Starting phenix.real_space_refine on Wed Mar 20 05:31:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdv_19076/03_2024/8rdv_19076.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdv_19076/03_2024/8rdv_19076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdv_19076/03_2024/8rdv_19076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdv_19076/03_2024/8rdv_19076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdv_19076/03_2024/8rdv_19076.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rdv_19076/03_2024/8rdv_19076.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4409 5.49 5 S 175 5.16 5 C 71916 2.51 5 N 26282 2.21 5 O 39281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 310": "OE1" <-> "OE2" Residue "H GLU 360": "OE1" <-> "OE2" Residue "H GLU 364": "OE1" <-> "OE2" Residue "R3 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A4 ASP 158": "OD1" <-> "OD2" Residue "A4 ASP 224": "OD1" <-> "OD2" Residue "L6 ASP 109": "OD1" <-> "OD2" Residue "F7 TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F7 ASP 23": "OD1" <-> "OD2" Residue "F7 GLU 82": "OE1" <-> "OE2" Residue "F7 ASP 123": "OD1" <-> "OD2" Residue "F7 ASP 142": "OD1" <-> "OD2" Residue "F7 ASP 147": "OD1" <-> "OD2" Residue "F7 GLU 165": "OE1" <-> "OE2" Residue "E9 GLU 12": "OE1" <-> "OE2" Residue "E9 GLU 121": "OE1" <-> "OE2" Residue "E9 ASP 183": "OD1" <-> "OD2" Residue "E9 GLU 197": "OE1" <-> "OE2" Residue "MB GLU 49": "OE1" <-> "OE2" Residue "UC ASP 12": "OD1" <-> "OD2" Residue "UC GLU 16": "OE1" <-> "OE2" Residue "UC GLU 58": "OE1" <-> "OE2" Residue "WD GLU 41": "OE1" <-> "OE2" Residue "XE GLU 20": "OE1" <-> "OE2" Residue "RF GLU 23": "OE1" <-> "OE2" Residue "VH GLU 44": "OE1" <-> "OE2" Residue "fJ TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OL ASP 37": "OD1" <-> "OD2" Residue "OL ASP 67": "OD1" <-> "OD2" Residue "SP GLU 20": "OE1" <-> "OE2" Residue "GS GLU 64": "OE1" <-> "OE2" Residue "CT TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT GLU 41": "OE1" <-> "OE2" Residue "NV GLU 10": "OE1" <-> "OE2" Residue "NV ASP 31": "OD1" <-> "OD2" Residue "NV GLU 39": "OE1" <-> "OE2" Residue "NV TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IX PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IX ASP 71": "OD1" <-> "OD2" Residue "QZ GLU 69": "OE1" <-> "OE2" Residue "Nc TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Kd GLU 83": "OE1" <-> "OE2" Residue "Je GLU 9": "OE1" <-> "OE2" Residue "Je GLU 120": "OE1" <-> "OE2" Residue "Af GLU 179": "OE1" <-> "OE2" Residue "Lg GLU 107": "OE1" <-> "OE2" Residue "Oi GLU 12": "OE1" <-> "OE2" Residue "Oi GLU 46": "OE1" <-> "OE2" Residue "Oi GLU 84": "OE1" <-> "OE2" Residue "Oi GLU 114": "OE1" <-> "OE2" Residue "Pj TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bk GLU 47": "OE1" <-> "OE2" Residue "Cl TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cl ASP 72": "OD1" <-> "OD2" Residue "Cl GLU 120": "OE1" <-> "OE2" Residue "Dm TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Sn TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Sn GLU 54": "OE1" <-> "OE2" Residue "Sn TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "To ASP 59": "OD1" <-> "OD2" Residue "To ASP 63": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142063 Number of models: 1 Model: "" Number of chains: 56 Chain: "B" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2829 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 985 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "H" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1409 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "Z2" Number of atoms: 58145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2710, 58145 Classifications: {'RNA': 2710} Modifications used: {'rna2p_pur': 267, 'rna2p_pyr': 151, 'rna3p_pur': 1299, 'rna3p_pyr': 993} Link IDs: {'rna2p': 418, 'rna3p': 2291} 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: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 717 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} 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: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 637 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} 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: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1688 Classifications: {'peptide': 212} 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: "V" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1521 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 10, 'rna3p_pur': 1, 'rna3p_pyr': 64} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "Y" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna3p': 5} 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: "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: 4 Time building chain proxies: 55.43, per 1000 atoms: 0.39 Number of scatterers: 142063 At special positions: 0 Unit cell: (221.961, 236.421, 276.186, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 175 16.00 P 4409 15.00 O 39281 8.00 N 26282 7.00 C 71916 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: 59.69 Conformation dependent library (CDL) restraints added in 7.3 seconds 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11180 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 77 sheets defined 36.4% alpha, 22.4% beta 1476 base pairs and 2366 stacking pairs defined. Time for finding SS restraints: 50.22 Creating SS restraints... Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 32 through 52 Processing helix chain 'B' and resid 53 through 69 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.870A pdb=" N ASN B 76 " --> pdb=" O HIS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 183 through 205 removed outlier: 4.188A pdb=" N GLU B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 254 through 279 removed outlier: 3.794A pdb=" N LEU B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'F' and resid 33 through 37 Processing helix chain 'F' and resid 39 through 52 Proline residue: F 49 - end of helix Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 69 through 89 removed outlier: 3.577A pdb=" N ALA F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 100 removed outlier: 4.536A pdb=" N ALA F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 319 Processing helix chain 'R3' and resid 25 through 31 removed outlier: 4.236A pdb=" N GLNR3 31 " --> pdb=" O GLUR3 27 " (cutoff:3.500A) Processing helix chain 'R3' and resid 41 through 46 Processing helix chain 'R3' and resid 48 through 65 Processing helix chain 'A4' and resid 10 through 18 removed outlier: 4.067A pdb=" N LEUA4 14 " --> pdb=" O GLUA4 10 " (cutoff:3.500A) Processing helix chain 'A4' and resid 29 through 33 Processing helix chain 'A4' and resid 47 through 68 removed outlier: 3.538A pdb=" N LYSA4 53 " --> pdb=" O GLUA4 49 " (cutoff:3.500A) Processing helix chain 'A4' and resid 78 through 80 No H-bonds generated for 'chain 'A4' and resid 78 through 80' Processing helix chain 'A4' and resid 81 through 93 removed outlier: 3.888A pdb=" N ILEA4 85 " --> pdb=" O ALAA4 81 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALAA4 86 " --> pdb=" O SERA4 82 " (cutoff:3.500A) Processing helix chain 'A4' and resid 108 through 129 removed outlier: 3.527A pdb=" N LEUA4 112 " --> pdb=" O ASNA4 108 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLNA4 114 " --> pdb=" O LYSA4 110 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SERA4 115 " --> pdb=" O THRA4 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASPA4 128 " --> pdb=" O LYSA4 124 " (cutoff:3.500A) Processing helix chain 'A4' and resid 135 through 153 Processing helix chain 'A4' and resid 155 through 159 removed outlier: 4.292A pdb=" N ASPA4 158 " --> pdb=" O GLYA4 155 " (cutoff:3.500A) Processing helix chain 'A4' and resid 174 through 185 Processing helix chain 'A4' and resid 211 through 234 Processing helix chain 'A4' and resid 235 through 237 No H-bonds generated for 'chain 'A4' and resid 235 through 237' Processing helix chain 'E5' and resid 60 through 75 removed outlier: 3.594A pdb=" N ARGE5 74 " --> pdb=" O GLUE5 70 " (cutoff:3.500A) Processing helix chain 'E5' and resid 113 through 124 removed outlier: 3.596A 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 'L6' and resid 3 through 10 Processing helix chain 'L6' and resid 21 through 25 Processing helix chain 'L6' and resid 113 through 117 Processing helix chain 'F7' and resid 3 through 9 Processing helix chain 'F7' and resid 11 through 21 Processing helix chain 'F7' and resid 48 through 62 Processing helix chain 'F7' and resid 93 through 106 Processing helix chain 'F7' and resid 107 through 111 removed outlier: 3.611A pdb=" N VALF7 111 " --> pdb=" O ILEF7 108 " (cutoff:3.500A) Processing helix chain 'F7' and resid 134 through 138 removed outlier: 3.570A pdb=" N VALF7 137 " --> pdb=" O GLUF7 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHEF7 138 " --> pdb=" O GLNF7 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'F7' and resid 134 through 138' Processing helix chain 'F7' and resid 162 through 173 removed outlier: 3.642A pdb=" N PHEF7 173 " --> pdb=" O LEUF7 169 " (cutoff:3.500A) Processing helix chain 'E9' and resid 14 through 19 Processing helix chain 'E9' and resid 23 through 38 Processing helix chain 'E9' and resid 96 through 114 Processing helix chain 'E9' and resid 129 through 140 removed outlier: 3.676A pdb=" N LEUE9 133 " --> pdb=" O LYSE9 129 " (cutoff:3.500A) Processing helix chain 'E9' and resid 155 through 161 Processing helix chain 'E9' and resid 172 through 174 No H-bonds generated for 'chain 'E9' and resid 172 through 174' Processing helix chain 'E9' and resid 175 through 182 removed outlier: 3.761A pdb=" N PHEE9 182 " --> pdb=" O SERE9 178 " (cutoff:3.500A) Processing helix chain 'E9' and resid 189 through 199 Processing helix chain 'aA' and resid 9 through 17 Processing helix chain 'aA' and resid 18 through 20 No H-bonds generated for 'chain 'aA' and resid 18 through 20' Processing helix chain 'MB' and resid 13 through 32 Processing helix chain 'MB' and resid 38 through 56 removed outlier: 3.716A pdb=" N ARGMB 45 " --> pdb=" O ALAMB 41 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARGMB 46 " --> pdb=" O LYSMB 42 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VALMB 47 " --> pdb=" O GLUMB 43 " (cutoff:3.500A) Proline residue: MB 50 - end of helix Processing helix chain 'MB' and resid 59 through 71 Processing helix chain 'MB' and resid 72 through 83 Processing helix chain 'UC' and resid 14 through 18 removed outlier: 3.645A pdb=" N GLNUC 18 " --> pdb=" O ALAUC 15 " (cutoff:3.500A) Processing helix chain 'UC' and resid 19 through 28 Processing helix chain 'UC' and resid 50 through 59 removed outlier: 3.906A pdb=" N PHEUC 59 " --> pdb=" O LYSUC 55 " (cutoff:3.500A) Processing helix chain 'UC' and resid 60 through 65 removed outlier: 3.886A pdb=" N PHEUC 63 " --> pdb=" O GLUUC 60 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HISUC 65 " --> pdb=" O PHEUC 62 " (cutoff:3.500A) Processing helix chain 'WD' and resid 53 through 63 Processing helix chain 'WD' and resid 63 through 75 removed outlier: 3.527A pdb=" N ASPWD 70 " --> pdb=" O LYSWD 66 " (cutoff:3.500A) Processing helix chain 'XE' and resid 3 through 8 removed outlier: 4.257A pdb=" N ASPXE 8 " --> pdb=" O SERXE 4 " (cutoff:3.500A) Processing helix chain 'XE' and resid 10 through 35 Processing helix chain 'XE' and resid 41 through 63 Processing helix chain 'RF' and resid 13 through 25 removed outlier: 3.939A pdb=" N LEURF 19 " --> pdb=" O GLNRF 15 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VALRF 20 " --> pdb=" O LYSRF 16 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLURF 23 " --> pdb=" O LEURF 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VALRF 24 " --> pdb=" O VALRF 20 " (cutoff:3.500A) Processing helix chain 'RF' and resid 28 through 39 Processing helix chain 'RF' and resid 42 through 61 removed outlier: 3.849A pdb=" N PHERF 46 " --> pdb=" O LYSRF 42 " (cutoff:3.500A) Processing helix chain 'RF' and resid 65 through 69 Processing helix chain 'RF' and resid 89 through 91 No H-bonds generated for 'chain 'RF' and resid 89 through 91' Processing helix chain 'FG' and resid 12 through 16 removed outlier: 4.405A pdb=" N ASPFG 16 " --> pdb=" O ASPFG 13 " (cutoff:3.500A) Processing helix chain 'FG' and resid 17 through 32 removed outlier: 3.601A pdb=" N TYRFG 25 " --> pdb=" O METFG 21 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASNFG 32 " --> pdb=" O LEUFG 28 " (cutoff:3.500A) Processing helix chain 'FG' and resid 67 through 82 removed outlier: 4.579A pdb=" N ASPFG 82 " --> pdb=" O PHEFG 78 " (cutoff:3.500A) Processing helix chain 'fJ' and resid 72 through 76 Processing helix chain 'HK' and resid 3 through 20 removed outlier: 3.742A pdb=" N GLUHK 16 " --> pdb=" O LYSHK 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VALHK 17 " --> pdb=" O ARGHK 13 " (cutoff:3.500A) Processing helix chain 'HK' and resid 20 through 33 Processing helix chain 'HK' and resid 37 through 51 Processing helix chain 'HK' and resid 52 through 56 Processing helix chain 'HK' and resid 80 through 91 Processing helix chain 'OL' and resid 3 through 14 Processing helix chain 'OL' and resid 23 through 45 removed outlier: 4.242A pdb=" N ASNOL 40 " --> pdb=" O ASNOL 36 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HISOL 41 " --> pdb=" O ASPOL 37 " (cutoff:3.500A) Processing helix chain 'OL' and resid 48 through 73 removed outlier: 3.744A pdb=" N GLYOL 54 " --> pdb=" O HISOL 50 " (cutoff:3.500A) Processing helix chain 'OL' and resid 73 through 85 Processing helix chain 'MM' and resid 14 through 19 Processing helix chain 'MM' and resid 20 through 22 No H-bonds generated for 'chain 'MM' and resid 20 through 22' Processing helix chain 'MM' and resid 27 through 38 Processing helix chain 'MM' and resid 49 through 61 Processing helix chain 'MM' and resid 65 through 82 removed outlier: 3.902A pdb=" N ARGMM 71 " --> pdb=" O GLYMM 67 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEUMM 80 " --> pdb=" O ASNMM 76 " (cutoff:3.500A) Processing helix chain 'MM' and resid 85 through 93 removed outlier: 3.674A pdb=" N ARGMM 93 " --> pdb=" O ILEMM 89 " (cutoff:3.500A) Processing helix chain 'PO' and resid 6 through 21 Processing helix chain 'PO' and resid 25 through 30 Processing helix chain 'PO' and resid 31 through 72 removed outlier: 4.278A pdb=" N GLNPO 37 " --> pdb=" O ARGPO 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARGPO 51 " --> pdb=" O TYRPO 47 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYSPO 54 " --> pdb=" O ARGPO 50 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARGPO 58 " --> pdb=" O LYSPO 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARGPO 59 " --> pdb=" O ARGPO 55 " (cutoff:3.500A) Processing helix chain 'PO' and resid 75 through 87 Processing helix chain 'PO' and resid 91 through 102 Processing helix chain 'PO' and resid 102 through 116 Processing helix chain 'SP' and resid 12 through 21 Processing helix chain 'SP' and resid 41 through 45 removed outlier: 3.547A pdb=" N METSP 44 " --> pdb=" O LEUSP 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VALSP 45 " --> pdb=" O PROSP 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'SP' and resid 41 through 45' Processing helix chain 'SP' and resid 63 through 67 removed outlier: 3.580A pdb=" N METSP 66 " --> pdb=" O SERSP 63 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VALSP 67 " --> pdb=" O GLUSP 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'SP' and resid 63 through 67' Processing helix chain 'SP' and resid 70 through 75 removed outlier: 3.683A pdb=" N PHESP 74 " --> pdb=" O LEUSP 71 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 5 through 20 Processing helix chain 'BQ' and resid 30 through 44 Processing helix chain 'BQ' and resid 97 through 101 Processing helix chain 'BQ' and resid 114 through 122 Processing helix chain 'GR' and resid 58 through 81 removed outlier: 3.612A pdb=" N THRGR 67 " --> pdb=" O METGR 63 " (cutoff:3.500A) Processing helix chain 'GR' and resid 137 through 150 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: 4.221A pdb=" N PHEGS 62 " --> pdb=" O ASPGS 58 " (cutoff:3.500A) Processing helix chain 'GS' and resid 93 through 110 Processing helix chain 'GS' and resid 116 through 131 Processing helix chain 'GS' and resid 133 through 150 Processing helix chain 'CT' and resid 6 through 11 Processing helix chain 'CT' and resid 27 through 47 removed outlier: 4.565A pdb=" N GLUCT 31 " --> pdb=" O LYSCT 27 " (cutoff:3.500A) Processing helix chain 'CT' and resid 72 through 78 removed outlier: 3.817A pdb=" N VALCT 76 " --> pdb=" O ARGCT 72 " (cutoff:3.500A) Processing helix chain 'CT' and resid 82 through 94 removed outlier: 3.585A pdb=" N ARGCT 86 " --> pdb=" O GLUCT 82 " (cutoff:3.500A) Processing helix chain 'CT' and resid 112 through 126 Processing helix chain 'CT' and resid 129 through 145 Processing helix chain 'CT' and resid 156 through 160 removed outlier: 3.552A pdb=" N ALACT 160 " --> pdb=" O LEUCT 157 " (cutoff:3.500A) Processing helix chain 'KU' and resid 48 through 50 No H-bonds generated for 'chain 'KU' and resid 48 through 50' Processing helix chain 'KU' and resid 55 through 58 Processing helix chain 'KU' and resid 59 through 75 Processing helix chain 'KU' and resid 90 through 93 removed outlier: 3.697A pdb=" N ARGKU 93 " --> pdb=" O GLYKU 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'KU' and resid 90 through 93' Processing helix chain 'KU' and resid 94 through 103 removed outlier: 3.548A pdb=" N ARGKU 98 " --> pdb=" O GLUKU 94 " (cutoff:3.500A) Processing helix chain 'NV' and resid 11 through 26 Processing helix chain 'NV' and resid 27 through 35 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 50 removed outlier: 3.578A pdb=" N METYW 46 " --> pdb=" O SERYW 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VALYW 50 " --> pdb=" O METYW 46 " (cutoff:3.500A) Processing helix chain 'IX' and resid 7 through 11 Processing helix chain 'IX' and resid 24 through 38 removed outlier: 3.855A pdb=" N GLNIX 31 " --> pdb=" O ARGIX 27 " (cutoff:3.500A) Processing helix chain 'IX' and resid 58 through 62 removed outlier: 3.740A pdb=" N ILEIX 62 " --> pdb=" O ALAIX 59 " (cutoff:3.500A) Processing helix chain 'IX' and resid 67 through 72 Processing helix chain 'IX' and resid 89 through 96 Processing helix chain 'IX' and resid 98 through 109 Processing helix chain 'IX' and resid 112 through 120 Processing helix chain 'JY' and resid 14 through 31 removed outlier: 3.581A pdb=" N ASPJY 19 " --> pdb=" O HISJY 15 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLNJY 20 " --> pdb=" O ARGJY 16 " (cutoff:3.500A) Processing helix chain 'JY' and resid 80 through 90 removed outlier: 3.927A pdb=" N ALAJY 86 " --> pdb=" O LYSJY 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEUJY 90 " --> pdb=" O ALAJY 86 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 8 through 17 Processing helix chain 'Ba' and resid 17 through 23 Processing helix chain 'Ba' and resid 24 through 38 Processing helix chain 'Nc' and resid 5 through 23 removed outlier: 4.942A pdb=" N LYSNc 14 " --> pdb=" O ARGNc 10 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THRNc 15 " --> pdb=" O ARGNc 11 " (cutoff:3.500A) Processing helix chain 'Nc' and resid 56 through 61 removed outlier: 4.679A pdb=" N SERNc 61 " --> pdb=" O GLYNc 57 " (cutoff:3.500A) Processing helix chain 'Nc' and resid 66 through 83 Processing helix chain 'Nc' and resid 100 through 112 Processing helix chain 'Kd' and resid 39 through 43 Processing helix chain 'Kd' and resid 58 through 63 Processing helix chain 'Kd' and resid 82 through 87 removed outlier: 3.982A pdb=" N ASNKd 85 " --> pdb=" O SERKd 82 " (cutoff:3.500A) Processing helix chain 'Kd' and resid 93 through 100 Processing helix chain 'Kd' and resid 130 through 140 Processing helix chain 'Je' and resid 103 through 107 removed outlier: 3.602A pdb=" N LEUJe 106 " --> pdb=" O THRJe 103 " (cutoff:3.500A) Processing helix chain 'Je' and resid 111 through 118 Processing helix chain 'Af' and resid 40 through 45 Processing helix chain 'Af' and resid 57 through 61 Processing helix chain 'Af' and resid 62 through 73 removed outlier: 3.564A pdb=" N ALAAf 72 " --> pdb=" O HISAf 68 " (cutoff:3.500A) Processing helix chain 'Af' and resid 100 through 104 Processing helix chain 'Af' and resid 123 through 129 Processing helix chain 'Lg' and resid 44 through 59 Processing helix chain 'Lg' and resid 110 through 123 removed outlier: 3.586A pdb=" N ALALg 123 " --> pdb=" O THRLg 119 " (cutoff:3.500A) Processing helix chain 'dh' and resid 8 through 13 Processing helix chain 'dh' and resid 37 through 44 Processing helix chain 'dh' and resid 51 through 62 removed outlier: 4.419A pdb=" N ALAdh 56 " --> pdb=" O LYSdh 52 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALAdh 57 " --> pdb=" O SERdh 53 " (cutoff:3.500A) Processing helix chain 'Oi' and resid 5 through 14 removed outlier: 3.626A pdb=" N VALOi 11 " --> pdb=" O LEUOi 7 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALAOi 14 " --> pdb=" O ALAOi 10 " (cutoff:3.500A) Processing helix chain 'Oi' and resid 55 through 58 Processing helix chain 'Oi' and resid 99 through 105 Processing helix chain 'Pj' and resid 53 through 64 Processing helix chain 'Pj' and resid 68 through 79 removed outlier: 3.689A pdb=" N SERPj 73 " --> pdb=" O ASPPj 69 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 30 through 32 No H-bonds generated for 'chain 'Cl' and resid 30 through 32' Processing helix chain 'Cl' and resid 133 through 135 No H-bonds generated for 'chain 'Cl' and resid 133 through 135' Processing helix chain 'Cl' and resid 199 through 203 Processing helix chain 'Cl' and resid 207 through 214 removed outlier: 3.813A pdb=" N SERCl 211 " --> pdb=" O LYSCl 207 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARGCl 214 " --> pdb=" O ALACl 210 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 221 through 225 Processing helix chain 'Cl' and resid 263 through 265 No H-bonds generated for 'chain 'Cl' and resid 263 through 265' Processing helix chain 'Dm' and resid 8 through 16 Processing helix chain 'Dm' and resid 27 through 33 removed outlier: 3.685A pdb=" N THRDm 32 " --> pdb=" O TYRDm 28 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 50 through 67 Processing helix chain 'Dm' and resid 69 through 81 Processing helix chain 'Dm' and resid 86 through 97 Processing helix chain 'Dm' and resid 98 through 107 Processing helix chain 'Dm' and resid 111 through 121 Processing helix chain 'Dm' and resid 159 through 173 removed outlier: 3.860A pdb=" N GLUDm 167 " --> pdb=" O LYSDm 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEUDm 168 " --> pdb=" O ASNDm 164 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 203 through 211 removed outlier: 3.856A pdb=" N ILEDm 207 " --> pdb=" O ASNDm 203 " (cutoff:3.500A) Processing helix chain 'Sn' and resid 3 through 7 removed outlier: 3.907A pdb=" N TYRSn 7 " --> pdb=" O ASNSn 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'Sn' and resid 3 through 7' Processing helix chain 'Sn' and resid 16 through 26 Processing helix chain 'Sn' and resid 38 through 50 Processing helix chain 'To' and resid 4 through 41 removed outlier: 3.559A pdb=" N LYSTo 16 " --> pdb=" O ARGTo 12 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLNTo 24 " --> pdb=" O ASNTo 20 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARGTo 34 " --> pdb=" O THRTo 30 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VALTo 35 " --> pdb=" O TYRTo 31 " (cutoff:3.500A) Processing helix chain 'To' and resid 43 through 53 removed outlier: 3.792A pdb=" N LYSTo 53 " --> pdb=" O GLUTo 49 " (cutoff:3.500A) Processing helix chain 'To' and resid 54 through 65 Processing helix chain 'To' and resid 68 through 85 removed outlier: 3.554A pdb=" N THRTo 82 " --> pdb=" O ARGTo 78 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLYTo 85 " --> pdb=" O LYSTo 81 " (cutoff:3.500A) Processing helix chain 'ep' and resid 30 through 33 Processing helix chain 'C1' and resid 22 through 29 Processing helix chain 'C1' and resid 40 through 49 removed outlier: 3.689A pdb=" N GLUC1 45 " --> pdb=" O ALAC1 41 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYSC1 46 " --> pdb=" O ALAC1 42 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALAC1 49 " --> pdb=" O GLUC1 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 89 through 94 removed outlier: 3.513A pdb=" N ARG B 101 " --> pdb=" O PHE B 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.582A pdb=" N GLU B 137 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.582A pdb=" N GLU B 137 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL B 211 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR B 124 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 213 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 126 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 210 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 234 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 282 through 283 removed outlier: 6.406A pdb=" N GLU B 299 " --> pdb=" O LYS B 348 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 350 " --> pdb=" O GLU B 299 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 301 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 323 removed outlier: 3.704A pdb=" N THR B 319 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 314 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 9 Processing sheet with id=AA7, first strand: chain 'H' and resid 214 through 223 removed outlier: 4.053A pdb=" N THR H 228 " --> pdb=" O LEU H 281 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY H 260 " --> pdb=" O LEU H 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 238 through 239 Processing sheet with id=AA9, first strand: chain 'H' and resid 312 through 313 removed outlier: 6.447A pdb=" N ILE H 379 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALA H 388 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE H 377 " --> pdb=" O ALA H 388 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA H 378 " --> pdb=" O TYR H 334 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N ASP H 339 " --> pdb=" O PRO H 368 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR H 341 " --> pdb=" O ILE H 366 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N LEU H 365 " --> pdb=" O ASP H 308 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N ASP H 308 " --> pdb=" O LEU H 365 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N HIS H 367 " --> pdb=" O LYS H 306 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS H 306 " --> pdb=" O HIS H 367 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR H 302 " --> pdb=" O MET H 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A4' and resid 21 through 24 removed outlier: 6.601A pdb=" N PHEA4 21 " --> pdb=" O ILEA4 46 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILEA4 46 " --> pdb=" O PHEA4 21 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HISA4 23 " --> pdb=" O HISA4 44 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLYA4 38 " --> pdb=" O ILEA4 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A4' and resid 96 through 97 removed outlier: 8.186A pdb=" N VALA4 97 " --> pdb=" O VALA4 72 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHEA4 74 " --> pdb=" O VALA4 97 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILEA4 166 " --> pdb=" O ILEA4 189 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILEA4 191 " --> pdb=" O ILEA4 166 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VALA4 168 " --> pdb=" O ILEA4 191 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VALA4 188 " --> pdb=" O TYRA4 203 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILEA4 205 " --> pdb=" O VALA4 188 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLYA4 190 " --> pdb=" O ILEA4 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E5' and resid 17 through 29 removed outlier: 4.940A pdb=" N GLUE5 18 " --> pdb=" O GLYE5 45 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLYE5 45 " --> pdb=" O GLUE5 18 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEUE5 20 " --> pdb=" O VALE5 43 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VALE5 43 " --> pdb=" O LEUE5 20 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E5' and resid 90 through 94 removed outlier: 3.596A pdb=" N SERE5 97 " --> pdb=" O HISE5 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L6' and resid 29 through 40 removed outlier: 5.769A pdb=" N CYSL6 34 " --> pdb=" O ARGL6 56 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARGL6 56 " --> pdb=" O CYSL6 34 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYSL6 51 " --> pdb=" O ILEL6 67 " (cutoff:3.500A) removed outlier: 10.222A pdb=" N TYRL6 95 " --> pdb=" O GLUL6 62 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SERL6 64 " --> pdb=" O TYRL6 95 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THRL6 97 " --> pdb=" O SERL6 64 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYRL6 66 " --> pdb=" O THRL6 97 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEUL6 81 " --> pdb=" O VALL6 98 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SERL6 78 " --> pdb=" O CYSL6 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F7' and resid 66 through 69 Processing sheet with id=AB7, first strand: chain 'E9' and resid 2 through 4 Processing sheet with id=AB8, first strand: chain 'E9' and resid 117 through 120 Processing sheet with id=AB9, first strand: chain 'aA' and resid 27 through 29 Processing sheet with id=AC1, first strand: chain 'MB' and resid 33 through 37 removed outlier: 5.233A pdb=" N METMB 110 " --> pdb=" O CYSMB 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'UC' and resid 7 through 12 removed outlier: 7.919A pdb=" N ASNUC 9 " --> pdb=" O LYSUC 49 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYSUC 49 " --> pdb=" O ASNUC 9 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N LEUUC 31 " --> pdb=" O METUC 93 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ALAUC 95 " --> pdb=" O LEUUC 31 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N PHEUC 97 " --> pdb=" O PROUC 33 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILEUC 35 " --> pdb=" O PHEUC 97 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ARGUC 99 " --> pdb=" O ILEUC 35 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYRUC 37 " --> pdb=" O ARGUC 99 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARGUC 85 " --> pdb=" O PROUC 92 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HISUC 94 " --> pdb=" O LEUUC 83 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEUUC 83 " --> pdb=" O HISUC 94 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASPUC 96 " --> pdb=" O LYSUC 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'WD' and resid 13 through 18 Processing sheet with id=AC4, first strand: chain 'WD' and resid 33 through 40 Processing sheet with id=AC5, first strand: chain 'RF' and resid 2 through 10 removed outlier: 5.429A pdb=" N CYSRF 101 " --> pdb=" O GLYRF 9 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLYRF 108 " --> pdb=" O VALRF 71 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VALRF 71 " --> pdb=" O GLYRF 108 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'RF' and resid 82 through 87 Processing sheet with id=AC7, first strand: chain 'FG' and resid 35 through 51 removed outlier: 5.585A pdb=" N ILEFG 36 " --> pdb=" O GLUFG 65 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLUFG 65 " --> pdb=" O ILEFG 36 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYRFG 59 " --> pdb=" O TRPFG 42 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARGFG 44 " --> pdb=" O ALAFG 57 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALAFG 57 " --> pdb=" O ARGFG 44 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLNFG 46 " --> pdb=" O HISFG 55 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N HISFG 55 " --> pdb=" O GLNFG 46 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HISFG 3 " --> pdb=" O ARGFG 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'VH' and resid 22 through 23 removed outlier: 6.605A pdb=" N LEUVH 59 " --> pdb=" O ILEVH 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'VH' and resid 30 through 31 Processing sheet with id=AD1, first strand: chain 'TI' and resid 63 through 64 removed outlier: 6.771A pdb=" N ARGTI 31 " --> pdb=" O VALTI 27 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VALTI 27 " --> pdb=" O ARGTI 31 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYSTI 33 " --> pdb=" O GLNTI 25 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THRTI 9 " --> pdb=" O LEUTI 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILETI 70 " --> pdb=" O ASPTI 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'TI' and resid 39 through 44 Processing sheet with id=AD3, first strand: chain 'TI' and resid 81 through 86 Processing sheet with id=AD4, first strand: chain 'fJ' and resid 21 through 27 removed outlier: 7.559A pdb=" N ASPfJ 11 " --> pdb=" O PROfJ 43 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYRfJ 45 " --> pdb=" O ASPfJ 11 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEUfJ 13 " --> pdb=" O TYRfJ 45 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEUfJ 47 " --> pdb=" O LEUfJ 13 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N HISfJ 15 " --> pdb=" O LEUfJ 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'HK' and resid 97 through 98 removed outlier: 5.608A pdb=" N LYSJY 71 " --> pdb=" O PROJY 43 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N METJY 73 " --> pdb=" O PROJY 41 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N ASPJY 75 " --> pdb=" O PROJY 39 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VALJY 77 " --> pdb=" O CYSJY 37 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N CYSJY 37 " --> pdb=" O VALJY 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'HK' and resid 97 through 98 Processing sheet with id=AD7, first strand: chain 'SP' and resid 31 through 33 removed outlier: 6.642A pdb=" N ILESP 31 " --> pdb=" O SERSP 50 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HISSP 52 " --> pdb=" O ILESP 31 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THRSP 33 " --> pdb=" O HISSP 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'BQ' and resid 24 through 28 removed outlier: 3.824A pdb=" N LYSBQ 58 " --> pdb=" O GLUBQ 54 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SERBQ 48 " --> pdb=" O GLUBQ 64 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'BQ' and resid 67 through 68 Processing sheet with id=AE1, first strand: chain 'BQ' and resid 76 through 79 Processing sheet with id=AE2, first strand: chain 'BQ' and resid 76 through 79 removed outlier: 5.612A pdb=" N VALBQ 127 " --> pdb=" O SERBQ 107 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SERBQ 107 " --> pdb=" O VALBQ 127 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALABQ 129 " --> pdb=" O ILEBQ 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'GR' and resid 9 through 10 Processing sheet with id=AE4, first strand: chain 'GR' and resid 16 through 19 Processing sheet with id=AE5, first strand: chain 'GR' and resid 121 through 124 Processing sheet with id=AE6, first strand: chain 'GR' and resid 95 through 99 removed outlier: 3.502A pdb=" N LYSGR 102 " --> pdb=" O THRGR 99 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'GS' and resid 74 through 81 Processing sheet with id=AE8, first strand: chain 'CT' and resid 56 through 58 removed outlier: 3.799A pdb=" N GLUCT 58 " --> pdb=" O LYSCT 65 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALACT 64 " --> pdb=" O GLNCT 100 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ASNCT 102 " --> pdb=" O ALACT 64 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILECT 66 " --> pdb=" O ASNCT 102 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLUCT 104 " --> pdb=" O ILECT 66 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILECT 68 " --> pdb=" O GLUCT 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'CT' and resid 164 through 171 Processing sheet with id=AF1, first strand: chain 'KU' and resid 41 through 46 removed outlier: 6.724A pdb=" N ILEKU 34 " --> pdb=" O LEUKU 42 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRPKU 44 " --> pdb=" O VALKU 32 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VALKU 32 " --> pdb=" O TRPKU 44 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLYKU 19 " --> pdb=" O ASPKU 83 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEUKU 85 " --> pdb=" O GLYKU 19 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALAKU 21 " --> pdb=" O LEUKU 85 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILEKU 82 " --> pdb=" O ASNKU 108 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILEKU 110 " --> pdb=" O ILEKU 82 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VALKU 84 " --> pdb=" O ILEKU 110 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ASPKU 112 " --> pdb=" O VALKU 84 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VALKU 86 " --> pdb=" O ASPKU 112 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'YW' and resid 34 through 38 Processing sheet with id=AF3, first strand: chain 'IX' and resid 122 through 124 removed outlier: 6.359A pdb=" N ILEIX 54 " --> pdb=" O LYSIX 123 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TRPIX 15 " --> pdb=" O LYSIX 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'IX' and resid 73 through 77 Processing sheet with id=AF5, first strand: chain 'QZ' and resid 13 through 23 removed outlier: 16.747A pdb=" N VALQZ 13 " --> pdb=" O LEUQZ 34 " (cutoff:3.500A) removed outlier: 13.097A pdb=" N LEUQZ 34 " --> pdb=" O VALQZ 13 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THRQZ 15 " --> pdb=" O GLUQZ 32 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLUQZ 32 " --> pdb=" O THRQZ 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARGQZ 17 " --> pdb=" O LEUQZ 30 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THRQZ 28 " --> pdb=" O VALQZ 19 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASPQZ 21 " --> pdb=" O SERQZ 26 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SERQZ 26 " --> pdb=" O ASPQZ 21 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N LYSQZ 77 " --> pdb=" O LYSQZ 49 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LYSQZ 51 " --> pdb=" O LYSQZ 77 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TRPQZ 79 " --> pdb=" O LYSQZ 51 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEUQZ 81 " --> pdb=" O LYSQZ 68 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYSQZ 68 " --> pdb=" O LEUQZ 81 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEUQZ 64 " --> pdb=" O VALQZ 85 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Qb' and resid 10 through 15 removed outlier: 3.844A pdb=" N METQb 40 " --> pdb=" O VALQb 4 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Qb' and resid 19 through 23 removed outlier: 6.760A pdb=" N TYRQb 93 " --> pdb=" O HISQb 66 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HISQb 66 " --> pdb=" O TYRQb 93 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEUQb 95 " --> pdb=" O ILEQb 64 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLUQb 60 " --> pdb=" O LYSQb 99 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILEQb 101 " --> pdb=" O SERQb 58 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SERQb 58 " --> pdb=" O ILEQb 101 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Qb' and resid 72 through 78 removed outlier: 4.124A pdb=" N TYRQb 83 " --> pdb=" O ASNQb 78 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Nc' and resid 48 through 53 removed outlier: 3.808A pdb=" N ALANc 50 " --> pdb=" O ILENc 40 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEUNc 27 " --> pdb=" O ASPNc 92 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Kd' and resid 76 through 80 Processing sheet with id=AG2, first strand: chain 'Kd' and resid 91 through 92 Processing sheet with id=AG3, first strand: chain 'Je' and resid 7 through 10 removed outlier: 6.500A pdb=" N ARGJe 17 " --> pdb=" O VALJe 10 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLUJe 45 " --> pdb=" O ARGJe 17 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VALJe 19 " --> pdb=" O VALJe 43 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VALJe 43 " --> pdb=" O VALJe 19 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYSJe 21 " --> pdb=" O VALJe 41 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALJe 41 " --> pdb=" O CYSJe 21 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYSJe 23 " --> pdb=" O ILEJe 39 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILEJe 39 " --> pdb=" O LYSJe 23 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASNJe 59 " --> pdb=" O LEUJe 87 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALAJe 83 " --> pdb=" O VALJe 63 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALAJe 84 " --> pdb=" O METJe 7 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLUJe 9 " --> pdb=" O ALAJe 84 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEUJe 86 " --> pdb=" O GLUJe 9 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Je' and resid 69 through 70 removed outlier: 3.791A pdb=" N VALJe 76 " --> pdb=" O ALAOi 75 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALAOi 60 " --> pdb=" O LYSOi 52 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYSOi 52 " --> pdb=" O ALAOi 60 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THROi 62 " --> pdb=" O ILEOi 50 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILEOi 66 " --> pdb=" O GLUOi 46 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLUOi 46 " --> pdb=" O ILEOi 66 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THROi 27 " --> pdb=" O LYSOi 89 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SEROi 85 " --> pdb=" O GLNOi 31 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYSOi 33 " --> pdb=" O ILEOi 83 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILEOi 83 " --> pdb=" O LYSOi 33 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Af' and resid 5 through 16 removed outlier: 6.186A pdb=" N VALAf 27 " --> pdb=" O CYSAf 10 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N METAf 12 " --> pdb=" O VALAf 25 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VALAf 25 " --> pdb=" O METAf 12 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARGAf 14 " --> pdb=" O ILEAf 23 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILEAf 23 " --> pdb=" O ARGAf 14 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYSAf 193 " --> pdb=" O VALAf 180 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VALAf 180 " --> pdb=" O LYSAf 193 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THRAf 174 " --> pdb=" O GLYAf 114 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLYAf 114 " --> pdb=" O THRAf 174 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLNAf 176 " --> pdb=" O VALAf 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VALAf 112 " --> pdb=" O GLNAf 176 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASNAf 115 " --> pdb=" O ASPAf 203 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASPAf 203 " --> pdb=" O ASNAf 115 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Af' and resid 79 through 84 removed outlier: 3.890A pdb=" N GLYAf 79 " --> pdb=" O THRAf 53 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THRAf 53 " --> pdb=" O GLYAf 79 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THRAf 52 " --> pdb=" O ILEAf 35 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILEAf 35 " --> pdb=" O THRAf 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Af' and resid 118 through 122 removed outlier: 5.560A pdb=" N METAf 168 " --> pdb=" O LYSAf 119 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHEAf 121 " --> pdb=" O GLYAf 166 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLYAf 166 " --> pdb=" O PHEAf 121 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Lg' and resid 63 through 66 removed outlier: 6.833A pdb=" N LEULg 34 " --> pdb=" O LEULg 103 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLULg 105 " --> pdb=" O PHELg 32 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHELg 32 " --> pdb=" O GLULg 105 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Lg' and resid 40 through 43 Processing sheet with id=AH1, first strand: chain 'dh' and resid 16 through 17 Processing sheet with id=AH2, first strand: chain 'Oi' and resid 92 through 93 removed outlier: 4.327A pdb=" N ARGOi 113 " --> pdb=" O ALAOi 93 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Pj' and resid 50 through 52 removed outlier: 6.395A pdb=" N VALPj 19 " --> pdb=" O ILEPj 36 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHEPj 38 " --> pdb=" O TYRPj 17 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYRPj 17 " --> pdb=" O PHEPj 38 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VALPj 2 " --> pdb=" O GLNPj 66 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'bk' and resid 16 through 21 Processing sheet with id=AH5, first strand: chain 'Cl' and resid 3 through 5 Processing sheet with id=AH6, first strand: chain 'Cl' and resid 34 through 35 Processing sheet with id=AH7, first strand: chain 'Cl' and resid 101 through 105 removed outlier: 3.781A pdb=" N ARGCl 80 " --> pdb=" O LEUCl 93 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYSCl 95 " --> pdb=" O VALCl 78 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VALCl 78 " --> pdb=" O LYSCl 95 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Cl' and resid 129 through 131 removed outlier: 5.752A pdb=" N LEUCl 164 " --> pdb=" O ARGCl 175 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARGCl 175 " --> pdb=" O LEUCl 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLYCl 166 " --> pdb=" O ILECl 173 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARGCl 183 " --> pdb=" O ILECl 267 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILECl 267 " --> pdb=" O ARGCl 183 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Cl' and resid 144 through 145 removed outlier: 6.141A pdb=" N ILECl 144 " --> pdb=" O GLNCl 153 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Dm' and resid 135 through 136 removed outlier: 3.769A pdb=" N ASPDm 148 " --> pdb=" O PHEDm 189 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Sn' and resid 10 through 13 removed outlier: 4.055A pdb=" N LYSSn 81 " --> pdb=" O ILESn 33 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Sn' and resid 69 through 70 Processing sheet with id=AI4, first strand: chain 'ep' and resid 2 through 4 removed outlier: 6.234A pdb=" N LYSep 2 " --> pdb=" O ARGep 36 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VALep 23 " --> pdb=" O GLNep 37 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C1' and resid 18 through 20 2103 hydrogen bonds defined for protein. 5889 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3681 hydrogen bonds 5714 hydrogen bond angles 0 basepair planarities 1476 basepair parallelities 2366 stacking parallelities Total time for adding SS restraints: 213.98 Time building geometry restraints manager: 64.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16497 1.32 - 1.44: 65152 1.44 - 1.57: 63248 1.57 - 1.69: 8804 1.69 - 1.81: 321 Bond restraints: 154022 Sorted by residual: bond pdb=" CB ARGPO 55 " pdb=" CG ARGPO 55 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.30e+00 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.87e+00 bond pdb=" CB ARGE9 48 " pdb=" CG ARGE9 48 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.39e+00 bond pdb=" CG1 ILEL6 82 " pdb=" CD1 ILEL6 82 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.04e+00 bond pdb=" CA PRO B 99 " pdb=" CB PRO B 99 " ideal model delta sigma weight residual 1.533 1.561 -0.028 1.26e-02 6.30e+03 4.90e+00 ... (remaining 154017 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.93: 20137 104.93 - 112.72: 90940 112.72 - 120.52: 65444 120.52 - 128.32: 46463 128.32 - 136.11: 6704 Bond angle restraints: 229688 Sorted by residual: angle pdb=" CA PRO B 99 " pdb=" N PRO B 99 " pdb=" CD PRO B 99 " ideal model delta sigma weight residual 112.00 101.18 10.82 1.40e+00 5.10e-01 5.98e+01 angle pdb=" O4' GZ2 495 " pdb=" C1' GZ2 495 " pdb=" N9 GZ2 495 " ideal model delta sigma weight residual 108.20 114.58 -6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" N HISVH 3 " pdb=" CA HISVH 3 " pdb=" C HISVH 3 " ideal model delta sigma weight residual 111.11 116.19 -5.08 1.20e+00 6.94e-01 1.79e+01 angle pdb=" C ALATo 54 " pdb=" N ILETo 55 " pdb=" CA ILETo 55 " ideal model delta sigma weight residual 120.33 123.66 -3.33 8.00e-01 1.56e+00 1.74e+01 angle pdb=" C GLUOi 18 " pdb=" N ARGOi 19 " pdb=" CA ARGOi 19 " ideal model delta sigma weight residual 123.11 115.68 7.43 1.79e+00 3.12e-01 1.72e+01 ... (remaining 229683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 85981 35.96 - 71.92: 11178 71.92 - 107.88: 1040 107.88 - 143.84: 18 143.84 - 179.80: 20 Dihedral angle restraints: 98237 sinusoidal: 80860 harmonic: 17377 Sorted by residual: dihedral pdb=" O4' CZ2 702 " pdb=" C1' CZ2 702 " pdb=" N1 CZ2 702 " pdb=" C2 CZ2 702 " ideal model delta sinusoidal sigma weight residual 200.00 20.29 179.71 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 17.01 -177.01 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UZ21208 " pdb=" C1' UZ21208 " pdb=" N1 UZ21208 " pdb=" C2 UZ21208 " ideal model delta sinusoidal sigma weight residual 200.00 25.62 174.38 1 1.50e+01 4.44e-03 8.51e+01 ... (remaining 98234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 24886 0.059 - 0.117: 3884 0.117 - 0.176: 453 0.176 - 0.234: 74 0.234 - 0.293: 15 Chirality restraints: 29312 Sorted by residual: chirality pdb=" C1' AZ2 712 " pdb=" O4' AZ2 712 " pdb=" C2' AZ2 712 " pdb=" N9 AZ2 712 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB THRbk 18 " pdb=" CA THRbk 18 " pdb=" OG1 THRbk 18 " pdb=" CG2 THRbk 18 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB VALPO 31 " pdb=" CA VALPO 31 " pdb=" CG1 VALPO 31 " pdb=" CG2 VALPO 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 29309 not shown) Planarity restraints: 12786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GZ2 495 " 0.063 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" N9 GZ2 495 " -0.054 2.00e-02 2.50e+03 pdb=" C8 GZ2 495 " -0.006 2.00e-02 2.50e+03 pdb=" N7 GZ2 495 " -0.004 2.00e-02 2.50e+03 pdb=" C5 GZ2 495 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GZ2 495 " 0.014 2.00e-02 2.50e+03 pdb=" O6 GZ2 495 " 0.011 2.00e-02 2.50e+03 pdb=" N1 GZ2 495 " 0.014 2.00e-02 2.50e+03 pdb=" C2 GZ2 495 " -0.003 2.00e-02 2.50e+03 pdb=" N2 GZ2 495 " -0.004 2.00e-02 2.50e+03 pdb=" N3 GZ2 495 " -0.019 2.00e-02 2.50e+03 pdb=" C4 GZ2 495 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEURF 7 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C LEURF 7 " 0.075 2.00e-02 2.50e+03 pdb=" O LEURF 7 " -0.028 2.00e-02 2.50e+03 pdb=" N ARGRF 8 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GZ2 34 " -0.059 2.00e-02 2.50e+03 2.43e-02 1.77e+01 pdb=" N9 GZ2 34 " 0.052 2.00e-02 2.50e+03 pdb=" C8 GZ2 34 " 0.006 2.00e-02 2.50e+03 pdb=" N7 GZ2 34 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GZ2 34 " 0.003 2.00e-02 2.50e+03 pdb=" C6 GZ2 34 " -0.009 2.00e-02 2.50e+03 pdb=" O6 GZ2 34 " -0.017 2.00e-02 2.50e+03 pdb=" N1 GZ2 34 " -0.006 2.00e-02 2.50e+03 pdb=" C2 GZ2 34 " 0.005 2.00e-02 2.50e+03 pdb=" N2 GZ2 34 " -0.002 2.00e-02 2.50e+03 pdb=" N3 GZ2 34 " 0.011 2.00e-02 2.50e+03 pdb=" C4 GZ2 34 " 0.017 2.00e-02 2.50e+03 ... (remaining 12783 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 763 2.54 - 3.13: 98852 3.13 - 3.72: 285279 3.72 - 4.31: 414712 4.31 - 4.90: 543594 Nonbonded interactions: 1343200 Sorted by model distance: nonbonded pdb=" O2' UZ2 671 " pdb=" O PHEBa 5 " model vdw 1.944 2.440 nonbonded pdb=" O2' UZ22618 " pdb=" OE1 GLUAf 82 " model vdw 2.063 2.440 nonbonded pdb=" O ILEE5 111 " pdb=" OG1 THRE5 130 " model vdw 2.089 2.440 nonbonded pdb=" O2' GZ2 562 " pdb=" OP1 AZ21238 " model vdw 2.116 2.440 nonbonded pdb=" N7 AZ2 281 " pdb=" N2 GZ2 331 " model vdw 2.118 2.600 ... (remaining 1343195 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: 9.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 35.170 Check model and map are aligned: 1.600 Set scattering table: 1.000 Process input model: 481.800 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 545.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 154022 Z= 0.391 Angle : 0.695 15.811 229688 Z= 0.366 Chirality : 0.043 0.293 29312 Planarity : 0.006 0.135 12786 Dihedral : 23.309 179.802 87057 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 4.14 % Allowed : 21.69 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.80 (0.10), residues: 5994 helix: 0.39 (0.11), residues: 1991 sheet: -0.54 (0.14), residues: 1213 loop : -1.14 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPCl 248 HIS 0.014 0.002 HISYW 14 PHE 0.023 0.002 PHEAf 121 TYR 0.019 0.002 TYRL6 117 ARG 0.025 0.001 ARGL6 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 731 time to evaluate : 6.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8422 (m) REVERT: B 355 GLU cc_start: 0.7191 (pm20) cc_final: 0.6859 (pt0) REVERT: H 269 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6401 (t0) REVERT: PO 13 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7404 (mtp85) REVERT: IX 90 THR cc_start: 0.8958 (t) cc_final: 0.8665 (m) REVERT: Je 45 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: Af 29 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: dh 17 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7553 (tpt-90) REVERT: Cl 259 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6682 (m-70) outliers start: 207 outliers final: 156 residues processed: 907 average time/residue: 2.1267 time to fit residues: 2746.0783 Evaluate side-chains 850 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 688 time to evaluate : 6.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 86 VAL 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 151 ASN Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 235 GLU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 293 GLN Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 316 LYS Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain E5 residue 70 GLU Chi-restraints excluded: chain E5 residue 91 LYS Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 59 SER Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 123 LYS Chi-restraints excluded: chain F7 residue 5 LYS Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 19 GLU Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 47 LYS Chi-restraints excluded: chain F7 residue 49 LEU Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 64 LYS Chi-restraints excluded: chain F7 residue 66 VAL Chi-restraints excluded: chain F7 residue 74 ILE Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 100 LEU Chi-restraints excluded: chain F7 residue 103 LEU Chi-restraints excluded: chain F7 residue 120 LYS Chi-restraints excluded: chain F7 residue 130 LEU Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 137 VAL Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain F7 residue 159 SER Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 13 SER Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 70 LYS Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain VH residue 9 SER Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain TI residue 56 ILE Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 28 THR Chi-restraints excluded: chain fJ residue 29 VAL Chi-restraints excluded: chain fJ residue 33 THR Chi-restraints excluded: chain fJ residue 53 SER Chi-restraints excluded: chain fJ residue 76 ARG Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain MM residue 7 VAL Chi-restraints excluded: chain MM residue 18 SER Chi-restraints excluded: chain MM residue 29 THR Chi-restraints excluded: chain MM residue 45 VAL Chi-restraints excluded: chain MM residue 46 SER Chi-restraints excluded: chain MM residue 47 GLN Chi-restraints excluded: chain MM residue 48 LEU Chi-restraints excluded: chain MM residue 53 LEU Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 72 GLU Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain MM residue 89 ILE Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain SP residue 4 SER Chi-restraints excluded: chain SP residue 6 LYS Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 25 THR Chi-restraints excluded: chain SP residue 28 ARG Chi-restraints excluded: chain SP residue 37 ARG Chi-restraints excluded: chain SP residue 38 SER Chi-restraints excluded: chain SP residue 41 LEU Chi-restraints excluded: chain SP residue 43 GLN Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 35 SER Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GR residue 155 GLU Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 57 ILE Chi-restraints excluded: chain CT residue 59 ARG Chi-restraints excluded: chain CT residue 70 THR Chi-restraints excluded: chain CT residue 75 ILE Chi-restraints excluded: chain CT residue 76 VAL Chi-restraints excluded: chain CT residue 92 THR Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 107 THR Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 122 SER Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 149 ILE Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 34 ILE Chi-restraints excluded: chain NV residue 7 LYS Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain QZ residue 20 SER Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain dh residue 17 ARG Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain bk residue 18 THR Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Cl residue 259 HIS Chi-restraints excluded: chain Dm residue 135 VAL Chi-restraints excluded: chain Dm residue 183 SER Chi-restraints excluded: chain Dm residue 188 THR Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 866 optimal weight: 40.0000 chunk 777 optimal weight: 4.9990 chunk 431 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 524 optimal weight: 20.0000 chunk 415 optimal weight: 10.0000 chunk 804 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 488 optimal weight: 10.0000 chunk 598 optimal weight: 30.0000 chunk 931 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN H 293 GLN F7 9 ASN ** F7 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN ** F7 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E9 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E9 194 GLN UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 59 GLN HK 62 ASN BQ 18 GLN GR 88 GLN GR 106 ASN ** GS 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JY 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Nc 66 ASN Je 29 HIS Oi 3 ASN Oi 15 GLN Oi 54 ASN Pj 66 GLN Cl 153 GLN Cl 187 ASN Dm 117 GLN ** Dm 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Sn 2 ASN To 3 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 154022 Z= 0.459 Angle : 0.728 11.992 229688 Z= 0.374 Chirality : 0.046 0.306 29312 Planarity : 0.006 0.101 12786 Dihedral : 23.272 179.886 75475 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.88 % Rotamer: Outliers : 6.58 % Allowed : 20.09 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.58 (0.10), residues: 5994 helix: 0.60 (0.11), residues: 1989 sheet: -0.43 (0.14), residues: 1207 loop : -1.03 (0.11), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPCl 248 HIS 0.013 0.002 HISYW 14 PHE 0.021 0.002 PHEAf 121 TYR 0.021 0.002 TYRL6 117 ARG 0.011 0.001 ARGA4 12 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 693 time to evaluate : 6.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 2 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5173 (mtpt) REVERT: F 11 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7780 (ptmt) REVERT: F 110 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: H 250 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7933 (mm) REVERT: H 364 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: A4 35 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7333 (p90) REVERT: A4 153 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7855 (mt) REVERT: L6 56 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7776 (ttp80) REVERT: E9 136 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7706 (tptm) REVERT: E9 173 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6638 (pt0) REVERT: RF 95 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6230 (tpm170) REVERT: VH 72 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7879 (pttm) REVERT: TI 25 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: TI 84 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: OL 58 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8207 (ptp) REVERT: MM 87 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7104 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7395 (mtp85) REVERT: SP 43 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: BQ 78 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: CT 55 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8590 (tp) REVERT: NV 49 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7658 (tmtm) REVERT: IX 31 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7285 (mm-40) REVERT: IX 90 THR cc_start: 0.8965 (t) cc_final: 0.8688 (m) REVERT: Nc 20 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7889 (tpp-160) REVERT: Je 64 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8609 (ptt-90) REVERT: dh 17 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8275 (tpt170) REVERT: Cl 5 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8393 (mmmm) REVERT: Dm 143 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: Sn 20 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7350 (tm-30) outliers start: 329 outliers final: 165 residues processed: 921 average time/residue: 2.1150 time to fit residues: 2799.8128 Evaluate side-chains 869 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 678 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET 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 151 ASN Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 11 LYS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 235 GLU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 293 GLN Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 51 LYS Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 56 ARG Chi-restraints excluded: chain L6 residue 64 SER Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 47 LYS Chi-restraints excluded: chain F7 residue 49 LEU Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 108 ILE Chi-restraints excluded: chain F7 residue 130 LEU Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 16 THR Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain E9 residue 173 GLU Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 89 ASN Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 2 GLU Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain VH residue 9 SER Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 5 ARG Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 37 ILE Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 84 GLN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 28 THR Chi-restraints excluded: chain fJ residue 29 VAL Chi-restraints excluded: chain fJ residue 33 THR Chi-restraints excluded: chain fJ residue 72 SER Chi-restraints excluded: chain HK residue 6 MET Chi-restraints excluded: chain HK residue 58 VAL Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain MM residue 7 VAL Chi-restraints excluded: chain MM residue 18 SER Chi-restraints excluded: chain MM residue 29 THR Chi-restraints excluded: chain MM residue 45 VAL Chi-restraints excluded: chain MM residue 47 GLN Chi-restraints excluded: chain MM residue 53 LEU Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain MM residue 89 ILE Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 77 SER Chi-restraints excluded: chain PO residue 87 ASN Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 41 LEU Chi-restraints excluded: chain SP residue 43 GLN Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 32 TYR Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 56 MET Chi-restraints excluded: chain CT residue 76 VAL Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 151 VAL Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 26 SER Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 35 THR Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 1 MET Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 52 VAL Chi-restraints excluded: chain Je residue 58 MET Chi-restraints excluded: chain Je residue 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 60 ARG Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 64 ILE Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 17 ARG Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 85 SER Chi-restraints excluded: chain Oi residue 87 GLU Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain Cl residue 5 LYS Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Cl residue 259 HIS Chi-restraints excluded: chain Dm residue 143 GLN Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain C1 residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 517 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 775 optimal weight: 6.9990 chunk 634 optimal weight: 30.0000 chunk 257 optimal weight: 5.9990 chunk 933 optimal weight: 10.0000 chunk 1008 optimal weight: 10.0000 chunk 831 optimal weight: 3.9990 chunk 925 optimal weight: 10.0000 chunk 318 optimal weight: 6.9990 chunk 748 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN H 293 GLN ** F7 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN ** F7 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UC 77 GLN XE 22 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN VH 46 HIS TI 59 GLN HK 62 ASN BQ 18 GLN GR 88 GLN GR 106 ASN GS 29 HIS GS 149 ASN CT 3 GLN JY 58 ASN JY 78 GLN Nc 66 ASN Je 29 HIS Pj 66 GLN Cl 134 ASN Cl 187 ASN Dm 117 GLN ** Dm 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 171 GLN To 3 ASN ep 33 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 154022 Z= 0.315 Angle : 0.626 9.865 229688 Z= 0.327 Chirality : 0.040 0.281 29312 Planarity : 0.005 0.082 12786 Dihedral : 23.150 179.983 75341 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 6.24 % Allowed : 20.85 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.33 (0.10), residues: 5994 helix: 0.84 (0.11), residues: 1990 sheet: -0.31 (0.14), residues: 1217 loop : -0.90 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPCl 248 HIS 0.009 0.001 HISYW 14 PHE 0.018 0.002 PHEFG 62 TYR 0.016 0.002 TYRL6 117 ARG 0.006 0.001 ARGQZ 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 697 time to evaluate : 6.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8485 (m) REVERT: B 352 MET cc_start: 0.8348 (mmm) cc_final: 0.7891 (mmm) REVERT: F 11 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7553 (ptmt) REVERT: H 250 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.7888 (mm) REVERT: H 255 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7368 (mtmt) REVERT: H 364 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7107 (tt0) REVERT: A4 35 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7608 (p90) REVERT: A4 153 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7824 (mt) REVERT: L6 56 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: E9 136 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7689 (tptm) REVERT: E9 144 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7565 (ptp-170) REVERT: UC 55 LYS cc_start: 0.8816 (tptp) cc_final: 0.8615 (tptp) REVERT: UC 58 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: RF 95 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6074 (tpm170) REVERT: VH 72 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7884 (pttm) REVERT: TI 25 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: TI 84 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: MM 87 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7060 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7385 (mtp85) REVERT: BQ 78 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: CT 55 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8591 (tp) REVERT: NV 14 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7605 (mp) REVERT: NV 49 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7771 (tmtm) REVERT: IX 31 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7386 (mm-40) REVERT: IX 90 THR cc_start: 0.8939 (t) cc_final: 0.8674 (m) REVERT: IX 98 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: Nc 115 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6858 (pp20) REVERT: Je 64 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8600 (ptt-90) REVERT: Lg 52 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7784 (mtp180) REVERT: Lg 102 MET cc_start: 0.7792 (mmm) cc_final: 0.7364 (mmm) REVERT: dh 17 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8155 (tpt170) REVERT: Oi 115 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7915 (tptp) REVERT: bk 41 GLN cc_start: 0.8296 (mt0) cc_final: 0.8068 (mm110) REVERT: Cl 18 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7692 (ptmt) REVERT: Dm 34 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.5594 (mttt) REVERT: Dm 143 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: Sn 20 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: C1 1 MET cc_start: 0.7180 (ttt) cc_final: 0.6929 (ttt) outliers start: 312 outliers final: 158 residues processed: 908 average time/residue: 2.1522 time to fit residues: 2787.1593 Evaluate side-chains 863 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 674 time to evaluate : 6.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET 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 151 ASN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 11 LYS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 235 GLU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 255 LYS Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 293 GLN Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain L6 residue 8 ILE Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 56 ARG Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 108 ILE Chi-restraints excluded: chain F7 residue 130 LEU Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 16 THR Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 58 GLU Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 65 ASP Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 9 SER Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 5 ARG Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 56 ILE Chi-restraints excluded: chain TI residue 84 GLN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 28 THR Chi-restraints excluded: chain fJ residue 33 THR Chi-restraints excluded: chain HK residue 6 MET Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain MM residue 18 SER Chi-restraints excluded: chain MM residue 45 VAL Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain MM residue 89 ILE Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 38 SER Chi-restraints excluded: chain SP residue 67 VAL Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 76 VAL Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 34 ILE Chi-restraints excluded: chain KU residue 35 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 1 MET Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 98 GLU Chi-restraints excluded: chain QZ residue 26 SER Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Kd residue 118 VAL Chi-restraints excluded: chain Je residue 45 GLU Chi-restraints excluded: chain Je residue 47 ILE Chi-restraints excluded: chain Je residue 52 VAL Chi-restraints excluded: chain Je residue 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Je residue 103 THR Chi-restraints excluded: chain Je residue 110 GLN Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 60 ARG Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Lg residue 26 THR Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 64 ILE Chi-restraints excluded: chain Lg residue 76 ASN Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 17 ARG Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 87 GLU Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Cl residue 259 HIS Chi-restraints excluded: chain Dm residue 34 LYS Chi-restraints excluded: chain Dm residue 106 MET Chi-restraints excluded: chain Dm residue 143 GLN Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 39 ILE Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain C1 residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 922 optimal weight: 20.0000 chunk 701 optimal weight: 0.4980 chunk 484 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 445 optimal weight: 3.9990 chunk 626 optimal weight: 0.0470 chunk 936 optimal weight: 10.0000 chunk 991 optimal weight: 10.0000 chunk 489 optimal weight: 4.9990 chunk 887 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 overall best weight: 3.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN H 293 GLN A4 88 GLN ** F7 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F7 24 ASN ** F7 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 59 GLN HK 62 ASN MM 47 GLN BQ 18 GLN GR 106 ASN GS 149 ASN CT 3 GLN Nc 66 ASN Je 29 HIS Pj 66 GLN Cl 134 ASN Cl 187 ASN Dm 117 GLN ** Dm 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dm 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 171 GLN Sn 59 ASN To 3 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 154022 Z= 0.252 Angle : 0.580 13.583 229688 Z= 0.306 Chirality : 0.038 0.269 29312 Planarity : 0.005 0.063 12786 Dihedral : 23.077 179.607 75299 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 5.70 % Allowed : 21.79 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.12 (0.11), residues: 5994 helix: 1.04 (0.12), residues: 1993 sheet: -0.21 (0.14), residues: 1194 loop : -0.79 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCl 248 HIS 0.008 0.001 HISYW 14 PHE 0.018 0.001 PHEFG 62 TYR 0.013 0.001 TYRL6 117 ARG 0.007 0.000 ARGQZ 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 693 time to evaluate : 6.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6420 (tpp) REVERT: F 11 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7437 (ptmt) REVERT: H 250 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7840 (mm) REVERT: H 262 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: H 287 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: H 364 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: A4 35 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7652 (p90) REVERT: A4 153 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7831 (mt) REVERT: L6 56 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7750 (ttp80) REVERT: E9 136 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7681 (tptm) REVERT: E9 144 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7545 (ptp-170) REVERT: UC 58 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: RF 95 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6064 (tpm170) REVERT: VH 11 ARG cc_start: 0.6126 (OUTLIER) cc_final: 0.5842 (tmm160) REVERT: VH 72 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7865 (pttm) REVERT: TI 25 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: TI 84 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: PO 13 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7382 (mtp85) REVERT: BQ 78 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: CT 55 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8578 (tp) REVERT: NV 14 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7593 (mp) REVERT: NV 49 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7725 (tmtm) REVERT: IX 90 THR cc_start: 0.8909 (t) cc_final: 0.8660 (m) REVERT: Nc 115 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6841 (pp20) REVERT: Je 64 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8587 (ptt-90) REVERT: Af 29 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: Lg 52 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7782 (mtp180) REVERT: Lg 111 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: dh 17 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8155 (tpt170) REVERT: Oi 115 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7892 (tptp) REVERT: bk 41 GLN cc_start: 0.8284 (mt0) cc_final: 0.8061 (mm110) REVERT: Cl 18 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7642 (ptmt) REVERT: Cl 110 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: Dm 34 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.5453 (mttt) REVERT: Dm 143 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: Sn 20 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: C1 5 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8366 (mm) outliers start: 283 outliers final: 165 residues processed: 879 average time/residue: 2.1864 time to fit residues: 2735.4138 Evaluate side-chains 871 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 672 time to evaluate : 6.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 11 LYS Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 235 GLU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 293 GLN Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 146 MET Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 8 ILE Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 56 ARG Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 11 GLU Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 100 LEU Chi-restraints excluded: chain F7 residue 108 ILE Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 16 THR Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 89 ASN Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 58 GLU Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 65 ASP Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 9 SER Chi-restraints excluded: chain VH residue 11 ARG Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 37 ILE Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 56 ILE Chi-restraints excluded: chain TI residue 84 GLN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 28 THR Chi-restraints excluded: chain fJ residue 33 THR Chi-restraints excluded: chain fJ residue 72 SER Chi-restraints excluded: chain HK residue 6 MET Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 40 ASN Chi-restraints excluded: chain OL residue 69 LEU Chi-restraints excluded: chain MM residue 45 VAL Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 89 ILE Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 112 LYS Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 32 TYR Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 56 MET Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 16 VAL Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 34 ILE Chi-restraints excluded: chain KU residue 35 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 1 MET Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain JY residue 77 VAL Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 61 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Kd residue 83 GLU Chi-restraints excluded: chain Kd residue 118 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 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Je residue 110 GLN Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 60 ARG Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 64 ILE Chi-restraints excluded: chain Lg residue 76 ASN Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 119 THR Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 17 ARG Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 87 GLU Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain bk residue 32 MET Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 36 SER Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Dm residue 34 LYS Chi-restraints excluded: chain Dm residue 143 GLN Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain C1 residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 825 optimal weight: 6.9990 chunk 562 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 738 optimal weight: 10.0000 chunk 409 optimal weight: 10.0000 chunk 846 optimal weight: 10.0000 chunk 685 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 506 optimal weight: 3.9990 chunk 890 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN A4 63 ASN F7 10 ASN F7 24 ASN F7 27 GLN ** F7 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aA 20 HIS UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 59 GLN HK 62 ASN OL 9 GLN BQ 18 GLN GR 106 ASN CT 3 GLN Nc 66 ASN Je 29 HIS Af 139 ASN Cl 134 ASN Cl 187 ASN Dm 117 GLN ** Dm 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 171 GLN Sn 59 ASN To 3 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 154022 Z= 0.265 Angle : 0.582 9.232 229688 Z= 0.306 Chirality : 0.038 0.274 29312 Planarity : 0.005 0.066 12786 Dihedral : 23.021 179.880 75284 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 5.96 % Allowed : 21.91 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: 0.00 (0.11), residues: 5994 helix: 1.16 (0.12), residues: 1991 sheet: -0.14 (0.15), residues: 1189 loop : -0.72 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCl 248 HIS 0.008 0.001 HISYW 14 PHE 0.018 0.001 PHEFG 62 TYR 0.013 0.002 TYRL6 117 ARG 0.015 0.000 ARGA4 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 710 time to evaluate : 6.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7704 (ptm160) REVERT: H 250 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7847 (mm) REVERT: H 255 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7340 (mtmt) REVERT: H 262 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: H 287 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: H 364 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: A4 35 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7633 (p90) REVERT: A4 153 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7807 (mt) REVERT: L6 18 LYS cc_start: 0.7112 (pttp) cc_final: 0.6900 (pptt) REVERT: L6 56 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7751 (ttp80) REVERT: F7 94 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: E9 136 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7709 (tptm) REVERT: E9 144 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7532 (ptp-170) REVERT: E9 173 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6636 (pt0) REVERT: WD 4 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8572 (t) REVERT: WD 48 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8025 (ttt180) REVERT: WD 54 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8613 (tttp) REVERT: RF 95 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6046 (tpm170) REVERT: VH 11 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.5829 (tmm160) REVERT: VH 72 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7860 (pttm) REVERT: TI 25 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: TI 84 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: MM 87 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7150 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7354 (mtp85) REVERT: PO 117 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.6353 (mp) REVERT: BQ 78 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: CT 55 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8586 (tp) REVERT: NV 14 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7588 (mp) REVERT: NV 49 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7732 (tmtm) REVERT: IX 31 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7450 (mm110) REVERT: IX 90 THR cc_start: 0.8925 (t) cc_final: 0.8683 (m) REVERT: Qb 79 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7319 (ptm160) REVERT: Nc 115 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6848 (pp20) REVERT: Je 64 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8582 (ptt-90) REVERT: Af 29 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: Lg 52 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7767 (mtp180) REVERT: Lg 111 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: Oi 40 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6219 (tm-30) REVERT: Oi 115 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7899 (tptp) REVERT: bk 41 GLN cc_start: 0.8300 (mt0) cc_final: 0.8073 (mm110) REVERT: Cl 5 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8123 (mtmm) REVERT: Cl 18 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7641 (ptmt) REVERT: Cl 110 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: Dm 34 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6329 (mmtt) REVERT: Dm 143 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: Sn 20 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7365 (tm-30) outliers start: 296 outliers final: 153 residues processed: 911 average time/residue: 2.1619 time to fit residues: 2807.8752 Evaluate side-chains 863 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 668 time to evaluate : 6.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 255 LYS Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 8 ILE Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 56 ARG Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 108 ILE Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain E9 residue 173 GLU Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 89 ASN Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 4 VAL Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 48 ARG Chi-restraints excluded: chain WD residue 54 LYS Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 11 ARG Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 56 ILE Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 84 GLN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 28 THR Chi-restraints excluded: chain fJ residue 29 VAL Chi-restraints excluded: chain fJ residue 72 SER Chi-restraints excluded: chain HK residue 58 VAL Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 9 GLN Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 69 LEU Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 112 LYS Chi-restraints excluded: chain PO residue 117 LEU Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 32 TYR Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 56 MET Chi-restraints excluded: chain CT residue 80 LYS Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 16 VAL Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 35 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain JY residue 77 VAL Chi-restraints excluded: chain QZ residue 20 SER Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 61 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 83 GLU Chi-restraints excluded: chain Kd residue 118 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 64 ARG Chi-restraints excluded: chain Je residue 103 THR Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 40 ASN Chi-restraints excluded: chain Af residue 60 ARG Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 76 ASN Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 119 THR Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain Oi residue 40 GLU Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain bk residue 32 MET Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain Cl residue 5 LYS Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 36 SER Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Dm residue 23 SER Chi-restraints excluded: chain Dm residue 34 LYS Chi-restraints excluded: chain Dm residue 143 GLN Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 333 optimal weight: 10.0000 chunk 893 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 582 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 992 optimal weight: 10.0000 chunk 824 optimal weight: 5.9990 chunk 459 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 521 optimal weight: 6.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN R3 54 GLN F7 24 ASN ** F7 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 59 GLN HK 62 ASN BQ 18 GLN GR 106 ASN GS 149 ASN CT 3 GLN JY 99 GLN Qb 77 HIS Nc 66 ASN ** Je 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 139 ASN Cl 134 ASN Cl 187 ASN Dm 117 GLN Dm 171 GLN To 3 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 154022 Z= 0.529 Angle : 0.773 11.269 229688 Z= 0.392 Chirality : 0.048 0.327 29312 Planarity : 0.007 0.120 12786 Dihedral : 23.172 179.281 75260 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 6.14 % Allowed : 22.31 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.24 (0.10), residues: 5994 helix: 0.89 (0.11), residues: 1986 sheet: -0.28 (0.14), residues: 1238 loop : -0.81 (0.11), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPCl 248 HIS 0.012 0.002 HISVH 3 PHE 0.020 0.002 PHEKd 66 TYR 0.021 0.002 TYRL6 117 ARG 0.009 0.001 ARGIX 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 693 time to evaluate : 6.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 352 MET cc_start: 0.8421 (mmm) cc_final: 0.8064 (mmm) REVERT: H 250 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7883 (mm) REVERT: H 262 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7541 (pm20) REVERT: H 287 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: H 336 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.5663 (mtm180) REVERT: H 364 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: A4 35 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7501 (p90) REVERT: A4 135 THR cc_start: 0.5205 (OUTLIER) cc_final: 0.4732 (t) REVERT: A4 153 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8022 (mt) REVERT: F7 94 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: E9 136 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7746 (tptm) REVERT: E9 144 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7527 (ptp-170) REVERT: E9 173 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6672 (pt0) REVERT: WD 48 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7617 (ttt180) REVERT: WD 54 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8642 (tttp) REVERT: RF 1 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5878 (ptp) REVERT: RF 95 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6236 (tpm170) REVERT: VH 72 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7915 (pttm) REVERT: TI 25 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: TI 84 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: MM 87 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7091 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7424 (mtp85) REVERT: BQ 78 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: GR 36 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6911 (ttt-90) REVERT: GR 124 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: CT 55 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8599 (tp) REVERT: CT 112 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7667 (t70) REVERT: CT 157 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8269 (mt) REVERT: NV 14 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7646 (mp) REVERT: NV 49 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7668 (tmtm) REVERT: IX 31 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7428 (mm110) REVERT: IX 90 THR cc_start: 0.8985 (t) cc_final: 0.8733 (m) REVERT: IX 98 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: Qb 79 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7276 (ptm160) REVERT: Nc 115 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6945 (pp20) REVERT: Je 47 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7306 (mp) REVERT: Je 64 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8671 (ptt-90) REVERT: Lg 52 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7814 (mtp180) REVERT: Lg 111 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: Oi 115 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7943 (tptp) REVERT: bk 49 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7844 (mtpt) REVERT: Cl 5 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8271 (mtmm) REVERT: Dm 143 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: Sn 20 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7352 (tm-30) outliers start: 305 outliers final: 178 residues processed: 906 average time/residue: 2.2097 time to fit residues: 2865.0734 Evaluate side-chains 893 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 674 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 151 ASN 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 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 70 GLU Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 64 SER Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 86 ARG Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 100 LEU Chi-restraints excluded: chain F7 residue 108 ILE Chi-restraints excluded: chain F7 residue 130 LEU Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 89 GLN Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain E9 residue 173 GLU Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 14 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 48 ARG Chi-restraints excluded: chain WD residue 54 LYS Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 1 MET Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 21 MET Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 3 HIS Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 37 ILE Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 84 GLN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 28 THR Chi-restraints excluded: chain fJ residue 29 VAL Chi-restraints excluded: chain fJ residue 72 SER Chi-restraints excluded: chain HK residue 4 LYS Chi-restraints excluded: chain HK residue 58 VAL Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 40 ASN Chi-restraints excluded: chain OL residue 69 LEU Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 73 VAL Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 36 ARG Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GR residue 124 GLU Chi-restraints excluded: chain GR residue 176 LYS Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 80 LYS Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 149 ILE Chi-restraints excluded: chain CT residue 157 LEU Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain KU residue 16 VAL Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 35 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 1 MET Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 98 GLU Chi-restraints excluded: chain JY residue 60 ASP Chi-restraints excluded: chain JY residue 77 VAL Chi-restraints excluded: chain QZ residue 20 SER Chi-restraints excluded: chain QZ residue 66 ARG Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 61 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Kd residue 83 GLU 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 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Je residue 110 GLN Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 64 ILE Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 119 THR Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain dh residue 38 SER Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 85 SER Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 5 LYS Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 36 SER Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 71 LYS Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Dm residue 23 SER Chi-restraints excluded: chain Dm residue 143 GLN Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 957 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 565 optimal weight: 30.0000 chunk 724 optimal weight: 10.0000 chunk 561 optimal weight: 50.0000 chunk 835 optimal weight: 20.0000 chunk 554 optimal weight: 0.9990 chunk 988 optimal weight: 20.0000 chunk 618 optimal weight: 40.0000 chunk 602 optimal weight: 8.9990 chunk 456 optimal weight: 0.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN F7 10 ASN F7 24 ASN ** F7 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 59 GLN BQ 18 GLN GR 106 ASN CT 3 GLN Nc 66 ASN ** Je 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 139 ASN Pj 66 GLN Cl 134 ASN Cl 187 ASN Dm 117 GLN ** Dm 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 171 GLN To 3 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 154022 Z= 0.399 Angle : 0.679 9.953 229688 Z= 0.351 Chirality : 0.043 0.298 29312 Planarity : 0.006 0.098 12786 Dihedral : 23.133 179.615 75258 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 5.78 % Allowed : 23.11 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.18 (0.11), residues: 5994 helix: 0.94 (0.11), residues: 1987 sheet: -0.25 (0.14), residues: 1236 loop : -0.77 (0.11), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPCl 248 HIS 0.009 0.001 HISYW 14 PHE 0.019 0.002 PHEFG 62 TYR 0.019 0.002 TYRGR 115 ARG 0.007 0.001 ARGBa 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 681 time to evaluate : 6.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7649 (ptm160) REVERT: H 250 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7871 (mm) REVERT: H 255 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7547 (mtmt) REVERT: H 262 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: H 287 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: H 336 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.5644 (mtm180) REVERT: H 364 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7164 (tt0) REVERT: A4 35 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7451 (p90) REVERT: A4 55 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: A4 135 THR cc_start: 0.5190 (OUTLIER) cc_final: 0.4772 (t) REVERT: A4 153 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7847 (mt) REVERT: L6 99 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.6916 (mmm160) REVERT: F7 94 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: E9 136 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7719 (tptm) REVERT: E9 144 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7556 (ptp-170) REVERT: E9 173 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6656 (pt0) REVERT: WD 48 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8016 (ttt180) REVERT: WD 54 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8631 (tttp) REVERT: RF 1 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5881 (ptp) REVERT: RF 95 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6217 (tpm170) REVERT: VH 72 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7910 (pttm) REVERT: TI 25 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: TI 84 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: OL 58 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8201 (ptp) REVERT: MM 87 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7099 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7423 (mtp85) REVERT: BQ 78 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: GR 36 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6907 (ttt-90) REVERT: GR 85 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7305 (tpt90) REVERT: CT 55 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8592 (tp) REVERT: CT 112 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7671 (t70) REVERT: CT 157 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8280 (mt) REVERT: NV 14 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7618 (mp) REVERT: NV 49 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7734 (tmtm) REVERT: IX 31 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7413 (mm110) REVERT: IX 90 THR cc_start: 0.8959 (t) cc_final: 0.8710 (m) REVERT: IX 98 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: Qb 79 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7287 (ptm160) REVERT: Nc 115 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: Je 47 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7276 (mp) REVERT: Je 64 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8592 (ptt-90) REVERT: Lg 6 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.5893 (ptm160) REVERT: Lg 52 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7804 (mtp180) REVERT: Lg 111 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: Oi 40 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6285 (tm-30) REVERT: Oi 115 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7924 (tptp) REVERT: Cl 5 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8249 (mtmm) REVERT: Sn 20 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: To 58 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8309 (mp) outliers start: 287 outliers final: 176 residues processed: 885 average time/residue: 2.0443 time to fit residues: 2586.9701 Evaluate side-chains 893 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 670 time to evaluate : 6.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 151 ASN 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 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 255 LYS Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 76 MET Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 57 LEU Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 86 ARG Chi-restraints excluded: chain L6 residue 99 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 23 ASP Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 100 LEU Chi-restraints excluded: chain F7 residue 108 ILE Chi-restraints excluded: chain F7 residue 130 LEU Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 89 GLN Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain E9 residue 173 GLU Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 14 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 89 ASN Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 48 ARG Chi-restraints excluded: chain WD residue 54 LYS Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 1 MET Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 84 GLN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 28 THR Chi-restraints excluded: chain HK residue 4 LYS Chi-restraints excluded: chain HK residue 58 VAL Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 40 ASN Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 69 LEU Chi-restraints excluded: chain MM residue 18 SER Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 87 ASN Chi-restraints excluded: chain SP residue 4 SER Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 38 SER Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 73 VAL Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 36 ARG Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 32 TYR Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 55 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 157 LEU Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 191 THR Chi-restraints excluded: chain KU residue 16 VAL Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 35 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 98 GLU Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 77 VAL Chi-restraints excluded: chain QZ residue 20 SER Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 61 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Kd residue 83 GLU Chi-restraints excluded: chain Kd residue 118 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 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Je residue 110 GLN Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 64 ILE Chi-restraints excluded: chain Lg residue 110 SER Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 119 THR Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain dh residue 38 SER Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 40 GLU Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain Cl residue 5 LYS Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 36 SER Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 71 LYS Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Dm residue 23 SER Chi-restraints excluded: chain Dm residue 106 MET Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 19 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 611 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 590 optimal weight: 9.9990 chunk 297 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 628 optimal weight: 8.9990 chunk 673 optimal weight: 6.9990 chunk 488 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 777 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN F7 24 ASN F7 135 GLN UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 29 ASN TI 59 GLN HK 62 ASN BQ 18 GLN BQ 52 ASN GR 106 ASN CT 3 GLN Nc 66 ASN ** Je 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cl 134 ASN Cl 187 ASN Dm 117 GLN ** Dm 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 171 GLN Dm 182 HIS To 3 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 154022 Z= 0.362 Angle : 0.653 12.212 229688 Z= 0.339 Chirality : 0.042 0.290 29312 Planarity : 0.006 0.093 12786 Dihedral : 23.091 179.989 75257 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.92 % Favored : 96.01 % Rotamer: Outliers : 5.74 % Allowed : 23.15 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.12 (0.11), residues: 5994 helix: 0.99 (0.11), residues: 1987 sheet: -0.20 (0.14), residues: 1213 loop : -0.74 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPCl 248 HIS 0.009 0.001 HISYW 14 PHE 0.018 0.002 PHEFG 62 TYR 0.018 0.002 TYRGR 115 ARG 0.008 0.001 ARGQZ 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 675 time to evaluate : 6.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 16 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7809 (ptm160) REVERT: H 250 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7851 (mm) REVERT: H 255 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7597 (mtmt) REVERT: H 262 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: H 287 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: H 336 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.5656 (mtm180) REVERT: H 364 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: A4 35 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7436 (p90) REVERT: A4 55 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: A4 135 THR cc_start: 0.5210 (OUTLIER) cc_final: 0.4799 (t) REVERT: A4 153 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7910 (mt) REVERT: L6 99 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.6897 (mmm160) REVERT: F7 94 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: E9 136 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7734 (tptm) REVERT: E9 144 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7550 (ptp-170) REVERT: E9 173 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6657 (pt0) REVERT: MB 103 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8827 (ttm170) REVERT: WD 48 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8013 (ttt180) REVERT: WD 54 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8653 (tttp) REVERT: RF 1 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5919 (ptp) REVERT: RF 8 ARG cc_start: 0.7563 (mtp85) cc_final: 0.7320 (mtp85) REVERT: RF 95 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6105 (tpm170) REVERT: VH 11 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5803 (tmm160) REVERT: VH 72 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7891 (pttm) REVERT: TI 25 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: TI 84 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: OL 58 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8195 (ptp) REVERT: MM 87 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7105 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7408 (mtp85) REVERT: BQ 78 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: GR 36 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6926 (ttt-90) REVERT: GR 85 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7284 (tpt90) REVERT: GS 11 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6323 (pp20) REVERT: GS 136 MET cc_start: 0.8840 (tpp) cc_final: 0.8472 (tpp) REVERT: CT 112 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7671 (t70) REVERT: NV 14 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7624 (mp) REVERT: NV 49 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7791 (tmtm) REVERT: IX 31 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7421 (mm110) REVERT: IX 90 THR cc_start: 0.8958 (t) cc_final: 0.8707 (m) REVERT: IX 98 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: Qb 13 ARG cc_start: 0.7937 (tmm-80) cc_final: 0.7712 (tmm-80) REVERT: Qb 79 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.7346 (ptm160) REVERT: Nc 115 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6933 (pp20) REVERT: Je 47 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7230 (mp) REVERT: Je 64 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8626 (ptt-90) REVERT: Af 29 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: Lg 6 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.5840 (ptm160) REVERT: Lg 52 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7794 (mtp180) REVERT: Lg 111 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: Oi 115 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7910 (tptp) REVERT: bk 21 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8455 (ttmt) REVERT: bk 49 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7812 (mtpt) REVERT: Cl 5 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8216 (mtmm) REVERT: Cl 18 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7650 (ptmt) REVERT: Sn 20 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: To 58 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8336 (mp) outliers start: 285 outliers final: 179 residues processed: 874 average time/residue: 2.1702 time to fit residues: 2704.6450 Evaluate side-chains 899 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 669 time to evaluate : 6.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 151 ASN 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 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 235 GLU Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 255 LYS Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 76 MET Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 57 LEU Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain L6 residue 99 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 100 LEU Chi-restraints excluded: chain F7 residue 108 ILE Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain E9 residue 173 GLU Chi-restraints excluded: chain MB residue 14 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 89 ASN Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain MB residue 103 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 48 ARG Chi-restraints excluded: chain WD residue 54 LYS Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 1 MET Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 11 ARG Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 37 ILE Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain TI residue 84 GLN Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 33 THR Chi-restraints excluded: chain fJ residue 72 SER Chi-restraints excluded: chain HK residue 58 VAL Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 40 ASN Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 69 LEU Chi-restraints excluded: chain MM residue 18 SER Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 77 SER Chi-restraints excluded: chain PO residue 87 ASN Chi-restraints excluded: chain SP residue 4 SER Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 38 SER Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 73 VAL Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 36 ARG Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GS residue 11 GLU Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 32 TYR Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 77 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 149 ILE Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 191 THR Chi-restraints excluded: chain KU residue 16 VAL Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 35 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 98 GLU Chi-restraints excluded: chain IX residue 124 LEU Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 58 ASN Chi-restraints excluded: chain JY residue 77 VAL Chi-restraints excluded: chain QZ residue 20 SER Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 61 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Kd residue 83 GLU Chi-restraints excluded: chain Kd residue 118 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 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Je residue 103 THR Chi-restraints excluded: chain Je residue 110 GLN Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 64 ILE Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 119 THR Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain dh residue 38 SER Chi-restraints excluded: chain Oi residue 2 SER Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 85 SER Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain bk residue 21 LYS Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain bk residue 49 LYS Chi-restraints excluded: chain Cl residue 5 LYS Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 36 SER Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 71 LYS Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Dm residue 23 SER Chi-restraints excluded: chain Dm residue 106 MET Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain To residue 58 LEU Chi-restraints excluded: chain ep residue 19 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 899 optimal weight: 10.0000 chunk 947 optimal weight: 10.0000 chunk 864 optimal weight: 9.9990 chunk 921 optimal weight: 40.0000 chunk 554 optimal weight: 4.9990 chunk 401 optimal weight: 10.0000 chunk 723 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 832 optimal weight: 0.9990 chunk 871 optimal weight: 30.0000 chunk 918 optimal weight: 20.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN F7 24 ASN UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 29 ASN TI 59 GLN HK 62 ASN BQ 18 GLN GR 106 ASN CT 3 GLN Nc 66 ASN ** Je 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 139 ASN Pj 66 GLN Cl 134 ASN Cl 187 ASN Cl 259 HIS Dm 117 GLN Dm 171 GLN To 3 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 154022 Z= 0.398 Angle : 0.680 13.936 229688 Z= 0.351 Chirality : 0.043 0.297 29312 Planarity : 0.006 0.099 12786 Dihedral : 23.113 179.807 75254 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 5.54 % Allowed : 23.55 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.15 (0.11), residues: 5994 helix: 0.97 (0.11), residues: 1987 sheet: -0.22 (0.14), residues: 1228 loop : -0.77 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCl 248 HIS 0.009 0.001 HISYW 14 PHE 0.019 0.002 PHEFG 62 TYR 0.019 0.002 TYRGR 115 ARG 0.008 0.001 ARGQZ 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 675 time to evaluate : 6.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 11 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7493 (ptmt) REVERT: H 250 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7838 (mm) REVERT: H 262 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: H 287 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6697 (pm20) REVERT: H 336 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.5623 (mtm180) REVERT: H 364 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: A4 35 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7405 (p90) REVERT: A4 55 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: A4 135 THR cc_start: 0.5301 (OUTLIER) cc_final: 0.4849 (t) REVERT: A4 153 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7862 (mt) REVERT: L6 99 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.6907 (mmm160) REVERT: F7 94 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: E9 136 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7741 (tptm) REVERT: E9 144 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7549 (ptp-170) REVERT: E9 171 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8769 (m) REVERT: E9 173 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: MB 103 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8835 (ttm170) REVERT: WD 48 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7610 (ttt180) REVERT: WD 54 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8644 (tttp) REVERT: XE 2 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7367 (tttp) REVERT: RF 1 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5961 (ptp) REVERT: RF 95 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6215 (tpm170) REVERT: VH 11 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.5804 (tmm160) REVERT: VH 72 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7892 (pttm) REVERT: TI 25 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: OL 58 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8209 (ptp) REVERT: MM 87 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7117 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7418 (mtp85) REVERT: SP 39 MET cc_start: 0.7090 (ptm) cc_final: 0.6843 (ttp) REVERT: BQ 78 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: GR 36 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.6926 (ttt-90) REVERT: GR 85 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7295 (tpt90) REVERT: GS 11 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6310 (pp20) REVERT: GS 136 MET cc_start: 0.8860 (tpp) cc_final: 0.8632 (mmm) REVERT: CT 112 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7664 (t70) REVERT: CT 157 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8283 (mt) REVERT: NV 14 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7613 (mp) REVERT: NV 49 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7749 (tmtm) REVERT: IX 31 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7439 (mm110) REVERT: IX 90 THR cc_start: 0.8957 (t) cc_final: 0.8718 (m) REVERT: IX 98 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: Qb 79 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7285 (ptm160) REVERT: Nc 115 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6936 (pp20) REVERT: Je 47 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7265 (mp) REVERT: Je 64 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8604 (ptt-90) REVERT: Af 29 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7301 (tp30) REVERT: Lg 6 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5871 (ptm160) REVERT: Lg 52 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7796 (mtp180) REVERT: Lg 111 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: Oi 115 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7927 (tptp) REVERT: bk 21 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8454 (ttmt) REVERT: Cl 5 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8270 (mtmm) REVERT: Sn 20 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7354 (tm-30) outliers start: 275 outliers final: 181 residues processed: 870 average time/residue: 2.1536 time to fit residues: 2678.3977 Evaluate side-chains 889 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 659 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 151 ASN 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 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 11 LYS Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 235 GLU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 76 MET Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 57 LEU Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain L6 residue 99 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 23 ASP Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 100 LEU Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 171 THR Chi-restraints excluded: chain E9 residue 173 GLU Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 14 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain MB residue 103 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 48 ARG Chi-restraints excluded: chain WD residue 54 LYS Chi-restraints excluded: chain XE residue 2 LYS Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 1 MET Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 11 ARG Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 37 ILE Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 33 THR Chi-restraints excluded: chain fJ residue 72 SER Chi-restraints excluded: chain HK residue 4 LYS Chi-restraints excluded: chain HK residue 58 VAL Chi-restraints excluded: chain HK residue 67 THR Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 40 ASN Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 69 LEU Chi-restraints excluded: chain MM residue 18 SER Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 77 SER Chi-restraints excluded: chain PO residue 87 ASN Chi-restraints excluded: chain SP residue 4 SER Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 73 VAL Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 36 ARG Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GS residue 11 GLU Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 32 TYR Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 77 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 149 ILE Chi-restraints excluded: chain CT residue 157 LEU Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 191 THR Chi-restraints excluded: chain KU residue 16 VAL Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 98 GLU Chi-restraints excluded: chain IX residue 124 LEU Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 58 ASN Chi-restraints excluded: chain JY residue 77 VAL Chi-restraints excluded: chain QZ residue 20 SER Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 61 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Kd residue 83 GLU 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 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Je residue 103 THR Chi-restraints excluded: chain Je residue 110 GLN Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 119 THR Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain dh residue 38 SER Chi-restraints excluded: chain Oi residue 2 SER Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 85 SER Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain bk residue 21 LYS Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain Cl residue 5 LYS Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 36 SER Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 71 LYS Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Dm residue 23 SER Chi-restraints excluded: chain Dm residue 106 MET Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 605 optimal weight: 20.0000 chunk 974 optimal weight: 60.0000 chunk 594 optimal weight: 10.0000 chunk 462 optimal weight: 7.9990 chunk 677 optimal weight: 3.9990 chunk 1022 optimal weight: 10.0000 chunk 940 optimal weight: 10.0000 chunk 813 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 628 optimal weight: 8.9990 chunk 499 optimal weight: 5.9990 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 287 GLN F7 24 ASN UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN TI 29 ASN TI 59 GLN BQ 18 GLN GR 106 ASN CT 3 GLN Nc 66 ASN ** Je 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Pj 66 GLN Cl 134 ASN Cl 187 ASN Dm 117 GLN Dm 159 GLN Dm 171 GLN To 3 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 154022 Z= 0.433 Angle : 0.706 14.352 229688 Z= 0.363 Chirality : 0.045 0.303 29312 Planarity : 0.006 0.104 12786 Dihedral : 23.135 179.694 75250 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.88 % Rotamer: Outliers : 5.18 % Allowed : 24.01 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.20 (0.11), residues: 5994 helix: 0.94 (0.11), residues: 1984 sheet: -0.28 (0.14), residues: 1249 loop : -0.79 (0.11), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPCl 248 HIS 0.009 0.001 HISYW 14 PHE 0.019 0.002 PHEFG 62 TYR 0.022 0.002 TYRGR 115 ARG 0.008 0.001 ARGQZ 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11988 Ramachandran restraints generated. 5994 Oldfield, 0 Emsley, 5994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 671 time to evaluate : 6.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 250 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7862 (mm) REVERT: H 262 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: H 287 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6708 (pm20) REVERT: H 336 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.5677 (mtm180) REVERT: H 364 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: A4 35 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7381 (p90) REVERT: A4 55 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: A4 153 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8019 (mt) REVERT: L6 99 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.6926 (mmm160) REVERT: F7 94 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: E9 136 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7743 (tptm) REVERT: E9 144 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7535 (ptp-170) REVERT: E9 173 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6619 (pt0) REVERT: MB 103 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8781 (ttt180) REVERT: WD 48 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7618 (ttt180) REVERT: WD 54 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8641 (tttp) REVERT: RF 1 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5981 (ptp) REVERT: RF 95 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6227 (tpm170) REVERT: VH 72 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7910 (pttm) REVERT: TI 25 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: OL 58 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8208 (ptp) REVERT: MM 87 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7055 (ttp-110) REVERT: PO 13 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7428 (mtp85) REVERT: SP 39 MET cc_start: 0.7038 (ptm) cc_final: 0.6780 (ttp) REVERT: BQ 78 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: GR 36 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6913 (ttt-90) REVERT: GR 85 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7308 (tpt90) REVERT: GS 11 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6303 (pp20) REVERT: CT 112 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7671 (t70) REVERT: CT 114 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8101 (ttt90) REVERT: CT 157 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8280 (mt) REVERT: NV 14 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7659 (mp) REVERT: NV 49 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7719 (tmtm) REVERT: IX 31 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7413 (mm110) REVERT: IX 90 THR cc_start: 0.8969 (t) cc_final: 0.8718 (m) REVERT: IX 98 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: Qb 79 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7287 (ptm160) REVERT: Nc 115 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6959 (pp20) REVERT: Je 47 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7282 (mp) REVERT: Je 64 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8603 (ptt-90) REVERT: Lg 6 ARG cc_start: 0.6361 (OUTLIER) cc_final: 0.5875 (ptm160) REVERT: Lg 52 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7806 (mtp180) REVERT: Lg 111 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: Oi 115 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7928 (tptp) REVERT: bk 21 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8453 (ttmt) REVERT: Cl 5 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8263 (mtmm) REVERT: Sn 20 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7364 (tm-30) outliers start: 257 outliers final: 188 residues processed: 854 average time/residue: 2.1585 time to fit residues: 2630.7382 Evaluate side-chains 892 residues out of total 5026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 660 time to evaluate : 6.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 151 ASN 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 225 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 128 ARG Chi-restraints excluded: chain H residue 235 GLU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 262 GLU Chi-restraints excluded: chain H residue 270 GLU Chi-restraints excluded: chain H residue 279 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain H residue 287 GLU Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 317 GLU Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 336 ARG Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 339 ASP Chi-restraints excluded: chain H residue 357 ASP Chi-restraints excluded: chain H residue 364 GLU Chi-restraints excluded: chain H residue 390 VAL Chi-restraints excluded: chain R3 residue 42 SER Chi-restraints excluded: chain R3 residue 47 THR Chi-restraints excluded: chain A4 residue 35 TYR Chi-restraints excluded: chain A4 residue 55 PHE Chi-restraints excluded: chain A4 residue 135 THR Chi-restraints excluded: chain A4 residue 140 LEU Chi-restraints excluded: chain A4 residue 153 LEU Chi-restraints excluded: chain A4 residue 186 ILE Chi-restraints excluded: chain E5 residue 76 MET Chi-restraints excluded: chain E5 residue 116 MET Chi-restraints excluded: chain E5 residue 122 VAL Chi-restraints excluded: chain L6 residue 41 THR Chi-restraints excluded: chain L6 residue 47 SER Chi-restraints excluded: chain L6 residue 55 VAL Chi-restraints excluded: chain L6 residue 57 LEU Chi-restraints excluded: chain L6 residue 64 SER Chi-restraints excluded: chain L6 residue 75 GLN Chi-restraints excluded: chain L6 residue 94 ARG Chi-restraints excluded: chain L6 residue 99 ARG Chi-restraints excluded: chain L6 residue 109 ASP Chi-restraints excluded: chain F7 residue 23 ASP Chi-restraints excluded: chain F7 residue 25 VAL Chi-restraints excluded: chain F7 residue 28 VAL Chi-restraints excluded: chain F7 residue 50 LEU Chi-restraints excluded: chain F7 residue 88 LYS Chi-restraints excluded: chain F7 residue 94 GLU Chi-restraints excluded: chain F7 residue 96 MET Chi-restraints excluded: chain F7 residue 100 LEU Chi-restraints excluded: chain F7 residue 136 ILE Chi-restraints excluded: chain F7 residue 141 VAL Chi-restraints excluded: chain E9 residue 32 THR Chi-restraints excluded: chain E9 residue 136 LYS Chi-restraints excluded: chain E9 residue 144 ARG Chi-restraints excluded: chain E9 residue 173 GLU Chi-restraints excluded: chain MB residue 6 SER Chi-restraints excluded: chain MB residue 14 SER Chi-restraints excluded: chain MB residue 37 THR Chi-restraints excluded: chain MB residue 74 THR Chi-restraints excluded: chain MB residue 75 MET Chi-restraints excluded: chain MB residue 82 THR Chi-restraints excluded: chain MB residue 95 LEU Chi-restraints excluded: chain MB residue 103 ARG Chi-restraints excluded: chain UC residue 5 HIS Chi-restraints excluded: chain UC residue 65 HIS Chi-restraints excluded: chain WD residue 7 VAL Chi-restraints excluded: chain WD residue 48 ARG Chi-restraints excluded: chain WD residue 54 LYS Chi-restraints excluded: chain XE residue 39 ASN Chi-restraints excluded: chain XE residue 43 VAL Chi-restraints excluded: chain RF residue 1 MET Chi-restraints excluded: chain RF residue 4 THR Chi-restraints excluded: chain RF residue 29 ILE Chi-restraints excluded: chain RF residue 45 VAL Chi-restraints excluded: chain RF residue 66 ILE Chi-restraints excluded: chain RF residue 73 THR Chi-restraints excluded: chain RF residue 95 ARG Chi-restraints excluded: chain FG residue 6 VAL Chi-restraints excluded: chain FG residue 102 LEU Chi-restraints excluded: chain VH residue 51 VAL Chi-restraints excluded: chain VH residue 72 LYS Chi-restraints excluded: chain TI residue 25 GLN Chi-restraints excluded: chain TI residue 37 ILE Chi-restraints excluded: chain TI residue 41 THR Chi-restraints excluded: chain TI residue 57 LEU Chi-restraints excluded: chain fJ residue 3 LYS Chi-restraints excluded: chain fJ residue 11 ASP Chi-restraints excluded: chain fJ residue 33 THR Chi-restraints excluded: chain fJ residue 72 SER Chi-restraints excluded: chain HK residue 4 LYS Chi-restraints excluded: chain HK residue 58 VAL Chi-restraints excluded: chain HK residue 79 LEU Chi-restraints excluded: chain HK residue 100 SER Chi-restraints excluded: chain OL residue 23 SER Chi-restraints excluded: chain OL residue 40 ASN Chi-restraints excluded: chain OL residue 58 MET Chi-restraints excluded: chain OL residue 69 LEU Chi-restraints excluded: chain MM residue 18 SER Chi-restraints excluded: chain MM residue 68 ASP Chi-restraints excluded: chain MM residue 87 ARG Chi-restraints excluded: chain PO residue 31 VAL Chi-restraints excluded: chain PO residue 77 SER Chi-restraints excluded: chain PO residue 87 ASN Chi-restraints excluded: chain SP residue 4 SER Chi-restraints excluded: chain SP residue 12 ASP Chi-restraints excluded: chain SP residue 35 SER Chi-restraints excluded: chain SP residue 79 THR Chi-restraints excluded: chain BQ residue 73 VAL Chi-restraints excluded: chain BQ residue 78 GLN Chi-restraints excluded: chain BQ residue 108 THR Chi-restraints excluded: chain BQ residue 131 VAL Chi-restraints excluded: chain GR residue 15 VAL Chi-restraints excluded: chain GR residue 29 LYS Chi-restraints excluded: chain GR residue 36 ARG Chi-restraints excluded: chain GR residue 52 LEU Chi-restraints excluded: chain GR residue 85 ARG Chi-restraints excluded: chain GR residue 92 VAL Chi-restraints excluded: chain GS residue 11 GLU Chi-restraints excluded: chain GS residue 32 SER Chi-restraints excluded: chain CT residue 14 VAL Chi-restraints excluded: chain CT residue 32 TYR Chi-restraints excluded: chain CT residue 51 MET Chi-restraints excluded: chain CT residue 77 ILE Chi-restraints excluded: chain CT residue 101 VAL Chi-restraints excluded: chain CT residue 102 ASN Chi-restraints excluded: chain CT residue 112 ASP Chi-restraints excluded: chain CT residue 114 ARG Chi-restraints excluded: chain CT residue 124 LEU Chi-restraints excluded: chain CT residue 149 ILE Chi-restraints excluded: chain CT residue 157 LEU Chi-restraints excluded: chain CT residue 178 LEU Chi-restraints excluded: chain CT residue 191 THR Chi-restraints excluded: chain KU residue 16 VAL Chi-restraints excluded: chain KU residue 30 THR Chi-restraints excluded: chain KU residue 84 VAL Chi-restraints excluded: chain KU residue 87 LYS Chi-restraints excluded: chain NV residue 14 ILE Chi-restraints excluded: chain NV residue 49 LYS Chi-restraints excluded: chain YW residue 11 SER Chi-restraints excluded: chain YW residue 53 LEU Chi-restraints excluded: chain IX residue 31 GLN Chi-restraints excluded: chain IX residue 45 THR Chi-restraints excluded: chain IX residue 98 GLU Chi-restraints excluded: chain IX residue 124 LEU Chi-restraints excluded: chain JY residue 40 VAL Chi-restraints excluded: chain JY residue 58 ASN Chi-restraints excluded: chain JY residue 77 VAL Chi-restraints excluded: chain QZ residue 20 SER Chi-restraints excluded: chain Ba residue 4 THR Chi-restraints excluded: chain Qb residue 7 THR Chi-restraints excluded: chain Qb residue 18 GLU Chi-restraints excluded: chain Qb residue 21 LYS Chi-restraints excluded: chain Qb residue 38 VAL Chi-restraints excluded: chain Qb residue 61 VAL Chi-restraints excluded: chain Qb residue 72 ILE Chi-restraints excluded: chain Qb residue 79 ARG Chi-restraints excluded: chain Nc residue 72 SER Chi-restraints excluded: chain Nc residue 115 GLU Chi-restraints excluded: chain Kd residue 82 SER Chi-restraints excluded: chain Kd residue 83 GLU Chi-restraints excluded: chain Kd residue 118 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 64 ARG Chi-restraints excluded: chain Je residue 77 LEU Chi-restraints excluded: chain Je residue 103 THR Chi-restraints excluded: chain Je residue 110 GLN Chi-restraints excluded: chain Af residue 26 THR Chi-restraints excluded: chain Af residue 29 GLU Chi-restraints excluded: chain Af residue 86 ASN Chi-restraints excluded: chain Af residue 94 GLU Chi-restraints excluded: chain Af residue 210 VAL Chi-restraints excluded: chain Lg residue 6 ARG Chi-restraints excluded: chain Lg residue 25 SER Chi-restraints excluded: chain Lg residue 43 THR Chi-restraints excluded: chain Lg residue 52 ARG Chi-restraints excluded: chain Lg residue 64 ILE Chi-restraints excluded: chain Lg residue 111 GLU Chi-restraints excluded: chain Lg residue 119 THR Chi-restraints excluded: chain Lg residue 135 THR Chi-restraints excluded: chain dh residue 32 ILE Chi-restraints excluded: chain dh residue 38 SER Chi-restraints excluded: chain dh residue 52 LYS Chi-restraints excluded: chain Oi residue 2 SER Chi-restraints excluded: chain Oi residue 6 LEU Chi-restraints excluded: chain Oi residue 62 THR Chi-restraints excluded: chain Oi residue 70 VAL Chi-restraints excluded: chain Oi residue 85 SER Chi-restraints excluded: chain Oi residue 115 LYS Chi-restraints excluded: chain Pj residue 19 VAL Chi-restraints excluded: chain Pj residue 20 VAL Chi-restraints excluded: chain bk residue 21 LYS Chi-restraints excluded: chain bk residue 47 GLU Chi-restraints excluded: chain Cl residue 5 LYS Chi-restraints excluded: chain Cl residue 18 LYS Chi-restraints excluded: chain Cl residue 36 SER Chi-restraints excluded: chain Cl residue 51 THR Chi-restraints excluded: chain Cl residue 71 LYS Chi-restraints excluded: chain Cl residue 110 GLN Chi-restraints excluded: chain Cl residue 186 VAL Chi-restraints excluded: chain Cl residue 245 THR Chi-restraints excluded: chain Dm residue 23 SER Chi-restraints excluded: chain Dm residue 106 MET Chi-restraints excluded: chain Sn residue 20 GLN Chi-restraints excluded: chain Sn residue 28 VAL Chi-restraints excluded: chain Sn residue 35 SER Chi-restraints excluded: chain Sn residue 36 LYS Chi-restraints excluded: chain Sn residue 53 VAL Chi-restraints excluded: chain Sn residue 63 VAL Chi-restraints excluded: chain ep residue 19 ARG Chi-restraints excluded: chain C1 residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 646 optimal weight: 9.9990 chunk 867 optimal weight: 30.0000 chunk 249 optimal weight: 10.0000 chunk 750 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 815 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 837 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN F7 24 ASN UC 77 GLN ** FG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VH 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** VH 12 ASN HK 62 ASN BQ 18 GLN GR 106 ASN CT 3 GLN Nc 66 ASN ** Je 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Pj 66 GLN Cl 187 ASN Dm 117 GLN To 3 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125571 restraints weight = 159879.971| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.78 r_work: 0.3257 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 154022 Z= 0.275 Angle : 0.613 13.244 229688 Z= 0.322 Chirality : 0.039 0.280 29312 Planarity : 0.005 0.069 12786 Dihedral : 23.119 179.731 75249 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 4.86 % Allowed : 24.45 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.07 (0.11), residues: 5994 helix: 1.06 (0.12), residues: 1990 sheet: -0.21 (0.14), residues: 1226 loop : -0.73 (0.11), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPCl 248 HIS 0.008 0.001 HISYW 14 PHE 0.018 0.002 PHEFG 62 TYR 0.019 0.002 TYRGR 115 ARG 0.008 0.000 ARGQZ 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41023.58 seconds wall clock time: 714 minutes 17.78 seconds (42857.78 seconds total)