERT: R 3 LYS cc_start: 0.8587 (mtpt) cc_final: 0.7193 (mtmt) REVERT: R 7 GLU cc_start: 0.8241 (mp0) cc_final: 0.7588 (mp0) REVERT: V 22 ASP cc_start: 0.8391 (m-30) cc_final: 0.7682 (t0) REVERT: Z 45 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7653 (ptmt) outliers start: 144 outliers final: 124 residues processed: 1043 average time/residue: 1.2884 time to fit residues: 2357.3120 Evaluate side-chains 1080 residues out of total 4924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 948 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 200 TRP Chi-restraints excluded: chain d residue 43 LYS Chi-restraints excluded: chain d residue 95 ASP Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 122 ASP Chi-restraints excluded: chain d residue 133 VAL Chi-restraints excluded: chain e residue 26 VAL Chi-restraints excluded: chain e residue 35 THR Chi-restraints excluded: chain e residue 112 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 19 GLU Chi-restraints excluded: chain f residue 32 THR Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 44 LEU Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 ASN Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 47 SER Chi-restraints excluded: chain j residue 90 LEU Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 94 GLU Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 52 GLN Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 57 LEU Chi-restraints excluded: chain p residue 59 TRP Chi-restraints excluded: chain q residue 27 VAL Chi-restraints excluded: chain r residue 23 THR Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 11 VAL Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 44 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 155 LYS Chi-restraints excluded: chain v residue 234 THR Chi-restraints excluded: chain v residue 266 LEU Chi-restraints excluded: chain v residue 274 LEU Chi-restraints excluded: chain v residue 308 VAL Chi-restraints excluded: chain v residue 312 ASP Chi-restraints excluded: chain w residue 70 THR Chi-restraints excluded: chain w residue 81 ILE Chi-restraints excluded: chain w residue 88 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 15 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 42 LYS Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 131 ILE Chi-restraints excluded: chain P residue 132 ILE Chi-restraints excluded: chain Q residue 2 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 37 ASN Chi-restraints excluded: chain Q residue 62 ASP Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 75 LYS Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 100 VAL Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 2 residue 4 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 24 LEU Chi-restraints excluded: chain 4 residue 39 SER Chi-restraints excluded: chain 8 residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1022 random chunks: chunk 644 optimal weight: 50.0000 chunk 863 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 747 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 812 optimal weight: 5.9990 chunk 339 optimal weight: 2.9990 chunk 833 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 64 ASN c 133 GLN ** d 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 122 GLN ** l 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN Q 49 ASN Z 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.111361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085045 restraints weight = 302710.282| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.18 r_work: 0.3035 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1368 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: