Starting phenix.real_space_refine on Wed Mar 20 12:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdw_19077/03_2024/8rdw_19077_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdw_19077/03_2024/8rdw_19077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdw_19077/03_2024/8rdw_19077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdw_19077/03_2024/8rdw_19077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdw_19077/03_2024/8rdw_19077_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdw_19077/03_2024/8rdw_19077_updated.pdb" } resolution = 2.74 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= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 4349 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 72497 2.51 5 N 26506 2.21 5 O 39151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 26": "OE1" <-> "OE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H ASP 348": "OD1" <-> "OD2" Residue "R3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R3 GLU 35": "OE1" <-> "OE2" Residue "A4 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 ASP 172": "OD1" <-> "OD2" Residue "A4 ASP 224": "OD1" <-> "OD2" Residue "E5 ASP 24": "OD1" <-> "OD2" Residue "E5 GLU 60": "OE1" <-> "OE2" Residue "E5 GLU 70": "OE1" <-> "OE2" Residue "E5 ASP 127": "OD1" <-> "OD2" Residue "L6 GLU 70": "OE1" <-> "OE2" Residue "F7 TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F7 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E9 GLU 122": "OE1" <-> "OE2" Residue "E9 GLU 151": "OE1" <-> "OE2" Residue "E9 GLU 197": "OE1" <-> "OE2" Residue "aA ASP 30": "OD1" <-> "OD2" Residue "aA GLU 35": "OE1" <-> "OE2" Residue "MB GLU 30": "OE1" <-> "OE2" Residue "MB GLU 32": "OE1" <-> "OE2" Residue "MB GLU 49": "OE1" <-> "OE2" Residue "UC GLU 16": "OE1" <-> "OE2" Residue "UC GLU 42": "OE1" <-> "OE2" Residue "UC GLU 76": "OE1" <-> "OE2" Residue "WD ASP 65": "OD1" <-> "OD2" Residue "RF ASP 22": "OD1" <-> "OD2" Residue "fJ TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HK TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HK GLU 29": "OE1" <-> "OE2" Residue "OL TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OL GLU 25": "OE1" <-> "OE2" Residue "MM GLU 66": "OE1" <-> "OE2" Residue "PO GLU 111": "OE1" <-> "OE2" Residue "PO GLU 116": "OE1" <-> "OE2" Residue "SP ASP 12": "OD1" <-> "OD2" Residue "BQ GLU 43": "OE1" <-> "OE2" Residue "BQ GLU 69": "OE1" <-> "OE2" Residue "BQ GLU 75": "OE1" <-> "OE2" Residue "GS GLU 48": "OE1" <-> "OE2" Residue "CT PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KU PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NV GLU 39": "OE1" <-> "OE2" Residue "IX ASP 19": "OD1" <-> "OD2" Residue "JY ASP 63": "OD1" <-> "OD2" Residue "QZ ASP 63": "OD1" <-> "OD2" Residue "Qb GLU 23": "OE1" <-> "OE2" Residue "Qb GLU 70": "OE1" <-> "OE2" Residue "Nc TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Nc GLU 47": "OE1" <-> "OE2" Residue "Kd PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Je GLU 45": "OE1" <-> "OE2" Residue "Je ASP 56": "OD1" <-> "OD2" Residue "Je PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af ASP 44": "OD1" <-> "OD2" Residue "Af ASP 58": "OD1" <-> "OD2" Residue "Af GLU 91": "OE1" <-> "OE2" Residue "Af GLU 94": "OE1" <-> "OE2" Residue "Lg PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 91": "OE1" <-> "OE2" Residue "Lg GLU 111": "OE1" <-> "OE2" Residue "Lg GLU 116": "OE1" <-> "OE2" Residue "Oi ASP 26": "OD1" <-> "OD2" Residue "Oi TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Pj ASP 29": "OD1" <-> "OD2" Residue "Pj ASP 69": "OD1" <-> "OD2" Residue "bk ASP 3": "OD1" <-> "OD2" Residue "bk GLU 47": "OE1" <-> "OE2" Residue "Cl ASP 98": "OD1" <-> "OD2" Residue "Cl ASP 114": "OD1" <-> "OD2" Residue "Cl ASP 264": "OD1" <-> "OD2" Residue "Dm GLU 89": "OE1" <-> "OE2" Residue "Dm TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Dm ASP 146": "OD1" <-> "OD2" Residue "Sn GLU 17": "OE1" <-> "OE2" Residue "Sn ASP 34": "OD1" <-> "OD2" Residue "Sn TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "To ASP 36": "OD1" <-> "OD2" Residue "ep GLU 30": "OE1" <-> "OE2" Residue "C1 ASP 20": "OD1" <-> "OD2" Residue "C1 GLU 45": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142686 Number of models: 1 Model: "" Number of chains: 58 Chain: "B" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2871 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 356} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 127 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 965 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "H" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2918 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 367} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Z2" Number of atoms: 58553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2729, 58553 Classifications: {'RNA': 2729} Modifications used: {'rna2p_pur': 268, 'rna2p_pyr': 152, 'rna3p_pur': 1309, 'rna3p_pyr': 1000} Link IDs: {'rna2p': 420, 'rna3p': 2308} Chain breaks: 7 Chain: "R3" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "A4" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1816 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "E5" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1151 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "L6" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "F7" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1362 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 169} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D8" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2446 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 52, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 100} Chain: "E9" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1537 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "aA" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 442 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "MB" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "UC" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "WD" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 618 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "XE" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 502 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "RF" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "FG" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 849 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "VH" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 626 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "TI" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "fJ" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 493 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "HK" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 811 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "OL" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "MM" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "iN" Number of atoms: 32246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1503, 32246 Classifications: {'RNA': 1503} Modifications used: {'rna2p_pur': 120, 'rna2p_pyr': 84, 'rna3p_pur': 741, 'rna3p_pyr': 558} Link IDs: {'rna2p': 204, 'rna3p': 1298} Chain breaks: 3 Chain: "PO" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "SP" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "BQ" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 974 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "GR" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1357 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "GS" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1200 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 6, 'TRANS': 146} Chain: "CT" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "KU" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 842 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "NV" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 472 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "YW" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 438 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "IX" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1108 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "JY" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "QZ" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 632 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Ba" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 369 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Qb" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "Nc" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 852 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Kd" Number of atoms: 1062 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1058 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 144, 1055 Classifications: {'peptide': 144} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 140} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1058 Chain: "Je" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 937 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "Af" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1548 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "Lg" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "dh" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 519 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "Oi" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "Pj" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "bk" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Cl" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2107 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "Dm" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1689 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Sn" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "To" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "ep" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 298 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "C1" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 374 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 49.30, per 1000 atoms: 0.35 Number of scatterers: 142686 At special positions: 0 Unit cell: (219.792, 236.421, 276.909, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 182 16.00 P 4349 15.00 Mg 1 11.99 O 39151 8.00 N 26506 7.00 C 72497 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: 58.89 Conformation dependent library (CDL) restraints added in 7.2 seconds 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11642 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: 191 helices and 75 sheets defined 38.7% alpha, 20.0% beta 1468 base pairs and 2240 stacking pairs defined. Time for finding SS restraints: 73.02 Creating SS restraints... Processing helix chain 'B' and resid 4 through 12 removed outlier: 5.444A pdb=" N GLU B 10 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS B 12 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 52 removed outlier: 7.510A pdb=" N ASP B 31 " --> pdb=" O HIS B 27 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Proline residue: B 34 - end of helix Processing helix chain 'B' and resid 53 through 69 removed outlier: 4.153A pdb=" N ASP B 62 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 4.311A pdb=" N ALA B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 6.851A pdb=" N ASN B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 156' Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.609A pdb=" N THR B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 207 removed outlier: 4.292A pdb=" N GLU B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 246 through 280 removed outlier: 3.583A pdb=" N GLN B 255 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.663A pdb=" N GLY B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 removed outlier: 4.887A pdb=" N SER B 358 " --> pdb=" O GLN B 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'F' and resid 32 through 38 removed outlier: 4.262A pdb=" N SER F 38 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 54 Proline residue: F 49 - end of helix removed outlier: 3.740A pdb=" N LEU F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 90 removed outlier: 4.062A pdb=" N ALA F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP F 90 " --> pdb=" O ILE F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 100 removed outlier: 4.651A pdb=" N ALA F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 38 removed outlier: 3.757A pdb=" N ILE H 38 " --> pdb=" O THR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 53 removed outlier: 3.621A pdb=" N ILE H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 95 Processing helix chain 'H' and resid 113 through 127 Processing helix chain 'H' and resid 137 through 142 removed outlier: 3.547A pdb=" N VAL H 141 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP H 142 " --> pdb=" O CYS H 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 137 through 142' Processing helix chain 'H' and resid 143 through 162 removed outlier: 4.713A pdb=" N LEU H 147 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 181 Processing helix chain 'H' and resid 187 through 201 Processing helix chain 'H' and resid 207 through 212 removed outlier: 5.393A pdb=" N ALA H 212 " --> pdb=" O ASP H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 290 removed outlier: 3.956A pdb=" N VAL H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLN H 290 " --> pdb=" O ARG H 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 285 through 290' Processing helix chain 'R3' and resid 25 through 34 removed outlier: 4.289A pdb=" N GLNR3 31 " --> pdb=" O GLUR3 27 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYRR3 32 " --> pdb=" O LEUR3 28 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILER3 33 " --> pdb=" O LEUR3 29 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SERR3 34 " --> pdb=" O LYSR3 30 " (cutoff:3.500A) Processing helix chain 'R3' and resid 41 through 46 Processing helix chain 'R3' and resid 48 through 66 Processing helix chain 'A4' and resid 10 through 18 removed outlier: 4.177A pdb=" N LEUA4 14 " --> pdb=" O GLUA4 10 " (cutoff:3.500A) Processing helix chain 'A4' and resid 47 through 69 removed outlier: 3.776A pdb=" N GLYA4 64 " --> pdb=" O ASNA4 60 " (cutoff:3.500A) Processing helix chain 'A4' and resid 81 through 93 removed outlier: 4.005A pdb=" N ILEA4 85 " --> pdb=" O ALAA4 81 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALAA4 86 " --> pdb=" O SERA4 82 " (cutoff:3.500A) Processing helix chain 'A4' and resid 110 through 129 removed outlier: 4.765A pdb=" N GLNA4 114 " --> pdb=" O LYSA4 110 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SERA4 115 " --> pdb=" O THRA4 111 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASPA4 128 " --> pdb=" O LYSA4 124 " (cutoff:3.500A) Processing helix chain 'A4' and resid 130 through 135 removed outlier: 4.266A pdb=" N LEUA4 134 " --> pdb=" O THRA4 130 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N THRA4 135 " --> pdb=" O PHEA4 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A4' and resid 130 through 135' Processing helix chain 'A4' and resid 136 through 154 removed outlier: 3.687A pdb=" N LEUA4 140 " --> pdb=" O LYSA4 136 " (cutoff:3.500A) Processing helix chain 'A4' and resid 155 through 160 removed outlier: 4.711A pdb=" N META4 159 " --> pdb=" O GLYA4 155 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLYA4 160 " --> pdb=" O ILEA4 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A4' and resid 155 through 160' Processing helix chain 'A4' and resid 170 through 175 Processing helix chain 'A4' and resid 176 through 185 Processing helix chain 'A4' and resid 211 through 236 removed outlier: 3.807A pdb=" N THRA4 235 " --> pdb=" O GLUA4 231 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLNA4 236 " --> pdb=" O TYRA4 232 " (cutoff:3.500A) Processing helix chain 'A4' and resid 104 through 109 removed outlier: 3.887A pdb=" N TRPA4 109 " --> pdb=" O GLYA4 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A4' and resid 104 through 109' Processing helix chain 'E5' and resid 60 through 76 removed outlier: 3.696A pdb=" N ARGE5 74 " --> pdb=" O GLUE5 70 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASNE5 75 " --> pdb=" O ALAE5 71 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N METE5 76 " --> pdb=" O ALAE5 72 " (cutoff:3.500A) Processing helix chain 'E5' and resid 113 through 124 removed outlier: 3.781A pdb=" N VALE5 119 " --> pdb=" O ALAE5 115 " (cutoff:3.500A) Processing helix chain 'E5' and resid 137 through 152 Processing helix chain 'E5' and resid 154 through 163 Processing helix chain 'E5' and resid 165 through 170 removed outlier: 3.977A pdb=" N LEUE5 170 " --> pdb=" O VALE5 166 " (cutoff:3.500A) Processing helix chain 'L6' and resid 3 through 10 removed outlier: 3.686A pdb=" N ARGL6 9 " --> pdb=" O ASNL6 5 " (cutoff:3.500A) Processing helix chain 'L6' and resid 113 through 118 removed outlier: 3.646A pdb=" N TYRL6 117 " --> pdb=" O GLYL6 113 " (cutoff:3.500A) Processing helix chain 'F7' and resid 2 through 11 Processing helix chain 'F7' and resid 12 through 21 removed outlier: 3.597A pdb=" N LYSF7 17 " --> pdb=" O LYSF7 13 " (cutoff:3.500A) Processing helix chain 'F7' and resid 47 through 61 removed outlier: 5.606A pdb=" N GLUF7 51 " --> pdb=" O LYSF7 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLYF7 52 " --> pdb=" O LYSF7 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALAF7 59 " --> pdb=" O ALAF7 55 " (cutoff:3.500A) Processing helix chain 'F7' and resid 93 through 111 removed outlier: 3.641A pdb=" N TYRF7 97 " --> pdb=" O GLYF7 93 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALAF7 107 " --> pdb=" O LEUF7 103 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILEF7 108 " --> pdb=" O ILEF7 104 " (cutoff:3.500A) Proline residue: F7 109 - end of helix Processing helix chain 'F7' and resid 162 through 174 removed outlier: 3.881A pdb=" N PHEF7 173 " --> pdb=" O LEUF7 169 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLYF7 174 " --> pdb=" O LEUF7 170 " (cutoff:3.500A) Processing helix chain 'F7' and resid 134 through 139 removed outlier: 3.660A pdb=" N PHEF7 138 " --> pdb=" O GLNF7 135 " (cutoff:3.500A) Proline residue: F7 139 - end of helix Processing helix chain 'E9' and resid 23 through 40 removed outlier: 3.792A pdb=" N ARGE9 39 " --> pdb=" O LEUE9 35 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLNE9 40 " --> pdb=" O ALAE9 36 " (cutoff:3.500A) Processing helix chain 'E9' and resid 96 through 115 Processing helix chain 'E9' and resid 129 through 141 removed outlier: 3.638A pdb=" N LEUE9 133 " --> pdb=" O LYSE9 129 " (cutoff:3.500A) Processing helix chain 'E9' and resid 153 through 164 removed outlier: 4.434A pdb=" N LEUE9 158 " --> pdb=" O GLUE9 154 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASNE9 162 " --> pdb=" O LEUE9 158 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILEE9 163 " --> pdb=" O ALAE9 159 " (cutoff:3.500A) Proline residue: E9 164 - end of helix Processing helix chain 'E9' and resid 175 through 182 removed outlier: 3.610A pdb=" N ILEE9 180 " --> pdb=" O PROE9 176 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHEE9 182 " --> pdb=" O SERE9 178 " (cutoff:3.500A) Processing helix chain 'E9' and resid 188 through 199 Processing helix chain 'E9' and resid 15 through 20 Processing helix chain 'aA' and resid 9 through 19 removed outlier: 3.502A pdb=" N ARGaA 17 " --> pdb=" O ARGaA 13 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HISaA 19 " --> pdb=" O METaA 15 " (cutoff:3.500A) Processing helix chain 'MB' and resid 13 through 32 Processing helix chain 'MB' and resid 37 through 58 removed outlier: 3.754A pdb=" N ARGMB 45 " --> pdb=" O ALAMB 41 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARGMB 46 " --> pdb=" O LYSMB 42 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VALMB 47 " --> pdb=" O GLUMB 43 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLUMB 49 " --> pdb=" O ARGMB 45 " (cutoff:3.500A) Proline residue: MB 50 - end of helix removed outlier: 4.609A pdb=" N GLUMB 57 " --> pdb=" O THRMB 53 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASPMB 58 " --> pdb=" O METMB 54 " (cutoff:3.500A) Processing helix chain 'MB' and resid 59 through 71 Processing helix chain 'MB' and resid 72 through 88 removed outlier: 3.519A pdb=" N LEUMB 83 " --> pdb=" O LEUMB 79 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLYMB 84 " --> pdb=" O PHEMB 80 " (cutoff:3.500A) Proline residue: MB 85 - end of helix Processing helix chain 'UC' and resid 14 through 19 removed outlier: 3.584A pdb=" N GLNUC 18 " --> pdb=" O SERUC 14 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLYUC 19 " --> pdb=" O ALAUC 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'UC' and resid 14 through 19' Processing helix chain 'UC' and resid 20 through 30 removed outlier: 3.925A pdb=" N GLNUC 29 " --> pdb=" O ARGUC 25 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASNUC 30 " --> pdb=" O LEUUC 26 " (cutoff:3.500A) Processing helix chain 'UC' and resid 49 through 59 removed outlier: 4.061A pdb=" N PHEUC 59 " --> pdb=" O LYSUC 55 " (cutoff:3.500A) Processing helix chain 'UC' and resid 60 through 65 removed outlier: 4.876A pdb=" N SERUC 64 " --> pdb=" O GLUUC 60 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HISUC 65 " --> pdb=" O ALAUC 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'UC' and resid 60 through 65' Processing helix chain 'WD' and resid 52 through 62 Processing helix chain 'WD' and resid 63 through 75 removed outlier: 3.505A pdb=" N ASPWD 70 " --> pdb=" O LYSWD 66 " (cutoff:3.500A) Processing helix chain 'XE' and resid 2 through 9 removed outlier: 3.773A pdb=" N LEUXE 6 " --> pdb=" O LYSXE 2 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASPXE 8 " --> pdb=" O SERXE 4 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYSXE 9 " --> pdb=" O GLUXE 5 " (cutoff:3.500A) Processing helix chain 'XE' and resid 10 through 35 removed outlier: 3.745A pdb=" N GLUXE 20 " --> pdb=" O GLNXE 16 " (cutoff:3.500A) Processing helix chain 'XE' and resid 40 through 63 removed outlier: 5.488A pdb=" N ARGXE 44 " --> pdb=" O THRXE 40 " (cutoff:3.500A) Processing helix chain 'RF' and resid 13 through 25 removed outlier: 3.850A pdb=" N LEURF 19 " --> pdb=" O GLNRF 15 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VALRF 20 " --> pdb=" O LYSRF 16 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLURF 23 " --> pdb=" O LEURF 19 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VALRF 24 " --> pdb=" O VALRF 20 " (cutoff:3.500A) Processing helix chain 'RF' and resid 28 through 39 removed outlier: 3.636A pdb=" N LEURF 33 " --> pdb=" O ILERF 29 " (cutoff:3.500A) Processing helix chain 'RF' and resid 41 through 61 removed outlier: 4.209A pdb=" N VALRF 45 " --> pdb=" O LYSRF 41 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHERF 46 " --> pdb=" O LYSRF 42 " (cutoff:3.500A) Processing helix chain 'RF' and resid 65 through 70 removed outlier: 3.985A pdb=" N LEURF 69 " --> pdb=" O ASPRF 65 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYSRF 70 " --> pdb=" O ILERF 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'RF' and resid 65 through 70' Processing helix chain 'FG' and resid 14 through 33 removed outlier: 4.050A pdb=" N VALFG 18 " --> pdb=" O GLNFG 14 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VALFG 19 " --> pdb=" O SERFG 15 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLYFG 20 " --> pdb=" O ASPFG 16 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASNFG 32 " --> pdb=" O LEUFG 28 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASNFG 33 " --> pdb=" O VALFG 29 " (cutoff:3.500A) Processing helix chain 'FG' and resid 67 through 82 removed outlier: 4.786A pdb=" N ASPFG 82 " --> pdb=" O PHEFG 78 " (cutoff:3.500A) Processing helix chain 'TI' and resid 64 through 69 removed outlier: 4.117A pdb=" N VALTI 68 " --> pdb=" O HISTI 64 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALATI 69 " --> pdb=" O ILETI 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'TI' and resid 64 through 69' Processing helix chain 'HK' and resid 3 through 21 removed outlier: 3.741A pdb=" N GLUHK 16 " --> pdb=" O LYSHK 12 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VALHK 17 " --> pdb=" O ARGHK 13 " (cutoff:3.500A) Processing helix chain 'HK' and resid 22 through 33 Processing helix chain 'HK' and resid 37 through 51 Processing helix chain 'HK' and resid 80 through 91 removed outlier: 3.571A pdb=" N GLUHK 86 " --> pdb=" O ASNHK 82 " (cutoff:3.500A) Processing helix chain 'OL' and resid 3 through 15 removed outlier: 3.533A pdb=" N GLNOL 9 " --> pdb=" O SEROL 5 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILEOL 11 " --> pdb=" O ARGOL 7 " (cutoff:3.500A) Processing helix chain 'OL' and resid 23 through 43 removed outlier: 4.199A pdb=" N ASNOL 40 " --> pdb=" O ASNOL 36 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HISOL 41 " --> pdb=" O ASPOL 37 " (cutoff:3.500A) Processing helix chain 'OL' and resid 49 through 73 removed outlier: 3.913A pdb=" N GLYOL 54 " --> pdb=" O HISOL 50 " (cutoff:3.500A) Processing helix chain 'OL' and resid 74 through 85 Processing helix chain 'MM' and resid 14 through 22 removed outlier: 3.859A pdb=" N THRMM 20 " --> pdb=" O VALMM 16 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYRMM 21 " --> pdb=" O ILEMM 17 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILEMM 22 " --> pdb=" O SERMM 18 " (cutoff:3.500A) Processing helix chain 'MM' and resid 26 through 38 Processing helix chain 'MM' and resid 49 through 64 removed outlier: 3.507A pdb=" N ALAMM 61 " --> pdb=" O ARGMM 57 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASNMM 62 " --> pdb=" O ALAMM 58 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYRMM 63 " --> pdb=" O GLNMM 59 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N METMM 64 " --> pdb=" O VALMM 60 " (cutoff:3.500A) Processing helix chain 'MM' and resid 65 through 84 removed outlier: 3.641A pdb=" N ARGMM 71 " --> pdb=" O GLYMM 67 " (cutoff:3.500A) Processing helix chain 'MM' and resid 85 through 94 Processing helix chain 'MM' and resid 106 through 111 Processing helix chain 'PO' and resid 6 through 22 removed outlier: 3.688A pdb=" N LYSPO 22 " --> pdb=" O LEUPO 18 " (cutoff:3.500A) Processing helix chain 'PO' and resid 26 through 31 removed outlier: 3.697A pdb=" N ARGPO 30 " --> pdb=" O GLYPO 26 " (cutoff:3.500A) Processing helix chain 'PO' and resid 36 through 73 removed outlier: 3.618A pdb=" N ARGPO 51 " --> pdb=" O TYRPO 47 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYSPO 54 " --> pdb=" O ARGPO 50 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARGPO 58 " --> pdb=" O LYSPO 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARGPO 59 " --> pdb=" O ARGPO 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASNPO 72 " --> pdb=" O GLYPO 68 " (cutoff:3.500A) Processing helix chain 'PO' and resid 75 through 87 removed outlier: 3.535A pdb=" N ASNPO 81 " --> pdb=" O SERPO 77 " (cutoff:3.500A) Processing helix chain 'PO' and resid 91 through 102 Processing helix chain 'PO' and resid 103 through 117 removed outlier: 3.581A pdb=" N GLUPO 116 " --> pdb=" O LYSPO 112 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEUPO 117 " --> pdb=" O ALAPO 113 " (cutoff:3.500A) Processing helix chain 'SP' and resid 12 through 26 removed outlier: 3.762A pdb=" N ALASP 17 " --> pdb=" O ALASP 13 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYSSP 18 " --> pdb=" O HISSP 14 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLUSP 24 " --> pdb=" O GLUSP 20 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THRSP 25 " --> pdb=" O ASNSP 21 " (cutoff:3.500A) Processing helix chain 'SP' and resid 70 through 76 removed outlier: 4.717A pdb=" N PHESP 74 " --> pdb=" O LYSSP 70 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALASP 75 " --> pdb=" O LEUSP 71 " (cutoff:3.500A) Proline residue: SP 76 - end of helix No H-bonds generated for 'chain 'SP' and resid 70 through 76' Processing helix chain 'BQ' and resid 5 through 21 Processing helix chain 'BQ' and resid 30 through 44 Processing helix chain 'BQ' and resid 114 through 122 Processing helix chain 'GR' and resid 3 through 8 Proline residue: GR 8 - end of helix Processing helix chain 'GR' and resid 58 through 81 removed outlier: 3.616A pdb=" N GLYGR 66 " --> pdb=" O METGR 62 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THRGR 67 " --> pdb=" O METGR 63 " (cutoff:3.500A) Processing helix chain 'GR' and resid 137 through 153 removed outlier: 3.840A pdb=" N PHEGR 151 " --> pdb=" O LYSGR 147 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARGGR 152 " --> pdb=" O ILEGR 148 " (cutoff:3.500A) Proline residue: GR 153 - end of helix Processing helix chain 'GS' and resid 20 through 31 Processing helix chain 'GS' and resid 35 through 55 Processing helix chain 'GS' and resid 58 through 71 removed outlier: 4.174A pdb=" N PHEGS 62 " --> pdb=" O ASPGS 58 " (cutoff:3.500A) Processing helix chain 'GS' and resid 93 through 113 removed outlier: 3.504A pdb=" N ALAGS 106 " --> pdb=" O METGS 102 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSGS 111 " --> pdb=" O GLUGS 107 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARGGS 112 " --> pdb=" O ALAGS 108 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SERGS 113 " --> pdb=" O ALAGS 109 " (cutoff:3.500A) Processing helix chain 'GS' and resid 116 through 131 removed outlier: 3.531A pdb=" N GLUGS 130 " --> pdb=" O SERGS 126 " (cutoff:3.500A) Processing helix chain 'GS' and resid 133 through 150 Processing helix chain 'CT' and resid 6 through 12 removed outlier: 4.106A pdb=" N ARGCT 11 " --> pdb=" O PROCT 7 " (cutoff:3.500A) Processing helix chain 'CT' and resid 28 through 47 Processing helix chain 'CT' and resid 72 through 78 removed outlier: 3.504A pdb=" N VALCT 76 " --> pdb=" O ARGCT 72 " (cutoff:3.500A) Processing helix chain 'CT' and resid 81 through 95 removed outlier: 3.698A pdb=" N ARGCT 86 " --> pdb=" O GLUCT 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLUCT 90 " --> pdb=" O ARGCT 86 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYSCT 93 " --> pdb=" O LYSCT 89 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N METCT 94 " --> pdb=" O GLUCT 90 " (cutoff:3.500A) Processing helix chain 'CT' and resid 112 through 127 removed outlier: 3.692A pdb=" N ARGCT 127 " --> pdb=" O GLNCT 123 " (cutoff:3.500A) Processing helix chain 'CT' and resid 129 through 145 Processing helix chain 'KU' and resid 46 through 51 removed outlier: 3.734A pdb=" N GLNKU 50 " --> pdb=" O THRKU 46 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLYKU 51 " --> pdb=" O SERKU 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'KU' and resid 46 through 51' Processing helix chain 'KU' and resid 54 through 59 removed outlier: 3.865A pdb=" N SERKU 58 " --> pdb=" O GLYKU 54 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THRKU 59 " --> pdb=" O SERKU 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'KU' and resid 54 through 59' Processing helix chain 'KU' and resid 60 through 76 removed outlier: 4.133A pdb=" N GLUKU 76 " --> pdb=" O LYSKU 72 " (cutoff:3.500A) Processing helix chain 'KU' and resid 91 through 104 removed outlier: 4.314A pdb=" N SERKU 95 " --> pdb=" O PROKU 91 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VALKU 97 " --> pdb=" O ARGKU 93 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARGKU 98 " --> pdb=" O GLUKU 94 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLYKU 104 " --> pdb=" O LEUKU 100 " (cutoff:3.500A) Processing helix chain 'NV' and resid 11 through 27 Processing helix chain 'NV' and resid 28 through 37 removed outlier: 3.638A pdb=" N GLUNV 36 " --> pdb=" O VALNV 32 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHENV 37 " --> pdb=" O ARGNV 33 " (cutoff:3.500A) Processing helix chain 'NV' and resid 40 through 58 Processing helix chain 'YW' and resid 16 through 27 Processing helix chain 'YW' and resid 40 through 51 removed outlier: 3.546A pdb=" N METYW 46 " --> pdb=" O SERYW 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VALYW 50 " --> pdb=" O METYW 46 " (cutoff:3.500A) Processing helix chain 'IX' and resid 7 through 12 removed outlier: 3.653A pdb=" N VALIX 11 " --> pdb=" O LYSIX 7 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THRIX 12 " --> pdb=" O PROIX 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'IX' and resid 7 through 12' Processing helix chain 'IX' and resid 24 through 38 removed outlier: 4.041A pdb=" N GLNIX 31 " --> pdb=" O ARGIX 27 " (cutoff:3.500A) Processing helix chain 'IX' and resid 67 through 72 Processing helix chain 'IX' and resid 88 through 96 Processing helix chain 'IX' and resid 97 through 110 removed outlier: 4.324A pdb=" N LEUIX 101 " --> pdb=" O PROIX 97 " (cutoff:3.500A) Proline residue: IX 110 - end of helix Processing helix chain 'IX' and resid 112 through 123 removed outlier: 3.512A pdb=" N LYSIX 120 " --> pdb=" O TYRIX 116 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYSIX 121 " --> pdb=" O ALAIX 117 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEUIX 122 " --> pdb=" O METIX 118 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYSIX 123 " --> pdb=" O ILEIX 119 " (cutoff:3.500A) Processing helix chain 'JY' and resid 14 through 33 removed outlier: 3.799A pdb=" N ILEJY 18 " --> pdb=" O ASPJY 14 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASPJY 19 " --> pdb=" O HISJY 15 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLNJY 20 " --> pdb=" O ARGJY 16 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILEJY 25 " --> pdb=" O SERJY 21 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYSJY 30 " --> pdb=" O VALJY 26 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THRJY 32 " --> pdb=" O THRJY 28 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLYJY 33 " --> pdb=" O ALAJY 29 " (cutoff:3.500A) Processing helix chain 'JY' and resid 80 through 91 removed outlier: 4.107A pdb=" N ALAJY 86 " --> pdb=" O LYSJY 82 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEUJY 87 " --> pdb=" O THRJY 83 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N METJY 88 " --> pdb=" O VALJY 84 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYSJY 89 " --> pdb=" O ASPJY 85 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEUJY 90 " --> pdb=" O ALAJY 86 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASPJY 91 " --> pdb=" O LEUJY 87 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 8 through 16 Processing helix chain 'Ba' and resid 17 through 25 removed outlier: 4.258A pdb=" N THRBa 24 " --> pdb=" O ALABa 20 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYSBa 25 " --> pdb=" O ARGBa 21 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 26 through 38 Processing helix chain 'Nc' and resid 4 through 23 removed outlier: 3.531A pdb=" N LYSNc 13 " --> pdb=" O LEUNc 9 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYSNc 14 " --> pdb=" O ARGNc 10 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N THRNc 15 " --> pdb=" O ARGNc 11 " (cutoff:3.500A) Processing helix chain 'Nc' and resid 66 through 85 removed outlier: 3.662A pdb=" N GLUNc 79 " --> pdb=" O GLNNc 75 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLYNc 85 " --> pdb=" O ALANc 81 " (cutoff:3.500A) Processing helix chain 'Nc' and resid 100 through 113 removed outlier: 3.922A pdb=" N GLYNc 113 " --> pdb=" O ALANc 109 " (cutoff:3.500A) Processing helix chain 'Kd' and resid 39 through 44 removed outlier: 3.541A pdb=" N ARGKd 43 " --> pdb=" O GLYKd 39 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SERKd 44 " --> pdb=" O GLNKd 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'Kd' and resid 39 through 44' Processing helix chain 'Kd' and resid 58 through 64 removed outlier: 3.563A pdb=" N LEUKd 63 " --> pdb=" O LEUKd 59 " (cutoff:3.500A) Proline residue: Kd 64 - end of helix Processing helix chain 'Kd' and resid 70 through 77 removed outlier: 4.000A pdb=" N METKd 74 " --> pdb=" O SERKd 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THRKd 75 " --> pdb=" O LYSKd 71 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALAKd 77 " --> pdb=" O ALAKd 73 " (cutoff:3.500A) Processing helix chain 'Kd' and resid 80 through 85 removed outlier: 3.930A pdb=" N LEUKd 84 " --> pdb=" O ARGKd 80 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASNKd 85 " --> pdb=" O LEUKd 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'Kd' and resid 80 through 85' Processing helix chain 'Kd' and resid 93 through 101 Processing helix chain 'Kd' and resid 130 through 141 removed outlier: 3.535A pdb=" N ALAKd 140 " --> pdb=" O ALAKd 136 " (cutoff:3.500A) Processing helix chain 'Je' and resid 111 through 118 removed outlier: 3.514A pdb=" N VALJe 115 " --> pdb=" O PHEJe 111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUJe 117 " --> pdb=" O LYSJe 113 " (cutoff:3.500A) Processing helix chain 'Af' and resid 57 through 62 removed outlier: 5.210A pdb=" N THRAf 62 " --> pdb=" O ASPAf 58 " (cutoff:3.500A) Processing helix chain 'Af' and resid 63 through 73 removed outlier: 3.663A pdb=" N ALAAf 72 " --> pdb=" O HISAf 68 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 91 removed outlier: 4.228A pdb=" N GLUAf 91 " --> pdb=" O ASPAf 87 " (cutoff:3.500A) Processing helix chain 'Af' and resid 123 through 128 Processing helix chain 'Af' and resid 40 through 45 Processing helix chain 'Lg' and resid 43 through 59 removed outlier: 3.541A pdb=" N GLULg 48 " --> pdb=" O ALALg 44 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYSLg 57 " --> pdb=" O THRLg 53 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 110 through 126 removed outlier: 3.616A pdb=" N LEULg 120 " --> pdb=" O GLULg 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALALg 123 " --> pdb=" O THRLg 119 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYSLg 124 " --> pdb=" O LEULg 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEULg 125 " --> pdb=" O ALALg 121 " (cutoff:3.500A) Proline residue: Lg 126 - end of helix Processing helix chain 'dh' and resid 8 through 15 removed outlier: 3.902A pdb=" N LYSdh 13 " --> pdb=" O SERdh 9 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARGdh 14 " --> pdb=" O GLYdh 10 " (cutoff:3.500A) Processing helix chain 'dh' and resid 37 through 45 removed outlier: 4.086A pdb=" N ARGdh 45 " --> pdb=" O ILEdh 41 " (cutoff:3.500A) Processing helix chain 'dh' and resid 51 through 63 removed outlier: 4.483A pdb=" N ALAdh 56 " --> pdb=" O LYSdh 52 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALAdh 57 " --> pdb=" O SERdh 53 " (cutoff:3.500A) Proline residue: dh 63 - end of helix Processing helix chain 'Oi' and resid 5 through 16 removed outlier: 3.765A pdb=" N VALOi 11 " --> pdb=" O LEUOi 7 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLNOi 15 " --> pdb=" O VALOi 11 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILEOi 16 " --> pdb=" O GLUOi 12 " (cutoff:3.500A) Processing helix chain 'Oi' and resid 99 through 106 removed outlier: 4.800A pdb=" N ARGOi 103 " --> pdb=" O LEUOi 99 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLUOi 104 " --> pdb=" O TYROi 100 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARGOi 105 " --> pdb=" O TYROi 101 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SEROi 106 " --> pdb=" O LEUOi 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'Oi' and resid 99 through 106' Processing helix chain 'Pj' and resid 53 through 64 removed outlier: 3.592A pdb=" N ILEPj 61 " --> pdb=" O TYRPj 57 " (cutoff:3.500A) Processing helix chain 'Pj' and resid 68 through 81 removed outlier: 3.791A pdb=" N SERPj 73 " --> pdb=" O ASPPj 69 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYSPj 80 " --> pdb=" O ARGPj 76 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALAPj 81 " --> pdb=" O ALAPj 77 " (cutoff:3.500A) Processing helix chain 'bk' and resid 22 through 27 Proline residue: bk 27 - end of helix Processing helix chain 'Cl' and resid 10 through 15 removed outlier: 5.012A pdb=" N PHECl 15 " --> pdb=" O PROCl 11 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 131 through 136 removed outlier: 3.750A pdb=" N ILECl 135 " --> pdb=" O PROCl 131 " (cutoff:3.500A) Proline residue: Cl 136 - end of helix No H-bonds generated for 'chain 'Cl' and resid 131 through 136' Processing helix chain 'Cl' and resid 207 through 215 removed outlier: 3.881A pdb=" N SERCl 211 " --> pdb=" O LYSCl 207 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARGCl 214 " --> pdb=" O ALACl 210 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLYCl 215 " --> pdb=" O SERCl 211 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 221 through 226 removed outlier: 4.008A pdb=" N METCl 225 " --> pdb=" O ARGCl 221 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASNCl 226 " --> pdb=" O GLYCl 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cl' and resid 221 through 226' Processing helix chain 'Cl' and resid 260 through 265 removed outlier: 4.670A pdb=" N ASPCl 264 " --> pdb=" O ASNCl 260 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N SERCl 265 " --> pdb=" O LYSCl 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cl' and resid 260 through 265' Processing helix chain 'Dm' and resid 7 through 16 removed outlier: 4.424A pdb=" N LEUDm 11 " --> pdb=" O PRODm 7 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SERDm 12 " --> pdb=" O LYSDm 8 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARGDm 13 " --> pdb=" O LEUDm 9 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 27 through 33 removed outlier: 3.940A pdb=" N THRDm 32 " --> pdb=" O TYRDm 28 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 50 through 67 removed outlier: 3.576A pdb=" N GLUDm 58 " --> pdb=" O LEUDm 54 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VALDm 62 " --> pdb=" O GLUDm 58 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 69 through 83 removed outlier: 3.525A pdb=" N TYRDm 76 " --> pdb=" O GLNDm 72 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 86 through 98 removed outlier: 3.832A pdb=" N LEUDm 92 " --> pdb=" O GLYDm 88 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 99 through 107 removed outlier: 3.892A pdb=" N TYRDm 104 " --> pdb=" O ASPDm 100 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLYDm 107 " --> pdb=" O VALDm 103 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 111 through 122 removed outlier: 3.772A pdb=" N HISDm 121 " --> pdb=" O GLNDm 117 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARGDm 122 " --> pdb=" O LEUDm 118 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 159 through 173 removed outlier: 3.876A pdb=" N ASNDm 164 " --> pdb=" O LEUDm 160 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLUDm 167 " --> pdb=" O LYSDm 163 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLNDm 171 " --> pdb=" O GLUDm 167 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARGDm 172 " --> pdb=" O LEUDm 168 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 203 through 213 removed outlier: 3.882A pdb=" N ILEDm 207 " --> pdb=" O ASNDm 203 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SERDm 212 " --> pdb=" O VALDm 208 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYSDm 213 " --> pdb=" O GLUDm 209 " (cutoff:3.500A) Processing helix chain 'Sn' and resid 2 through 10 removed outlier: 4.502A pdb=" N LEUSn 6 " --> pdb=" O ASNSn 2 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYRSn 7 " --> pdb=" O ASNSn 3 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLNSn 8 " --> pdb=" O ALASn 4 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VALSn 9 " --> pdb=" O ARGSn 5 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEUSn 10 " --> pdb=" O LEUSn 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Sn' and resid 2 through 10' Processing helix chain 'Sn' and resid 16 through 26 Processing helix chain 'Sn' and resid 38 through 51 removed outlier: 3.549A pdb=" N GLUSn 47 " --> pdb=" O LYSSn 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUSn 48 " --> pdb=" O LYSSn 44 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLUSn 51 " --> pdb=" O GLUSn 47 " (cutoff:3.500A) Processing helix chain 'To' and resid 4 through 41 removed outlier: 3.549A pdb=" N THRTo 15 " --> pdb=" O ALATo 11 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYSTo 16 " --> pdb=" O ARGTo 12 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARGTo 17 " --> pdb=" O GLNTo 13 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SERTo 21 " --> pdb=" O ARGTo 17 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLNTo 24 " --> pdb=" O ASNTo 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N METTo 27 " --> pdb=" O SERTo 23 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEUTo 32 " --> pdb=" O VALTo 28 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VALTo 35 " --> pdb=" O TYRTo 31 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALATo 41 " --> pdb=" O ALATo 37 " (cutoff:3.500A) Processing helix chain 'To' and resid 44 through 65 removed outlier: 3.922A pdb=" N LYSTo 53 " --> pdb=" O GLUTo 49 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALATo 54 " --> pdb=" O ALATo 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILETo 55 " --> pdb=" O TYRTo 51 " (cutoff:3.500A) Proline residue: To 56 - end of helix removed outlier: 3.716A pdb=" N ALATo 62 " --> pdb=" O LEUTo 58 " (cutoff:3.500A) Processing helix chain 'To' and resid 68 through 88 removed outlier: 3.598A pdb=" N THRTo 82 " --> pdb=" O ARGTo 78 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLYTo 85 " --> pdb=" O LYSTo 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEUTo 86 " --> pdb=" O THRTo 82 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLNTo 87 " --> pdb=" O ILETo 83 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALATo 88 " --> pdb=" O LYSTo 84 " (cutoff:3.500A) Processing helix chain 'C1' and resid 22 through 28 Processing helix chain 'C1' and resid 29 through 34 Processing helix chain 'C1' and resid 40 through 49 removed outlier: 4.274A pdb=" N GLUC1 48 " --> pdb=" O ILEC1 44 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALAC1 49 " --> pdb=" O GLUC1 45 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 89 through 95 removed outlier: 4.807A pdb=" N ASP B 78 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 101 " --> pdb=" O PHE B 20 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.514A pdb=" N ASP B 131 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 132 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 234 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 281 through 284 removed outlier: 6.322A pdb=" N ALA B 281 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 3 through 9 removed outlier: 4.355A pdb=" N SER F 25 " --> pdb=" O TYR F 59 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'H' and resid 65 through 71 removed outlier: 5.478A pdb=" N CYS H 82 " --> pdb=" O THR H 17 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLY H 19 " --> pdb=" O CYS H 82 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY H 101 " --> pdb=" O ASN H 14 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'H' and resid 213 through 217 removed outlier: 6.825A pdb=" N PHE H 213 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN H 293 " --> pdb=" O ILE H 217 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP H 243 " --> pdb=" O CYS H 258 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'H' and resid 219 through 223 removed outlier: 3.729A pdb=" N THR H 228 " --> pdb=" O LEU H 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY H 232 " --> pdb=" O CYS H 277 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS H 277 " --> pdb=" O GLY H 232 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'H' and resid 332 through 335 removed outlier: 4.471A pdb=" N LEU H 375 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP H 308 " --> pdb=" O ALA H 392 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A4' and resid 20 through 23 removed outlier: 5.765A pdb=" N HISA4 20 " --> pdb=" O ILEA4 46 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HISA4 44 " --> pdb=" O GLYA4 22 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A4' and resid 95 through 98 Processing sheet with id= 11, first strand: chain 'E5' and resid 17 through 21 removed outlier: 6.807A pdb=" N LEUE5 41 " --> pdb=" O VALE5 21 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E5' and resid 89 through 93 removed outlier: 3.808A pdb=" N ALAE5 104 " --> pdb=" O ASPE5 127 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASPE5 127 " --> pdb=" O ALAE5 104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THRE5 130 " --> pdb=" O ILEE5 111 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E5' and resid 38 through 45 Processing sheet with id= 14, first strand: chain 'L6' and resid 29 through 32 removed outlier: 4.848A pdb=" N LEUL6 81 " --> pdb=" O VALL6 98 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'L6' and resid 36 through 41 removed outlier: 4.819A pdb=" N LYSL6 51 " --> pdb=" O ILEL6 67 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F7' and resid 65 through 69 removed outlier: 4.782A pdb=" N ILEF7 85 " --> pdb=" O VALF7 40 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYSF7 87 " --> pdb=" O METF7 38 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLYF7 39 " --> pdb=" O GLYF7 151 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLYF7 151 " --> pdb=" O GLYF7 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F7' and resid 72 through 75 removed outlier: 7.559A pdb=" N LYSF7 72 " --> pdb=" O GLUF7 81 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLUF7 81 " --> pdb=" O LYSF7 72 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E9' and resid 1 through 5 removed outlier: 3.681A pdb=" N METE9 1 " --> pdb=" O LEUE9 13 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALAE9 9 " --> pdb=" O THRE9 5 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E9' and resid 43 through 46 removed outlier: 6.892A pdb=" N ARGE9 43 " --> pdb=" O PROE9 88 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALAE9 86 " --> pdb=" O GLNE9 45 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E9' and resid 116 through 119 removed outlier: 3.808A pdb=" N LYSE9 184 " --> pdb=" O ARGE9 144 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'aA' and resid 28 through 31 removed outlier: 4.131A pdb=" N GLUaA 35 " --> pdb=" O ASPaA 30 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'MB' and resid 33 through 36 removed outlier: 5.130A pdb=" N ARGMB 103 " --> pdb=" O ASNMB 107 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLYMB 101 " --> pdb=" O PROMB 109 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALAMB 111 " --> pdb=" O LYSMB 99 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYSMB 99 " --> pdb=" O ALAMB 111 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VALMB 113 " --> pdb=" O ILEMB 97 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILEMB 97 " --> pdb=" O VALMB 113 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEUMB 115 " --> pdb=" O LEUMB 95 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEUMB 95 " --> pdb=" O LEUMB 115 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'UC' and resid 75 through 78 Processing sheet with id= 24, first strand: chain 'WD' and resid 12 through 19 removed outlier: 4.367A pdb=" N ASNWD 23 " --> pdb=" O SERWD 19 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'WD' and resid 34 through 41 Processing sheet with id= 26, first strand: chain 'RF' and resid 2 through 8 removed outlier: 3.515A pdb=" N ILERF 103 " --> pdb=" O LEURF 7 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'FG' and resid 38 through 42 removed outlier: 6.031A pdb=" N TYRFG 59 " --> pdb=" O TRPFG 42 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VALFG 6 " --> pdb=" O PHEFG 62 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'FG' and resid 43 through 47 removed outlier: 3.620A pdb=" N GLYFG 43 " --> pdb=" O TYRFG 59 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N HISFG 55 " --> pdb=" O LEUFG 47 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'VH' and resid 45 through 48 removed outlier: 5.754A pdb=" N VALVH 82 " --> pdb=" O GLYVH 48 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'VH' and resid 51 through 54 removed outlier: 4.017A pdb=" N THRVH 58 " --> pdb=" O GLYVH 54 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'TI' and resid 38 through 43 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'TI' and resid 80 through 86 removed outlier: 6.819A pdb=" N ARGTI 80 " --> pdb=" O ARGTI 96 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLNTI 92 " --> pdb=" O GLNTI 84 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYSTI 90 " --> pdb=" O GLYTI 86 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'fJ' and resid 23 through 27 removed outlier: 3.610A pdb=" N HISfJ 15 " --> pdb=" O TYRfJ 45 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'SP' and resid 30 through 34 removed outlier: 4.475A pdb=" N LEUSP 47 " --> pdb=" O VALSP 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BQ' and resid 23 through 29 removed outlier: 6.590A pdb=" N VALBQ 23 " --> pdb=" O LEUBQ 65 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALABQ 59 " --> pdb=" O SERBQ 29 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYSBQ 58 " --> pdb=" O GLUBQ 54 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SERBQ 48 " --> pdb=" O GLUBQ 64 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BQ' and resid 76 through 79 removed outlier: 3.612A pdb=" N THRBQ 76 " --> pdb=" O ALABQ 132 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILEBQ 105 " --> pdb=" O VALBQ 128 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'GR' and resid 16 through 19 Processing sheet with id= 38, first strand: chain 'GR' and resid 41 through 45 Processing sheet with id= 39, first strand: chain 'GR' and resid 94 through 98 Processing sheet with id= 40, first strand: chain 'GR' and resid 121 through 125 removed outlier: 5.861A pdb=" N THRGR 129 " --> pdb=" O LEUGR 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILEGR 90 " --> pdb=" O GLYGR 161 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'GS' and resid 73 through 80 removed outlier: 6.819A pdb=" N METGS 73 " --> pdb=" O VALGS 92 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'CT' and resid 54 through 59 removed outlier: 3.801A pdb=" N ASNCT 54 " --> pdb=" O ALACT 69 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLUCT 58 " --> pdb=" O LYSCT 65 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'CT' and resid 164 through 170 removed outlier: 3.505A pdb=" N GLYCT 155 " --> pdb=" O ARGCT 164 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLYCT 194 " --> pdb=" O THRCT 191 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'KU' and resid 42 through 45 removed outlier: 3.528A pdb=" N ALAKU 43 " --> pdb=" O ILEKU 34 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYSKU 87 " --> pdb=" O ILEKU 23 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'YW' and resid 32 through 38 removed outlier: 4.100A pdb=" N HISYW 33 " --> pdb=" O GLNYW 8 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYSYW 5 " --> pdb=" O GLUYW 57 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LEUYW 53 " --> pdb=" O LEUYW 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'IX' and resid 13 through 17 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'IX' and resid 74 through 78 removed outlier: 7.742A pdb=" N GLYIX 83 " --> pdb=" O SERIX 78 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'JY' and resid 5 through 13 removed outlier: 4.051A pdb=" N ILEJY 6 " --> pdb=" O ILEJY 76 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYSJY 71 " --> pdb=" O LEUJY 42 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N METJY 73 " --> pdb=" O VALJY 40 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'JY' and resid 44 through 53 removed outlier: 8.471A pdb=" N ALAJY 61 " --> pdb=" O THRJY 53 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'QZ' and resid 12 through 17 removed outlier: 5.823A pdb=" N SERQZ 12 " --> pdb=" O GLUQZ 69 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARGQZ 66 " --> pdb=" O VALQZ 82 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'QZ' and resid 25 through 37 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'Qb' and resid 11 through 15 removed outlier: 3.708A pdb=" N METQb 40 " --> pdb=" O VALQb 4 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEUQb 39 " --> pdb=" O GLYQb 50 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THRQb 46 " --> pdb=" O ASPQb 43 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Qb' and resid 18 through 23 removed outlier: 4.055A pdb=" N GLUQb 18 " --> pdb=" O ILEQb 98 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLUQb 65 " --> pdb=" O LEUQb 95 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Qb' and resid 71 through 78 removed outlier: 4.063A pdb=" N TYRQb 83 " --> pdb=" O ASNQb 78 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Nc' and resid 50 through 53 removed outlier: 3.867A pdb=" N ALANc 50 " --> pdb=" O ILENc 40 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Je' and resid 56 through 60 removed outlier: 4.462A pdb=" N ASPJe 56 " --> pdb=" O VALJe 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYSJe 40 " --> pdb=" O ILEJe 22 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SERJe 6 " --> pdb=" O CYSJe 21 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASNJe 82 " --> pdb=" O METJe 7 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Af' and resid 12 through 17 removed outlier: 3.813A pdb=" N ALAAf 21 " --> pdb=" O THRAf 17 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VALAf 27 " --> pdb=" O CYSAf 10 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLYAf 202 " --> pdb=" O LYSAf 9 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASPAf 203 " --> pdb=" O ASNAf 115 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASNAf 115 " --> pdb=" O ASPAf 203 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Af' and resid 33 through 36 removed outlier: 6.696A pdb=" N GLNAf 50 " --> pdb=" O THRAf 36 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLNAf 47 " --> pdb=" O ALAAf 85 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Af' and resid 182 through 185 Processing sheet with id= 60, first strand: chain 'Af' and resid 25 through 29 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'Lg' and resid 63 through 66 removed outlier: 3.811A pdb=" N TYRLg 104 " --> pdb=" O LEULg 34 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLNLg 31 " --> pdb=" O ARGLg 134 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARGLg 134 " --> pdb=" O GLNLg 31 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYSLg 128 " --> pdb=" O LEULg 37 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'dh' and resid 22 through 25 removed outlier: 5.597A pdb=" N PHEdh 22 " --> pdb=" O VALdh 50 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Oi' and resid 40 through 47 removed outlier: 6.531A pdb=" N THROi 27 " --> pdb=" O LYSOi 89 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SEROi 85 " --> pdb=" O GLNOi 31 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Oi' and resid 51 through 55 removed outlier: 3.822A pdb=" N ALAOi 51 " --> pdb=" O THROi 62 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARGOi 55 " --> pdb=" O ASNOi 58 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N SEROi 59 " --> pdb=" O LEUOi 78 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Pj' and resid 4 through 10 removed outlier: 4.380A pdb=" N PHEPj 16 " --> pdb=" O GLYPj 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLYPj 37 " --> pdb=" O VALPj 19 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'bk' and resid 16 through 21 Processing sheet with id= 67, first strand: chain 'Cl' and resid 2 through 6 removed outlier: 3.546A pdb=" N LYSCl 18 " --> pdb=" O VALCl 4 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N VALCl 16 " --> pdb=" O ALACl 6 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Cl' and resid 33 through 36 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'Cl' and resid 80 through 83 removed outlier: 6.509A pdb=" N LEUCl 93 " --> pdb=" O GLUCl 79 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILECl 74 " --> pdb=" O SERCl 118 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SERCl 118 " --> pdb=" O ILECl 74 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASPCl 114 " --> pdb=" O VALCl 78 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLYCl 127 " --> pdb=" O THRCl 115 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N METCl 117 " --> pdb=" O GLYCl 127 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Cl' and resid 162 through 165 removed outlier: 6.614A pdb=" N ILECl 173 " --> pdb=" O LEUCl 165 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLUCl 180 " --> pdb=" O LEUCl 176 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLYCl 179 " --> pdb=" O ALACl 271 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Cl' and resid 90 through 96 removed outlier: 5.234A pdb=" N HISCl 90 " --> pdb=" O ALACl 106 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLUCl 100 " --> pdb=" O TYRCl 96 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Dm' and resid 123 through 127 removed outlier: 7.216A pdb=" N THRDm 123 " --> pdb=" O GLNDm 153 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASPDm 148 " --> pdb=" O PHEDm 189 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILEDm 150 " --> pdb=" O GLYDm 187 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEUDm 185 " --> pdb=" O ILEDm 152 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Sn' and resid 28 through 32 removed outlier: 4.203A pdb=" N GLYSn 75 " --> pdb=" O LYSSn 68 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYSSn 66 " --> pdb=" O ARGSn 77 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASPSn 79 " --> pdb=" O LYSSn 64 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYSSn 64 " --> pdb=" O ASPSn 79 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYSSn 81 " --> pdb=" O ASNSn 62 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASNSn 62 " --> pdb=" O LYSSn 81 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALASn 83 " --> pdb=" O THRSn 60 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THRSn 60 " --> pdb=" O ALASn 83 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VALSn 85 " --> pdb=" O VALSn 58 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VALSn 58 " --> pdb=" O VALSn 85 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'ep' and resid 1 through 5 removed outlier: 6.430A pdb=" N HISep 33 " --> pdb=" O CYSep 27 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N CYSep 27 " --> pdb=" O HISep 33 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VALep 23 " --> pdb=" O GLNep 37 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'C1' and resid 17 through 21 removed outlier: 4.494A pdb=" N GLUC1 17 " --> pdb=" O LEUC1 5 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYSC1 35 " --> pdb=" O LEUC1 6 " (cutoff:3.500A) 2047 hydrogen bonds defined for protein. 6030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3659 hydrogen bonds 5688 hydrogen bond angles 0 basepair planarities 1468 basepair parallelities 2240 stacking parallelities Total time for adding SS restraints: 203.01 Time building geometry restraints manager: 63.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12441 1.30 - 1.43: 68211 1.43 - 1.56: 64892 1.56 - 1.69: 8687 1.69 - 1.82: 333 Bond restraints: 154564 Sorted by residual: bond pdb=" CG PROAf 165 " pdb=" CD PROAf 165 " ideal model delta sigma weight residual 1.503 1.229 0.274 3.40e-02 8.65e+02 6.48e+01 bond pdb=" C GLYKd 55 " pdb=" O GLYKd 55 " ideal model delta sigma weight residual 1.235 1.167 0.068 1.35e-02 5.49e+03 2.52e+01 bond pdb=" CA GLNKd 56 " pdb=" C GLNKd 56 " ideal model delta sigma weight residual 1.524 1.459 0.064 1.30e-02 5.92e+03 2.44e+01 bond pdb=" CB THRKd 57 " pdb=" CG2 THRKd 57 " ideal model delta sigma weight residual 1.521 1.367 0.154 3.30e-02 9.18e+02 2.18e+01 bond pdb=" CA PROAf 165 " pdb=" CB PROAf 165 " ideal model delta sigma weight residual 1.532 1.483 0.049 1.40e-02 5.10e+03 1.20e+01 ... (remaining 154559 not shown) Histogram of bond angle deviations from ideal: 85.14 - 95.22: 2 95.22 - 105.29: 20703 105.29 - 115.36: 108925 115.36 - 125.44: 84110 125.44 - 135.51: 16467 Bond angle restraints: 230207 Sorted by residual: angle pdb=" N PROAf 165 " pdb=" CD PROAf 165 " pdb=" CG PROAf 165 " ideal model delta sigma weight residual 103.20 85.49 17.71 1.50e+00 4.44e-01 1.39e+02 angle pdb=" CA PROAf 165 " pdb=" CB PROAf 165 " pdb=" CG PROAf 165 " ideal model delta sigma weight residual 104.50 85.14 19.36 1.90e+00 2.77e-01 1.04e+02 angle pdb=" N PROAf 165 " pdb=" CA PROAf 165 " pdb=" CB PROAf 165 " ideal model delta sigma weight residual 103.38 96.91 6.47 1.05e+00 9.07e-01 3.79e+01 angle pdb=" N SER B 7 " pdb=" CA SER B 7 " pdb=" C SER B 7 " ideal model delta sigma weight residual 114.62 107.64 6.98 1.14e+00 7.69e-01 3.74e+01 angle pdb=" N GLNKd 56 " pdb=" CA GLNKd 56 " pdb=" CB GLNKd 56 " ideal model delta sigma weight residual 109.97 118.48 -8.51 1.47e+00 4.63e-01 3.35e+01 ... (remaining 230202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 86447 35.75 - 71.50: 10784 71.50 - 107.25: 1109 107.25 - 143.00: 14 143.00 - 178.75: 25 Dihedral angle restraints: 98379 sinusoidal: 80280 harmonic: 18099 Sorted by residual: dihedral pdb=" O4' UZ21163 " pdb=" C1' UZ21163 " pdb=" N1 UZ21163 " pdb=" C2 UZ21163 " ideal model delta sinusoidal sigma weight residual 200.00 21.82 178.18 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UZ21729 " pdb=" C1' UZ21729 " pdb=" N1 UZ21729 " pdb=" C2 UZ21729 " ideal model delta sinusoidal sigma weight residual -160.00 16.69 -176.69 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UZ22767 " pdb=" C1' UZ22767 " pdb=" N1 UZ22767 " pdb=" C2 UZ22767 " ideal model delta sinusoidal sigma weight residual -160.00 12.37 -172.37 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 98376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 28039 0.085 - 0.170: 1193 0.170 - 0.256: 64 0.256 - 0.341: 4 0.341 - 0.426: 1 Chirality restraints: 29301 Sorted by residual: chirality pdb=" CA GLN B 255 " pdb=" N GLN B 255 " pdb=" C GLN B 255 " pdb=" CB GLN B 255 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C1' GZ2 733 " pdb=" O4' GZ2 733 " pdb=" C2' GZ2 733 " pdb=" N9 GZ2 733 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C1' GZ21434 " pdb=" O4' GZ21434 " pdb=" C2' GZ21434 " pdb=" N9 GZ21434 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 29298 not shown) Planarity restraints: 13066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AZ2 964 " -0.048 2.00e-02 2.50e+03 2.06e-02 1.17e+01 pdb=" N9 AZ2 964 " 0.043 2.00e-02 2.50e+03 pdb=" C8 AZ2 964 " 0.003 2.00e-02 2.50e+03 pdb=" N7 AZ2 964 " -0.002 2.00e-02 2.50e+03 pdb=" C5 AZ2 964 " 0.004 2.00e-02 2.50e+03 pdb=" C6 AZ2 964 " -0.007 2.00e-02 2.50e+03 pdb=" N6 AZ2 964 " -0.013 2.00e-02 2.50e+03 pdb=" N1 AZ2 964 " -0.005 2.00e-02 2.50e+03 pdb=" C2 AZ2 964 " 0.001 2.00e-02 2.50e+03 pdb=" N3 AZ2 964 " 0.010 2.00e-02 2.50e+03 pdb=" C4 AZ2 964 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GZ22814 " 0.045 2.00e-02 2.50e+03 1.95e-02 1.14e+01 pdb=" N9 GZ22814 " -0.048 2.00e-02 2.50e+03 pdb=" C8 GZ22814 " -0.005 2.00e-02 2.50e+03 pdb=" N7 GZ22814 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GZ22814 " 0.002 2.00e-02 2.50e+03 pdb=" C6 GZ22814 " 0.006 2.00e-02 2.50e+03 pdb=" O6 GZ22814 " 0.010 2.00e-02 2.50e+03 pdb=" N1 GZ22814 " 0.004 2.00e-02 2.50e+03 pdb=" C2 GZ22814 " -0.005 2.00e-02 2.50e+03 pdb=" N2 GZ22814 " -0.002 2.00e-02 2.50e+03 pdb=" N3 GZ22814 " -0.006 2.00e-02 2.50e+03 pdb=" C4 GZ22814 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GZ2 429 " -0.046 2.00e-02 2.50e+03 1.92e-02 1.10e+01 pdb=" N9 GZ2 429 " 0.044 2.00e-02 2.50e+03 pdb=" C8 GZ2 429 " 0.005 2.00e-02 2.50e+03 pdb=" N7 GZ2 429 " -0.003 2.00e-02 2.50e+03 pdb=" C5 GZ2 429 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GZ2 429 " -0.004 2.00e-02 2.50e+03 pdb=" O6 GZ2 429 " -0.011 2.00e-02 2.50e+03 pdb=" N1 GZ2 429 " -0.006 2.00e-02 2.50e+03 pdb=" C2 GZ2 429 " 0.000 2.00e-02 2.50e+03 pdb=" N2 GZ2 429 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GZ2 429 " 0.009 2.00e-02 2.50e+03 pdb=" C4 GZ2 429 " 0.009 2.00e-02 2.50e+03 ... (remaining 13063 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 1490 2.58 - 3.16: 107651 3.16 - 3.74: 289615 3.74 - 4.32: 405835 4.32 - 4.90: 533233 Nonbonded interactions: 1337824 Sorted by model distance: nonbonded pdb=" O1B GDP H 401 " pdb="MG MG H 402 " model vdw 2.002 2.170 nonbonded pdb=" O2' UZ2 671 " pdb=" O PHEBa 5 " model vdw 2.012 2.440 nonbonded pdb=" O6 GZ2 866 " pdb=" O4 UZ2 879 " model vdw 2.051 2.432 nonbonded pdb=" OH TYR H 47 " pdb=" O1A GDP H 401 " model vdw 2.078 2.440 nonbonded pdb=" OP1 UZ21925 " pdb=" O2' UZ22587 " model vdw 2.090 2.440 ... (remaining 1337819 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=0.50 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 31.740 Check model and map are aligned: 1.390 Set scattering table: 0.890 Process input model: 484.760 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.330 Set refine NCS operators: 0.010 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:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 540.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 0.274 154564 Z= 0.261 Angle : 0.606 19.355 230207 Z= 0.324 Chirality : 0.038 0.426 29301 Planarity : 0.005 0.071 13066 Dihedral : 23.099 178.745 86737 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 2.39 % Allowed : 15.44 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.60 (0.10), residues: 6246 helix: -0.81 (0.11), residues: 2013 sheet: -0.76 (0.14), residues: 1296 loop : -1.27 (0.11), residues: 2937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPA4 28 HIS 0.012 0.001 HISOi 5 PHE 0.021 0.002 PHEAf 121 TYR 0.020 0.002 TYRKd 60 ARG 0.009 0.001 ARGGR 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 753 time to evaluate : 6.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8478 (tp) cc_final: 0.8242 (tt) REVERT: H 345 GLN cc_start: 0.7585 (mt0) cc_final: 0.7311 (mt0) REVERT: UC 89 LYS cc_start: 0.8197 (mmmm) cc_final: 0.7832 (mmtt) REVERT: GS 136 MET cc_start: 0.7833 (tpp) cc_final: 0.7473 (mpp) REVERT: Nc 28 THR cc_start: 0.8989 (m) cc_final: 0.8740 (m) REVERT: Je 105 GLU cc_start: 0.7973 (mp0) cc_final: 0.7682 (mp0) outliers start: 124 outliers final: 88 residues processed: 853 average time/residue: 2.0777 time to fit residues: 2552.1643 Evaluate side-chains 786 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 698 time to evaluate : 6.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ARG Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain R3 residue 73 ASN Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 20 LYS Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 54 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 78 SER Chi-restraints excluded: chain L6 residue 86 ARG Chi-restraints excluded: chain F7 residue 159 SER Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 8 LEU Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 57 ILE Chi-restraints excluded: chain VH residue 14 ARG Chi-restraints excluded: chain HK residue 62 ASN Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain GR residue 175 LYS Chi-restraints excluded: chain GR residue 177 LYS Chi-restraints excluded: chain CT residue 19 ASN Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain KU residue 65 VAL Chi-restraints excluded: chain NV residue 7 LYS Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Kd residue 57 THR Chi-restraints excluded: chain Kd residue 96 THR Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Dm residue 25 VAL Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 32 THR Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 61 LYS Chi-restraints excluded: chain Dm residue 103 VAL Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 131 ARG Chi-restraints excluded: chain Dm residue 133 GLU Chi-restraints excluded: chain Dm residue 163 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 179 ASP Chi-restraints excluded: chain Dm residue 182 HIS Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Dm residue 195 ARG Chi-restraints excluded: chain Dm residue 207 ILE Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 880 optimal weight: 2.9990 chunk 790 optimal weight: 6.9990 chunk 438 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 533 optimal weight: 20.0000 chunk 422 optimal weight: 20.0000 chunk 817 optimal weight: 30.0000 chunk 316 optimal weight: 7.9990 chunk 497 optimal weight: 20.0000 chunk 608 optimal weight: 10.0000 chunk 947 optimal weight: 7.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 HIS ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 61 GLN A4 63 ASN F7 24 ASN F7 127 ASN E9 114 GLN aA 21 HIS VH 3 HIS VH 46 HIS TI 72 ASN fJ 10 HIS HK 82 ASN OL 83 GLN BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KU 118 HIS IX 70 GLN IX 136 GLN Kd 56 GLN Lg 31 GLN Lg 76 ASN Oi 3 ASN Oi 5 HIS ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pj 79 ASN bk 41 GLN Cl 110 GLN Cl 153 GLN Cl 163 GLN Sn 20 GLN To 19 GLN To 80 ASN C1 11 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 154564 Z= 0.466 Angle : 0.717 13.122 230207 Z= 0.368 Chirality : 0.045 0.329 29301 Planarity : 0.006 0.084 13066 Dihedral : 23.235 179.956 74628 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 5.15 % Allowed : 14.82 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.10), residues: 6246 helix: 0.00 (0.11), residues: 2054 sheet: -0.58 (0.14), residues: 1313 loop : -1.23 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPCl 248 HIS 0.015 0.002 HISdh 31 PHE 0.025 0.002 PHEAf 121 TYR 0.024 0.002 TYRL6 117 ARG 0.014 0.001 ARGMB 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 720 time to evaluate : 6.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ILE cc_start: 0.8457 (tp) cc_final: 0.8251 (tt) REVERT: B 74 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7910 (mtpt) REVERT: H 113 MET cc_start: 0.7570 (mmp) cc_final: 0.7365 (mmp) REVERT: H 263 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7344 (tpt) REVERT: H 345 GLN cc_start: 0.7568 (mt0) cc_final: 0.7347 (mt0) REVERT: F7 129 SER cc_start: 0.7734 (m) cc_final: 0.7314 (t) REVERT: MB 54 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8449 (ttp) REVERT: UC 16 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: UC 89 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7860 (mttp) REVERT: RF 62 HIS cc_start: 0.6982 (m170) cc_final: 0.6744 (m170) REVERT: VH 67 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8770 (t) REVERT: OL 72 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7334 (tptt) REVERT: PO 13 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7856 (ttp-110) REVERT: GS 87 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: CT 16 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7163 (mptp) REVERT: YW 55 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7601 (tppt) REVERT: Qb 79 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8315 (ptp-170) REVERT: dh 17 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7445 (tpt-90) REVERT: bk 49 LYS cc_start: 0.8297 (tmmt) cc_final: 0.7833 (tttt) REVERT: Cl 19 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8255 (t) REVERT: Dm 145 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: Dm 153 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: ep 9 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8244 (mttp) REVERT: C1 4 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8399 (pt) REVERT: C1 22 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7136 (mttt) outliers start: 267 outliers final: 133 residues processed: 888 average time/residue: 2.0372 time to fit residues: 2615.8310 Evaluate side-chains 837 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 686 time to evaluate : 6.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 82 ILE Chi-restraints excluded: chain L6 residue 87 VAL Chi-restraints excluded: chain F7 residue 40 VAL Chi-restraints excluded: chain F7 residue 57 MET Chi-restraints excluded: chain F7 residue 58 THR Chi-restraints excluded: chain F7 residue 152 MET Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain aA residue 53 LEU Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 14 SER Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain VH residue 9 SER Chi-restraints excluded: chain VH residue 14 ARG Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 72 LYS Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain SP residue 44 MET Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain GS residue 90 MET Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 59 THR Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain NV residue 32 VAL Chi-restraints excluded: chain YW residue 55 LYS Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 63 ASP Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 100 LEU Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Lg residue 18 THR Chi-restraints excluded: chain Lg residue 53 THR Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain Lg residue 137 MET Chi-restraints excluded: chain dh residue 17 ARG Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 72 VAL Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain Cl residue 19 VAL Chi-restraints excluded: chain Dm residue 25 VAL Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 103 VAL Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 133 GLU Chi-restraints excluded: chain Dm residue 145 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 182 HIS Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 4 ILE Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 526 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 788 optimal weight: 9.9990 chunk 644 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 948 optimal weight: 0.8980 chunk 1025 optimal weight: 10.0000 chunk 845 optimal weight: 10.0000 chunk 940 optimal weight: 4.9990 chunk 323 optimal weight: 4.9990 chunk 761 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 73 ASN ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN aA 21 HIS RF 40 ASN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN OL 83 GLN BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 123 GLN IX 70 GLN IX 136 GLN ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Qb 91 GLN Lg 31 GLN Lg 76 ASN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Cl 259 HIS Dm 164 ASN Dm 171 GLN To 19 GLN To 80 ASN C1 43 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 154564 Z= 0.296 Angle : 0.601 13.333 230207 Z= 0.314 Chirality : 0.039 0.295 29301 Planarity : 0.005 0.078 13066 Dihedral : 23.089 179.423 74537 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 4.78 % Allowed : 17.36 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.63 (0.10), residues: 6246 helix: 0.55 (0.11), residues: 2059 sheet: -0.42 (0.14), residues: 1299 loop : -1.06 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCl 248 HIS 0.008 0.001 HISYW 14 PHE 0.020 0.002 PHEFG 62 TYR 0.017 0.002 TYRL6 117 ARG 0.007 0.001 ARGBa 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 693 time to evaluate : 6.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7205 (ttp80) REVERT: B 259 GLU cc_start: 0.8085 (tp30) cc_final: 0.7883 (mm-30) REVERT: H 263 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7295 (tpt) REVERT: H 345 GLN cc_start: 0.7614 (mt0) cc_final: 0.7392 (mt0) REVERT: L6 10 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7160 (mmmm) REVERT: L6 31 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8277 (ttt-90) REVERT: F7 129 SER cc_start: 0.7730 (m) cc_final: 0.7282 (t) REVERT: MB 54 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8416 (ttp) REVERT: MB 118 ARG cc_start: 0.7206 (tpm170) cc_final: 0.6974 (tpp-160) REVERT: UC 16 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7180 (pp20) REVERT: UC 55 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.7977 (ttmm) REVERT: UC 89 LYS cc_start: 0.8223 (mmmm) cc_final: 0.7881 (mttp) REVERT: RF 62 HIS cc_start: 0.6990 (m170) cc_final: 0.6752 (m170) REVERT: VH 67 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8765 (t) REVERT: OL 72 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7385 (tptp) REVERT: PO 13 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7751 (ttp-110) REVERT: GS 87 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: CT 16 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7153 (mptp) REVERT: Qb 79 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8232 (ptp-170) REVERT: Je 113 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8015 (ptpt) REVERT: dh 17 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7436 (tpt-90) REVERT: Oi 35 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6926 (mtm110) REVERT: bk 49 LYS cc_start: 0.8290 (tmmt) cc_final: 0.7813 (tttt) REVERT: Cl 109 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8367 (ttpt) REVERT: Cl 205 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8491 (mp) REVERT: Dm 145 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: Dm 153 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: ep 9 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8235 (mttp) REVERT: C1 22 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7146 (mttt) outliers start: 248 outliers final: 126 residues processed: 852 average time/residue: 2.1086 time to fit residues: 2597.4938 Evaluate side-chains 816 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 668 time to evaluate : 6.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain F7 residue 40 VAL Chi-restraints excluded: chain F7 residue 58 THR Chi-restraints excluded: chain F7 residue 152 MET Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 16 THR Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 9 ASN Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain VH residue 9 SER Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain OL residue 3 THR Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 72 LYS Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 95 MET Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 64 VAL Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 63 ASP Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 96 THR Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 113 LYS Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 100 LEU Chi-restraints excluded: chain Lg residue 76 ASN Chi-restraints excluded: chain Lg residue 131 ILE Chi-restraints excluded: chain Lg residue 137 MET Chi-restraints excluded: chain dh residue 17 ARG Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 154 MET Chi-restraints excluded: chain Cl residue 205 LEU Chi-restraints excluded: chain Dm residue 25 VAL Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 145 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 937 optimal weight: 8.9990 chunk 713 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 452 optimal weight: 7.9990 chunk 637 optimal weight: 10.0000 chunk 952 optimal weight: 7.9990 chunk 1008 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 chunk 902 optimal weight: 8.9990 chunk 271 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 HIS ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 345 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN aA 21 HIS WD 44 ASN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TI 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HK 62 ASN ** OL 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 28 GLN CT 123 GLN ** KU 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN IX 136 GLN Af 86 ASN Lg 31 GLN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Cl 243 HIS Cl 259 HIS To 19 GLN To 80 ASN ep 24 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 154564 Z= 0.529 Angle : 0.762 13.975 230207 Z= 0.386 Chirality : 0.048 0.337 29301 Planarity : 0.006 0.103 13066 Dihedral : 23.182 178.825 74508 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 5.92 % Allowed : 17.36 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.10), residues: 6246 helix: 0.52 (0.11), residues: 2057 sheet: -0.41 (0.14), residues: 1303 loop : -1.10 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPCl 248 HIS 0.011 0.002 HISYW 14 PHE 0.025 0.002 PHEAf 121 TYR 0.024 0.002 TYRL6 117 ARG 0.011 0.001 ARGVH 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 705 time to evaluate : 6.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.7655 (ttpt) REVERT: B 137 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: B 249 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7128 (ttp80) REVERT: H 263 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7390 (tpt) REVERT: A4 35 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7042 (p90) REVERT: L6 31 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8312 (ttt-90) REVERT: F7 7 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8076 (tp) REVERT: F7 129 SER cc_start: 0.7846 (m) cc_final: 0.7423 (t) REVERT: E9 193 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8418 (mmmt) REVERT: MB 54 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8548 (ttp) REVERT: UC 16 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7228 (pp20) REVERT: UC 55 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.7834 (ttmm) REVERT: UC 89 LYS cc_start: 0.8278 (mmmm) cc_final: 0.7939 (mttp) REVERT: WD 71 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7829 (mp) REVERT: RF 62 HIS cc_start: 0.6990 (m170) cc_final: 0.6784 (m170) REVERT: VH 14 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8084 (ptt-90) REVERT: HK 54 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8250 (m-40) REVERT: OL 72 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7435 (tptp) REVERT: PO 13 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7905 (ttp-110) REVERT: GR 124 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: CT 16 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7191 (mptp) REVERT: IX 73 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7699 (mptt) REVERT: JY 52 LEU cc_start: 0.9088 (mp) cc_final: 0.8839 (mt) REVERT: Qb 79 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8016 (ptp-170) REVERT: Nc 47 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: Je 5 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: Je 9 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: Je 113 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8104 (ptpt) REVERT: dh 17 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7520 (tpt-90) REVERT: Oi 2 SER cc_start: 0.7663 (p) cc_final: 0.7200 (m) REVERT: Oi 35 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7075 (mtm110) REVERT: bk 49 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7801 (tttt) REVERT: Cl 109 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8328 (ttpt) REVERT: Cl 205 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8448 (mp) REVERT: Dm 145 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: Dm 153 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: Dm 155 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7615 (tttm) REVERT: ep 9 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8240 (mttt) REVERT: C1 22 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7214 (mttt) outliers start: 307 outliers final: 165 residues processed: 908 average time/residue: 2.0831 time to fit residues: 2740.1359 Evaluate side-chains 881 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 683 time to evaluate : 6.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 26 ARG Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 152 MET Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 33 VAL Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 87 VAL Chi-restraints excluded: chain F7 residue 7 LEU Chi-restraints excluded: chain F7 residue 40 VAL Chi-restraints excluded: chain F7 residue 58 THR Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 16 THR Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain aA residue 53 LEU Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 8 LEU Chi-restraints excluded: chain UC residue 9 ASN Chi-restraints excluded: chain UC residue 14 SER Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain UC residue 71 VAL Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain WD residue 71 LEU Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 21 MET Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain VH residue 9 SER Chi-restraints excluded: chain VH residue 14 ARG Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain HK residue 54 ASN Chi-restraints excluded: chain HK residue 62 ASN Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 72 LYS Chi-restraints excluded: chain PO residue 6 ARG Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain SP residue 44 MET Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain BQ residue 10 MET Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GR residue 124 GLU Chi-restraints excluded: chain GR residue 127 THR Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain GS residue 90 MET Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 122 SER Chi-restraints excluded: chain CT residue 141 SER Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 59 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 64 VAL Chi-restraints excluded: chain IX residue 73 LYS Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain JY residue 67 ILE Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 63 ASP Chi-restraints excluded: chain QZ residue 67 ILE Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Nc residue 47 GLU Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 96 THR Chi-restraints excluded: chain Je residue 5 GLU Chi-restraints excluded: chain Je residue 9 GLU Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 113 LYS Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 100 LEU Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Lg residue 53 THR Chi-restraints excluded: chain Lg residue 131 ILE Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain Lg residue 137 MET Chi-restraints excluded: chain dh residue 17 ARG Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 72 VAL Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 154 MET Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 205 LEU Chi-restraints excluded: chain Cl residue 259 HIS Chi-restraints excluded: chain Dm residue 25 VAL Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 145 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 155 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 34 ASP Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 85 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 839 optimal weight: 2.9990 chunk 572 optimal weight: 40.0000 chunk 14 optimal weight: 5.9990 chunk 750 optimal weight: 0.9980 chunk 415 optimal weight: 9.9990 chunk 860 optimal weight: 0.6980 chunk 696 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 514 optimal weight: 8.9990 chunk 904 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN aA 21 HIS ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN OL 83 GLN BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN CT 123 GLN IX 70 GLN IX 136 GLN ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 31 GLN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Cl 90 HIS Cl 259 HIS Sn 8 GLN To 3 ASN To 19 GLN To 24 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 154564 Z= 0.185 Angle : 0.543 13.955 230207 Z= 0.285 Chirality : 0.036 0.355 29301 Planarity : 0.004 0.071 13066 Dihedral : 23.038 178.999 74508 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 4.69 % Allowed : 19.37 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.25 (0.10), residues: 6246 helix: 0.95 (0.11), residues: 2076 sheet: -0.26 (0.14), residues: 1284 loop : -0.89 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPF7 83 HIS 0.012 0.001 HISCl 259 PHE 0.020 0.001 PHEFG 62 TYR 0.019 0.001 TYRDm 104 ARG 0.006 0.000 ARGE5 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 700 time to evaluate : 6.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7173 (ttp80) REVERT: H 263 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7296 (tpt) REVERT: A4 35 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7236 (p90) REVERT: L6 10 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7115 (mmmm) REVERT: L6 31 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8266 (ttt-90) REVERT: F7 129 SER cc_start: 0.7692 (m) cc_final: 0.7254 (t) REVERT: E9 193 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8349 (mmmt) REVERT: MB 54 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8379 (ttp) REVERT: UC 16 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7201 (pp20) REVERT: UC 55 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.7863 (ttmm) REVERT: UC 89 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7852 (mttp) REVERT: VH 67 VAL cc_start: 0.9027 (p) cc_final: 0.8809 (t) REVERT: OL 72 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7404 (tptp) REVERT: GS 87 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: CT 16 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7091 (mptp) REVERT: Qb 79 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8285 (ptp-170) REVERT: Je 5 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: Je 9 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: Je 113 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7960 (ptpt) REVERT: Oi 2 SER cc_start: 0.7603 (p) cc_final: 0.7084 (m) REVERT: Oi 35 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7033 (mtm110) REVERT: bk 49 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7780 (tttt) REVERT: Cl 109 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8345 (ttpt) REVERT: Dm 153 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: Dm 155 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7628 (tttm) REVERT: ep 9 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8232 (mttt) REVERT: C1 22 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7153 (mttt) outliers start: 243 outliers final: 108 residues processed: 856 average time/residue: 2.0821 time to fit residues: 2581.7566 Evaluate side-chains 789 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 659 time to evaluate : 6.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 18 GLU Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain F7 residue 152 MET Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain FG residue 61 LEU Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain OL residue 3 THR Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 72 LYS Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 19 ASN Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Je residue 5 GLU Chi-restraints excluded: chain Je residue 9 GLU Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 113 LYS Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 100 LEU Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 155 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 339 optimal weight: 10.0000 chunk 907 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 591 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 1009 optimal weight: 8.9990 chunk 837 optimal weight: 1.9990 chunk 467 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 333 optimal weight: 10.0000 chunk 529 optimal weight: 0.0970 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN F7 127 ASN E9 114 GLN WD 44 ASN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN HK 62 ASN ** OL 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN CT 123 GLN ** KU 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN IX 136 GLN ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 31 GLN Lg 76 ASN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Cl 259 HIS Sn 8 GLN To 19 GLN To 80 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 154564 Z= 0.323 Angle : 0.612 14.949 230207 Z= 0.317 Chirality : 0.040 0.316 29301 Planarity : 0.005 0.080 13066 Dihedral : 23.010 179.863 74499 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 5.21 % Allowed : 19.78 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.21 (0.10), residues: 6246 helix: 0.99 (0.11), residues: 2076 sheet: -0.25 (0.14), residues: 1294 loop : -0.88 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCl 248 HIS 0.007 0.001 HISE5 94 PHE 0.019 0.002 PHEFG 62 TYR 0.020 0.002 TYRDm 104 ARG 0.007 0.001 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 665 time to evaluate : 6.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7097 (ttp80) REVERT: H 263 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7325 (tpt) REVERT: A4 35 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7207 (p90) REVERT: L6 10 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7091 (mmtm) REVERT: L6 31 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8272 (ttt-90) REVERT: F7 129 SER cc_start: 0.7776 (m) cc_final: 0.7348 (t) REVERT: MB 54 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: UC 16 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7210 (pp20) REVERT: UC 55 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.7877 (ttmm) REVERT: UC 89 LYS cc_start: 0.8242 (mmmm) cc_final: 0.7905 (mttp) REVERT: XE 30 MET cc_start: 0.8443 (mmm) cc_final: 0.8168 (mmp) REVERT: VH 67 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8778 (t) REVERT: PO 13 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7521 (ttp-110) REVERT: GR 124 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7102 (pm20) REVERT: GR 175 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7515 (mttm) REVERT: GS 87 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: CT 16 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7161 (mptp) REVERT: IX 73 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7616 (mptt) REVERT: Qb 79 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8232 (ptp-170) REVERT: Nc 47 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: Je 5 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: Je 9 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: Je 113 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8024 (ptpt) REVERT: Oi 35 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7117 (mtm110) REVERT: Oi 87 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6833 (pp20) REVERT: bk 49 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7791 (tttt) REVERT: Cl 109 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8377 (ttpt) REVERT: Cl 205 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8511 (mp) REVERT: Dm 153 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: Dm 155 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7580 (tttm) REVERT: Sn 82 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8781 (pttt) REVERT: ep 9 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8243 (mttt) REVERT: C1 22 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7145 (mttt) outliers start: 270 outliers final: 147 residues processed: 846 average time/residue: 2.0998 time to fit residues: 2569.7796 Evaluate side-chains 829 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 652 time to evaluate : 6.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 124 GLN Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 18 GLU Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 132 CYS Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 86 ARG Chi-restraints excluded: chain L6 residue 87 VAL Chi-restraints excluded: chain F7 residue 152 MET Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain aA residue 53 LEU Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain UC residue 99 ARG Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 21 MET Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain FG residue 71 LEU Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain BQ residue 10 MET Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GR residue 124 GLU Chi-restraints excluded: chain GR residue 175 LYS Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 19 ASN Chi-restraints excluded: chain CT residue 122 SER Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 64 VAL Chi-restraints excluded: chain IX residue 73 LYS Chi-restraints excluded: chain IX residue 142 ILE Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 67 ILE Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Nc residue 47 GLU Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Je residue 5 GLU Chi-restraints excluded: chain Je residue 9 GLU Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 94 ILE Chi-restraints excluded: chain Je residue 113 LYS Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 53 THR Chi-restraints excluded: chain Lg residue 131 ILE Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 87 GLU Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 205 LEU Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 155 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 179 ASP Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 82 LYS Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 972 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 574 optimal weight: 10.0000 chunk 736 optimal weight: 9.9990 chunk 570 optimal weight: 20.0000 chunk 849 optimal weight: 50.0000 chunk 563 optimal weight: 8.9990 chunk 1005 optimal weight: 10.0000 chunk 629 optimal weight: 10.0000 chunk 612 optimal weight: 20.0000 chunk 464 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 HIS ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN WD 44 ASN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN HK 62 ASN ** OL 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 70 GLN IX 136 GLN ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 31 GLN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Sn 8 GLN To 19 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.105 154564 Z= 0.545 Angle : 0.765 16.431 230207 Z= 0.386 Chirality : 0.049 0.336 29301 Planarity : 0.006 0.085 13066 Dihedral : 23.147 179.392 74495 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 5.36 % Allowed : 20.03 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.43 (0.10), residues: 6246 helix: 0.78 (0.11), residues: 2066 sheet: -0.32 (0.14), residues: 1267 loop : -1.01 (0.11), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPCl 248 HIS 0.010 0.002 HISYW 14 PHE 0.023 0.002 PHEAf 121 TYR 0.026 0.002 TYRKd 60 ARG 0.011 0.001 ARGep 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 665 time to evaluate : 6.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.7698 (ttpt) REVERT: B 249 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7100 (ttp80) REVERT: H 263 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7437 (tpt) REVERT: A4 35 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7261 (p90) REVERT: L6 10 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.6587 (mmmm) REVERT: L6 31 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8330 (ttt-90) REVERT: F7 129 SER cc_start: 0.7872 (m) cc_final: 0.7469 (t) REVERT: MB 54 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8544 (ttp) REVERT: MB 95 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8844 (mt) REVERT: UC 16 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7247 (pp20) REVERT: UC 55 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.7822 (ttmm) REVERT: UC 76 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.6996 (mt-10) REVERT: UC 89 LYS cc_start: 0.8271 (mmmm) cc_final: 0.7955 (mttp) REVERT: PO 13 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7661 (ttp-110) REVERT: GR 124 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: GR 175 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7575 (mttm) REVERT: CT 16 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7523 (mptp) REVERT: YW 55 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7613 (tppt) REVERT: IX 73 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7688 (mptt) REVERT: JY 52 LEU cc_start: 0.9095 (mp) cc_final: 0.8847 (mt) REVERT: QZ 45 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6552 (ptp90) REVERT: Qb 79 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8075 (ptp-170) REVERT: Nc 47 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: Je 5 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: Je 9 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: Af 105 GLU cc_start: 0.7698 (pm20) cc_final: 0.7389 (pp20) REVERT: Af 187 LYS cc_start: 0.8032 (mtpp) cc_final: 0.7728 (ptpt) REVERT: Oi 35 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7042 (mtm110) REVERT: bk 49 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7806 (tttt) REVERT: Cl 109 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8331 (ttpt) REVERT: Cl 205 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8455 (mp) REVERT: Dm 145 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: Dm 153 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: Dm 155 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7618 (tttm) REVERT: Sn 82 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8805 (pttt) REVERT: ep 9 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8213 (mttt) REVERT: C1 22 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7186 (mttt) outliers start: 278 outliers final: 169 residues processed: 859 average time/residue: 2.0512 time to fit residues: 2546.8118 Evaluate side-chains 854 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 653 time to evaluate : 6.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 18 GLU Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 132 CYS Chi-restraints excluded: chain E5 residue 152 MET Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 82 ILE Chi-restraints excluded: chain L6 residue 86 ARG Chi-restraints excluded: chain L6 residue 87 VAL Chi-restraints excluded: chain F7 residue 35 THR Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 150 LYS Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain aA residue 53 LEU Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 9 ASN Chi-restraints excluded: chain UC residue 14 SER Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain UC residue 71 VAL Chi-restraints excluded: chain UC residue 76 GLU Chi-restraints excluded: chain UC residue 99 ARG Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 10 VAL Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain FG residue 71 LEU Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain TI residue 77 LYS Chi-restraints excluded: chain HK residue 62 ASN Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 26 VAL Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain PO residue 6 ARG Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain BQ residue 10 MET Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 72 LEU Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GR residue 124 GLU Chi-restraints excluded: chain GR residue 175 LYS Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 19 ASN Chi-restraints excluded: chain CT residue 122 SER Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 59 THR Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain YW residue 55 LYS Chi-restraints excluded: chain IX residue 11 VAL Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 64 VAL Chi-restraints excluded: chain IX residue 73 LYS Chi-restraints excluded: chain IX residue 142 ILE Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 45 ARG Chi-restraints excluded: chain QZ residue 67 ILE Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Nc residue 47 GLU Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 96 THR Chi-restraints excluded: chain Je residue 5 GLU Chi-restraints excluded: chain Je residue 9 GLU Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 58 MET Chi-restraints excluded: chain Je residue 94 ILE Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 53 THR Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 72 VAL Chi-restraints excluded: chain Oi residue 87 GLU Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 205 LEU Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 32 THR Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 145 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 155 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 179 ASP Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 34 ASP Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 67 THR Chi-restraints excluded: chain Sn residue 82 LYS Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 621 optimal weight: 10.0000 chunk 401 optimal weight: 5.9990 chunk 600 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 639 optimal weight: 10.0000 chunk 684 optimal weight: 30.0000 chunk 497 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 790 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN HK 62 ASN OL 83 GLN BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN CT 123 GLN IX 70 GLN IX 136 GLN Lg 31 GLN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Sn 8 GLN To 19 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 154564 Z= 0.425 Angle : 0.685 16.599 230207 Z= 0.351 Chirality : 0.044 0.329 29301 Planarity : 0.006 0.085 13066 Dihedral : 23.116 179.889 74495 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 4.90 % Allowed : 20.70 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.10), residues: 6246 helix: 0.86 (0.11), residues: 2065 sheet: -0.28 (0.14), residues: 1277 loop : -1.01 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPCl 248 HIS 0.008 0.001 HISYW 14 PHE 0.020 0.002 PHEFG 62 TYR 0.023 0.002 TYRDm 104 ARG 0.009 0.001 ARGBa 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 665 time to evaluate : 6.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.7717 (ttpt) REVERT: B 249 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7097 (ttp80) REVERT: H 263 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7447 (tpt) REVERT: A4 35 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7305 (p90) REVERT: L6 10 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.6815 (mmmm) REVERT: L6 31 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8301 (ttt-90) REVERT: F7 129 SER cc_start: 0.7849 (m) cc_final: 0.7434 (t) REVERT: MB 54 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8514 (ttp) REVERT: UC 16 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: UC 55 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.7792 (ttmm) REVERT: UC 89 LYS cc_start: 0.8274 (mmmm) cc_final: 0.7960 (mttp) REVERT: RF 62 HIS cc_start: 0.7135 (m170) cc_final: 0.6919 (m170) REVERT: VH 67 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8805 (t) REVERT: PO 13 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7588 (ttp-110) REVERT: PO 33 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7190 (mtm-85) REVERT: CT 16 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7215 (mptp) REVERT: YW 55 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7605 (tppt) REVERT: IX 73 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7654 (mptt) REVERT: JY 52 LEU cc_start: 0.9049 (mp) cc_final: 0.8813 (mt) REVERT: QZ 45 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6546 (ptp90) REVERT: Qb 65 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7737 (pp20) REVERT: Qb 79 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8187 (ptp-170) REVERT: Je 5 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.6658 (mt-10) REVERT: Je 9 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: Je 45 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: Af 105 GLU cc_start: 0.7677 (pm20) cc_final: 0.7373 (pp20) REVERT: Oi 35 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7004 (mtm110) REVERT: bk 49 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7811 (tttt) REVERT: Cl 109 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8308 (ttpt) REVERT: Cl 205 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8480 (mp) REVERT: Dm 153 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: Dm 155 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7616 (tttm) REVERT: Sn 82 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8790 (pttt) REVERT: ep 9 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8228 (mttt) REVERT: C1 22 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7167 (mttt) outliers start: 254 outliers final: 175 residues processed: 835 average time/residue: 2.1078 time to fit residues: 2542.7252 Evaluate side-chains 861 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 656 time to evaluate : 6.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 18 GLU Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 132 CYS Chi-restraints excluded: chain E5 residue 152 MET Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 82 ILE Chi-restraints excluded: chain L6 residue 86 ARG Chi-restraints excluded: chain L6 residue 87 VAL Chi-restraints excluded: chain F7 residue 16 ILE Chi-restraints excluded: chain F7 residue 152 MET Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain E9 residue 131 LYS Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain aA residue 53 LEU Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 9 ASN Chi-restraints excluded: chain UC residue 14 SER Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain UC residue 71 VAL Chi-restraints excluded: chain UC residue 99 ARG Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 10 VAL Chi-restraints excluded: chain FG residue 21 MET Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain FG residue 71 LEU Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain TI residue 77 LYS Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 26 VAL Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain PO residue 6 ARG Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 33 ARG Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain BQ residue 10 MET Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 72 LEU Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 19 ASN Chi-restraints excluded: chain CT residue 122 SER Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain YW residue 17 LYS Chi-restraints excluded: chain YW residue 55 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 64 VAL Chi-restraints excluded: chain IX residue 73 LYS Chi-restraints excluded: chain IX residue 142 ILE Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 45 ARG Chi-restraints excluded: chain QZ residue 67 ILE Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 65 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 37 VAL Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Kd residue 96 THR Chi-restraints excluded: chain Je residue 5 GLU Chi-restraints excluded: chain Je residue 9 GLU Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 58 MET Chi-restraints excluded: chain Je residue 94 ILE Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 53 THR Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 72 VAL Chi-restraints excluded: chain Oi residue 87 GLU Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 24 LEU Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 205 LEU Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 32 THR Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 155 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 179 ASP Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 67 THR Chi-restraints excluded: chain Sn residue 82 LYS Chi-restraints excluded: chain Sn residue 85 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain ep residue 18 ARG Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 914 optimal weight: 6.9990 chunk 963 optimal weight: 4.9990 chunk 878 optimal weight: 6.9990 chunk 936 optimal weight: 6.9990 chunk 962 optimal weight: 2.9990 chunk 563 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 735 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 846 optimal weight: 10.0000 chunk 886 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN aA 21 HIS ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN HK 62 ASN OL 83 GLN BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN CT 123 GLN IX 70 GLN IX 136 GLN ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 31 GLN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Sn 8 GLN To 19 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 154564 Z= 0.289 Angle : 0.614 16.424 230207 Z= 0.321 Chirality : 0.039 0.300 29301 Planarity : 0.005 0.086 13066 Dihedral : 23.127 179.419 74495 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.87 % Rotamer: Outliers : 4.40 % Allowed : 21.34 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.10), residues: 6246 helix: 0.98 (0.11), residues: 2066 sheet: -0.26 (0.14), residues: 1268 loop : -0.96 (0.11), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPF7 83 HIS 0.008 0.001 HISaA 21 PHE 0.031 0.002 PHEXE 26 TYR 0.025 0.002 TYRDm 104 ARG 0.009 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 666 time to evaluate : 6.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.7726 (ttpt) REVERT: B 249 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7090 (ttp80) REVERT: H 263 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7436 (tpt) REVERT: A4 35 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7314 (p90) REVERT: L6 10 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7032 (mmtm) REVERT: L6 31 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8292 (ttt-90) REVERT: F7 129 SER cc_start: 0.7812 (m) cc_final: 0.7405 (t) REVERT: MB 54 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8438 (ttp) REVERT: UC 16 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: UC 55 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.7783 (ttmm) REVERT: UC 89 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7952 (mttp) REVERT: RF 62 HIS cc_start: 0.7137 (m170) cc_final: 0.6914 (m170) REVERT: VH 67 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8804 (t) REVERT: PO 13 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7532 (ttp-110) REVERT: GR 124 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: CT 16 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7549 (mptp) REVERT: IX 73 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7781 (mttt) REVERT: JY 52 LEU cc_start: 0.9022 (mp) cc_final: 0.8774 (mt) REVERT: QZ 45 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6508 (ptp90) REVERT: Qb 65 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7721 (pp20) REVERT: Qb 79 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8207 (ptp-170) REVERT: Je 5 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: Je 9 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: Je 45 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: Af 105 GLU cc_start: 0.7676 (pm20) cc_final: 0.7374 (pp20) REVERT: Af 187 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7700 (ptpt) REVERT: Oi 35 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.6963 (mtm110) REVERT: bk 49 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7802 (tttt) REVERT: Cl 109 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8297 (ttpt) REVERT: Cl 205 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (mp) REVERT: Dm 145 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: Dm 153 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: Dm 155 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7604 (tttm) REVERT: Sn 82 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8752 (pttt) REVERT: ep 9 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8228 (mttt) REVERT: C1 22 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7144 (mttt) outliers start: 227 outliers final: 157 residues processed: 818 average time/residue: 2.0846 time to fit residues: 2460.8413 Evaluate side-chains 845 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 658 time to evaluate : 6.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 18 GLU Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 132 CYS Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 82 ILE Chi-restraints excluded: chain L6 residue 87 VAL Chi-restraints excluded: chain F7 residue 152 MET Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain aA residue 53 LEU Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 14 SER Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain UC residue 71 VAL Chi-restraints excluded: chain UC residue 99 ARG Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 10 VAL Chi-restraints excluded: chain FG residue 21 MET Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain FG residue 71 LEU Chi-restraints excluded: chain FG residue 77 LEU Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain TI residue 77 LYS Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain PO residue 6 ARG Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 72 LEU Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GR residue 124 GLU Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 19 ASN Chi-restraints excluded: chain CT residue 122 SER Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 17 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 64 VAL Chi-restraints excluded: chain IX residue 73 LYS Chi-restraints excluded: chain IX residue 142 ILE Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 45 ARG Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 65 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Kd residue 37 VAL Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Je residue 5 GLU Chi-restraints excluded: chain Je residue 9 GLU Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 58 MET Chi-restraints excluded: chain Je residue 94 ILE Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 53 THR Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 72 VAL Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 109 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 205 LEU Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 32 THR Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 145 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 155 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 179 ASP Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 82 LYS Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 933 optimal weight: 2.9990 chunk 615 optimal weight: 20.0000 chunk 990 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 469 optimal weight: 10.0000 chunk 688 optimal weight: 20.0000 chunk 1039 optimal weight: 9.9990 chunk 956 optimal weight: 10.0000 chunk 827 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 639 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 73 ASN ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN HK 62 ASN OL 83 GLN BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN CT 123 GLN IX 70 GLN IX 136 GLN ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Qb 102 ASN Lg 31 GLN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Sn 8 GLN To 19 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 154564 Z= 0.460 Angle : 0.711 17.468 230207 Z= 0.363 Chirality : 0.045 0.325 29301 Planarity : 0.006 0.087 13066 Dihedral : 23.125 179.996 74495 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 4.36 % Allowed : 21.49 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.37 (0.10), residues: 6246 helix: 0.87 (0.11), residues: 2067 sheet: -0.29 (0.14), residues: 1276 loop : -1.01 (0.11), residues: 2903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPF7 83 HIS 0.009 0.001 HISYW 14 PHE 0.027 0.002 PHEXE 26 TYR 0.029 0.002 TYRKd 60 ARG 0.009 0.001 ARGBa 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12492 Ramachandran restraints generated. 6246 Oldfield, 0 Emsley, 6246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 670 time to evaluate : 6.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.7700 (ttpt) REVERT: B 249 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7060 (ttp80) REVERT: H 263 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7457 (tpt) REVERT: A4 35 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7405 (p90) REVERT: L6 10 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.6767 (mmmm) REVERT: L6 31 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8317 (ttt-90) REVERT: F7 129 SER cc_start: 0.7875 (m) cc_final: 0.7474 (t) REVERT: MB 54 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8529 (ttp) REVERT: UC 16 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: UC 55 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.7803 (ttmm) REVERT: UC 89 LYS cc_start: 0.8267 (mmmm) cc_final: 0.7965 (mttp) REVERT: RF 62 HIS cc_start: 0.7142 (m170) cc_final: 0.6917 (m170) REVERT: PO 13 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7673 (ttp-110) REVERT: PO 33 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7226 (mtm-85) REVERT: GR 124 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: CT 16 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7172 (mptp) REVERT: IX 73 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7612 (mptt) REVERT: JY 52 LEU cc_start: 0.9058 (mp) cc_final: 0.8825 (mt) REVERT: QZ 45 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6557 (ptp90) REVERT: Qb 2 TYR cc_start: 0.8452 (p90) cc_final: 0.8016 (p90) REVERT: Qb 65 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7709 (pp20) REVERT: Qb 79 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8142 (ptp-170) REVERT: Je 5 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: Je 9 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: Je 45 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: Af 105 GLU cc_start: 0.7719 (pm20) cc_final: 0.7422 (pp20) REVERT: Af 187 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7805 (ptpt) REVERT: Lg 116 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: Oi 35 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7015 (mtm110) REVERT: Oi 87 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6884 (pp20) REVERT: bk 49 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7808 (tttt) REVERT: Cl 205 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8481 (mp) REVERT: Dm 145 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: Dm 153 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: Dm 155 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7591 (tttm) REVERT: Sn 82 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8790 (pttt) REVERT: ep 9 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8213 (mttt) REVERT: C1 22 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7171 (mttt) outliers start: 225 outliers final: 166 residues processed: 820 average time/residue: 2.0929 time to fit residues: 2472.9916 Evaluate side-chains 859 residues out of total 5232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 662 time to evaluate : 6.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 188 VAL Chi-restraints excluded: chain A4 residue 189 ILE Chi-restraints excluded: chain A4 residue 196 SER Chi-restraints excluded: chain E5 residue 18 GLU Chi-restraints excluded: chain E5 residue 37 SER Chi-restraints excluded: chain E5 residue 101 MET Chi-restraints excluded: chain E5 residue 119 VAL Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain E5 residue 132 CYS Chi-restraints excluded: chain E5 residue 152 MET Chi-restraints excluded: chain L6 residue 10 LYS Chi-restraints excluded: chain L6 residue 13 LYS Chi-restraints excluded: chain L6 residue 31 ARG Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 82 ILE Chi-restraints excluded: chain L6 residue 86 ARG Chi-restraints excluded: chain L6 residue 87 VAL Chi-restraints excluded: chain F7 residue 16 ILE Chi-restraints excluded: chain F7 residue 152 MET Chi-restraints excluded: chain F7 residue 158 THR Chi-restraints excluded: chain E9 residue 3 LEU Chi-restraints excluded: chain E9 residue 11 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 123 LEU Chi-restraints excluded: chain aA residue 23 THR Chi-restraints excluded: chain aA residue 53 LEU Chi-restraints excluded: chain MB residue 54 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 14 SER Chi-restraints excluded: chain UC residue 16 GLU Chi-restraints excluded: chain UC residue 55 LYS Chi-restraints excluded: chain UC residue 71 VAL Chi-restraints excluded: chain UC residue 99 ARG Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 25 THR Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 22 ASP Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 10 VAL Chi-restraints excluded: chain FG residue 21 MET Chi-restraints excluded: chain FG residue 56 LYS Chi-restraints excluded: chain FG residue 71 LEU Chi-restraints excluded: chain VH residue 43 THR Chi-restraints excluded: chain VH residue 63 ASN Chi-restraints excluded: chain VH residue 67 VAL Chi-restraints excluded: chain TI residue 12 VAL Chi-restraints excluded: chain TI residue 76 GLN Chi-restraints excluded: chain TI residue 77 LYS Chi-restraints excluded: chain HK residue 62 ASN Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 92 ASP Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 5 SER Chi-restraints excluded: chain OL residue 26 VAL Chi-restraints excluded: chain OL residue 37 ASP Chi-restraints excluded: chain OL residue 46 LYS Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain PO residue 6 ARG Chi-restraints excluded: chain PO residue 13 ARG Chi-restraints excluded: chain PO residue 33 ARG Chi-restraints excluded: chain SP residue 50 SER Chi-restraints excluded: chain BQ residue 86 ARG Chi-restraints excluded: chain BQ residue 128 VAL Chi-restraints excluded: chain GR residue 49 VAL Chi-restraints excluded: chain GR residue 72 LEU Chi-restraints excluded: chain GR residue 104 THR Chi-restraints excluded: chain GR residue 105 LEU Chi-restraints excluded: chain GR residue 106 ASN Chi-restraints excluded: chain GR residue 124 GLU Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain GS residue 87 GLN Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 16 LYS Chi-restraints excluded: chain CT residue 19 ASN Chi-restraints excluded: chain CT residue 122 SER Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 55 SER Chi-restraints excluded: chain KU residue 59 THR Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain KU residue 129 VAL Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 17 LYS Chi-restraints excluded: chain IX residue 17 VAL Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 64 VAL Chi-restraints excluded: chain IX residue 73 LYS Chi-restraints excluded: chain IX residue 142 ILE Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 44 THR Chi-restraints excluded: chain QZ residue 29 VAL Chi-restraints excluded: chain QZ residue 35 VAL Chi-restraints excluded: chain QZ residue 45 ARG Chi-restraints excluded: chain QZ residue 76 THR Chi-restraints excluded: chain QZ residue 85 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Ba residue 24 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 49 ILE Chi-restraints excluded: chain Qb residue 60 GLU Chi-restraints excluded: chain Qb residue 65 GLU Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 34 LYS Chi-restraints excluded: chain Kd residue 17 THR Chi-restraints excluded: chain Kd residue 37 VAL Chi-restraints excluded: chain Kd residue 75 THR Chi-restraints excluded: chain Je residue 5 GLU Chi-restraints excluded: chain Je residue 9 GLU Chi-restraints excluded: chain Je residue 43 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 58 MET Chi-restraints excluded: chain Je residue 94 ILE Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 42 ASP Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 53 THR Chi-restraints excluded: chain Lg residue 116 GLU Chi-restraints excluded: chain Lg residue 132 VAL Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 21 SER Chi-restraints excluded: chain Oi residue 35 ARG Chi-restraints excluded: chain Oi residue 66 ILE Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 72 VAL Chi-restraints excluded: chain Oi residue 87 GLU Chi-restraints excluded: chain Oi residue 89 LYS Chi-restraints excluded: chain Oi residue 106 SER Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain Pj residue 42 LEU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 116 VAL Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 205 LEU Chi-restraints excluded: chain Dm residue 29 ASP Chi-restraints excluded: chain Dm residue 32 THR Chi-restraints excluded: chain Dm residue 41 GLN Chi-restraints excluded: chain Dm residue 51 GLU Chi-restraints excluded: chain Dm residue 54 LEU Chi-restraints excluded: chain Dm residue 110 SER Chi-restraints excluded: chain Dm residue 111 THR Chi-restraints excluded: chain Dm residue 117 GLN Chi-restraints excluded: chain Dm residue 145 GLN Chi-restraints excluded: chain Dm residue 153 GLN Chi-restraints excluded: chain Dm residue 155 LYS Chi-restraints excluded: chain Dm residue 170 THR Chi-restraints excluded: chain Dm residue 179 ASP Chi-restraints excluded: chain Dm residue 194 ASP Chi-restraints excluded: chain Sn residue 16 SER Chi-restraints excluded: chain Sn residue 26 LEU Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain Sn residue 82 LYS Chi-restraints excluded: chain Sn residue 85 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 9 LYS Chi-restraints excluded: chain C1 residue 14 LYS Chi-restraints excluded: chain C1 residue 19 VAL Chi-restraints excluded: chain C1 residue 20 ASP Chi-restraints excluded: chain C1 residue 22 LYS Chi-restraints excluded: chain C1 residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 507 optimal weight: 7.9990 chunk 657 optimal weight: 10.0000 chunk 881 optimal weight: 0.0020 chunk 253 optimal weight: 10.0000 chunk 762 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 828 optimal weight: 2.9990 chunk 346 optimal weight: 7.9990 chunk 850 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 73 ASN ** E5 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN E9 114 GLN aA 21 HIS ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** TI 72 ASN HK 62 ASN OL 83 GLN BQ 18 GLN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 3 GLN CT 123 GLN IX 70 GLN IX 136 GLN ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Qb 102 ASN ** Nc 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 31 GLN ** Oi 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bk 41 GLN Sn 8 GLN To 19 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108883 restraints weight = 202230.663| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 0.43 r_work: 0.3170 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 154564 Z= 0.329 Angle : 0.641 17.414 230207 Z= 0.334 Chirality : 0.041 0.307 29301 Planarity : 0.005 0.087 13066 Dihedral : 23.128 179.572 74495 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 4.28 % Allowed : 21.76 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.30 (0.10), residues: 6246 helix: 0.96 (0.11), residues: 2067 sheet: -0.27 (0.14), residues: 1272 loop : -0.97 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPF7 83 HIS 0.008 0.001 HISE5 94 PHE 0.033 0.002 PHEXE 26 TYR 0.026 0.002 TYRKd 60 ARG 0.021 0.001 ARGHK 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39764.01 seconds wall clock time: 693 minutes 31.56 seconds (41611.56 seconds total)