Starting phenix.real_space_refine on Tue Mar 19 07:40:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceu_16613/03_2024/8ceu_16613_updated.pdb" } resolution = 1.83 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= 0.001 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: 8 Type Number sf(0) Gaussians K 81 8.98 5 Zn 1 6.06 5 P 2872 5.49 5 Mg 220 5.21 5 S 74 5.16 5 C 42552 2.51 5 N 16045 2.21 5 O 30993 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 ARG 4": "NH1" <-> "NH2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "e PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 11": "OE1" <-> "OE2" Residue "f PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "j ARG 98": "NH1" <-> "NH2" Residue "k ASP 91": "OD1" <-> "OD2" Residue "n GLU 20": "OE1" <-> "OE2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 56": "OE1" <-> "OE2" Residue "t PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Residue "w TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 5": "OE1" <-> "OE2" Residue "y PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92838 Number of models: 1 Model: "" Number of chains: 79 Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 59130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59130 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 7, 'rna2p_pur': 265, 'rna2p_pyr': 142, 'rna3p': 17, 'rna3p_pur': 1320, 'rna3p_pyr': 1002} Link IDs: {'rna2p': 413, 'rna3p': 2339} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1558 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1463 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain breaks: 1 Chain: "f" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 974 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 3 Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1291 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 98} Chain breaks: 1 Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 728 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 1 Chain: "u" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "v" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 576 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 444 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "V" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {'KBE': 1} Classifications: {'peptide': 5, 'undetermined': 1} Link IDs: {'TRANS': 5} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Planarities with less than four sites: {'UAL:plan-2': 1, 'MYN:plan-2': 1, 'DPP:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 320 Unusual residues: {' K': 75, ' MG': 209, 'G34': 1} Classifications: {'undetermined': 285} Link IDs: {None: 284} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "c" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 3, ' MG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "1" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "a" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5806, 5806 Classifications: {'water': 5806} Link IDs: {None: 5805} Chain: "b" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "c" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "d" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "e" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "i" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "j" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "k" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "l" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "m" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "n" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "o" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "p" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "r" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "s" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "t" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "u" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "v" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "w" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "x" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "y" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "z" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1373 SG CYS 3 11 161.404 58.558 96.693 1.00 43.48 S ATOM 1398 SG CYS 3 14 157.372 58.947 97.430 1.00 39.62 S ATOM 1501 SG CYS 3 27 159.896 56.853 99.528 1.00 42.31 S Time building chain proxies: 39.86, per 1000 atoms: 0.43 Number of scatterers: 92838 At special positions: 0 Unit cell: (196.56, 206.64, 237.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 K 81 19.00 S 74 16.00 P 2872 15.00 Mg 220 11.99 O 30993 8.00 N 16045 7.00 C 42552 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=26, symmetry=0 Number of additional bonds: simple=26, symmetry=0 Coordination: Other bonds: Time building additional restraints: 47.96 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " Number of angles added : 3 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB UAL V 3 " pdb=" CB KBE C 1 " pdb=" CB UAL C 3 " pdb=" CB KBE D 1 " pdb=" CB KBE E 1 " pdb=" CB KBE F 1 " pdb=" CB KBE G 1 " pdb=" CB UAL G 3 " pdb=" CB KBE I 1 " Number of C-beta restraints generated: 5588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 47 sheets defined 26.4% alpha, 20.1% beta 1001 base pairs and 1507 stacking pairs defined. Time for finding SS restraints: 49.66 Creating SS restraints... Processing helix chain '1' and resid 9 through 16 Processing helix chain '1' and resid 18 through 22 Processing helix chain '1' and resid 25 through 37 Processing helix chain '2' and resid 8 through 11 No H-bonds generated for 'chain '2' and resid 8 through 11' Processing helix chain '2' and resid 38 through 45 Processing helix chain '2' and resid 52 through 61 removed outlier: 4.545A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 33 No H-bonds generated for 'chain '3' and resid 31 through 33' Processing helix chain 'c' and resid 31 through 33 No H-bonds generated for 'chain 'c' and resid 31 through 33' Processing helix chain 'c' and resid 198 through 202 removed outlier: 3.977A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 214 removed outlier: 3.571A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 222 through 224 No H-bonds generated for 'chain 'c' and resid 222 through 224' Processing helix chain 'c' and resid 261 through 266 removed outlier: 4.664A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 261 through 266' Processing helix chain 'd' and resid 62 through 71 Processing helix chain 'd' and resid 98 through 101 Processing helix chain 'd' and resid 121 through 125 Processing helix chain 'e' and resid 16 through 19 No H-bonds generated for 'chain 'e' and resid 16 through 19' Processing helix chain 'e' and resid 25 through 38 Processing helix chain 'e' and resid 98 through 114 Processing helix chain 'e' and resid 131 through 141 Processing helix chain 'e' and resid 155 through 161 Processing helix chain 'e' and resid 172 through 174 No H-bonds generated for 'chain 'e' and resid 172 through 174' Processing helix chain 'e' and resid 177 through 182 Processing helix chain 'e' and resid 190 through 200 Processing helix chain 'f' and resid 5 through 10 removed outlier: 3.666A pdb=" N LYS f 9 " --> pdb=" O HIS f 5 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP f 10 " --> pdb=" O ASP f 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 5 through 10' Processing helix chain 'f' and resid 12 through 19 Processing helix chain 'f' and resid 25 through 27 No H-bonds generated for 'chain 'f' and resid 25 through 27' Processing helix chain 'f' and resid 58 through 61 No H-bonds generated for 'chain 'f' and resid 58 through 61' Processing helix chain 'f' and resid 93 through 101 removed outlier: 3.606A pdb=" N TRP f 97 " --> pdb=" O GLU f 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU f 98 " --> pdb=" O ARG f 95 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU f 101 " --> pdb=" O GLU f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 173 removed outlier: 3.728A pdb=" N ARG f 167 " --> pdb=" O ASP f 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 6 No H-bonds generated for 'chain 'g' and resid 3 through 6' Processing helix chain 'g' and resid 62 through 80 Processing helix chain 'g' and resid 138 through 151 removed outlier: 3.713A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 28 Processing helix chain 'i' and resid 8 through 10 No H-bonds generated for 'chain 'i' and resid 8 through 10' Processing helix chain 'i' and resid 25 through 37 removed outlier: 3.753A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 61 No H-bonds generated for 'chain 'i' and resid 59 through 61' Processing helix chain 'i' and resid 68 through 71 No H-bonds generated for 'chain 'i' and resid 68 through 71' Processing helix chain 'i' and resid 89 through 108 Proline residue: i 97 - end of helix removed outlier: 4.014A pdb=" N VAL i 100 " --> pdb=" O ARG i 96 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 121 removed outlier: 3.941A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 133 through 135 No H-bonds generated for 'chain 'i' and resid 133 through 135' Processing helix chain 'j' and resid 105 through 107 No H-bonds generated for 'chain 'j' and resid 105 through 107' Processing helix chain 'j' and resid 113 through 118 Processing helix chain 'k' and resid 38 through 40 No H-bonds generated for 'chain 'k' and resid 38 through 40' Processing helix chain 'k' and resid 57 through 60 No H-bonds generated for 'chain 'k' and resid 57 through 60' Processing helix chain 'k' and resid 69 through 73 removed outlier: 3.824A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 69 through 73' Processing helix chain 'k' and resid 79 through 83 removed outlier: 3.916A pdb=" N ALA k 83 " --> pdb=" O SER k 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 97 Processing helix chain 'k' and resid 129 through 137 Processing helix chain 'l' and resid 43 through 57 Processing helix chain 'l' and resid 110 through 123 removed outlier: 4.076A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 31 Processing helix chain 'm' and resid 38 through 56 removed outlier: 4.226A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix Processing helix chain 'm' and resid 60 through 70 Processing helix chain 'm' and resid 73 through 81 Processing helix chain 'm' and resid 83 through 86 No H-bonds generated for 'chain 'm' and resid 83 through 86' Processing helix chain 'n' and resid 3 through 21 removed outlier: 4.583A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 3.999A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 68 through 85 Processing helix chain 'n' and resid 101 through 113 Processing helix chain 'o' and resid 3 through 12 removed outlier: 4.037A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 56 No H-bonds generated for 'chain 'o' and resid 54 through 56' Processing helix chain 'o' and resid 98 through 102 Processing helix chain 'o' and resid 105 through 108 Processing helix chain 'p' and resid 7 through 20 Processing helix chain 'p' and resid 26 through 29 Processing helix chain 'p' and resid 32 through 71 removed outlier: 3.624A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 85 Processing helix chain 'p' and resid 92 through 101 Processing helix chain 'p' and resid 103 through 117 Processing helix chain 'r' and resid 14 through 24 removed outlier: 4.005A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 38 Processing helix chain 'r' and resid 42 through 60 Processing helix chain 'r' and resid 66 through 68 No H-bonds generated for 'chain 'r' and resid 66 through 68' Processing helix chain 'r' and resid 89 through 91 No H-bonds generated for 'chain 'r' and resid 89 through 91' Processing helix chain 's' and resid 4 through 10 removed outlier: 3.603A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 27 Processing helix chain 's' and resid 40 through 50 Processing helix chain 't' and resid 67 through 69 No H-bonds generated for 'chain 't' and resid 67 through 69' Processing helix chain 'u' and resid 14 through 23 Processing helix chain 'u' and resid 44 through 51 Processing helix chain 'u' and resid 55 through 58 No H-bonds generated for 'chain 'u' and resid 55 through 58' Processing helix chain 'w' and resid 53 through 62 Processing helix chain 'w' and resid 64 through 74 Processing helix chain 'x' and resid 3 through 8 removed outlier: 3.593A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 33 Processing helix chain 'x' and resid 40 through 61 removed outlier: 3.563A pdb=" N VAL x 46 " --> pdb=" O LEU x 43 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS x 54 " --> pdb=" O ALA x 51 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU x 57 " --> pdb=" O LYS x 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA x 61 " --> pdb=" O ASN x 58 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 27 Processing helix chain 'y' and resid 42 through 50 Processing helix chain 'y' and resid 52 through 54 No H-bonds generated for 'chain 'y' and resid 52 through 54' Processing helix chain 'z' and resid 10 through 19 removed outlier: 4.806A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 20 through 25 Processing sheet with id= B, first strand: chain '2' and resid 14 through 16 Processing sheet with id= C, first strand: chain '3' and resid 2 through 4 Processing sheet with id= D, first strand: chain '3' and resid 14 through 19 Processing sheet with id= E, first strand: chain 'c' and resid 3 through 5 Processing sheet with id= F, first strand: chain 'c' and resid 34 through 36 Processing sheet with id= G, first strand: chain 'c' and resid 101 through 105 removed outlier: 3.541A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 129 through 131 Processing sheet with id= I, first strand: chain 'c' and resid 181 through 185 removed outlier: 6.663A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 169 through 172 removed outlier: 4.544A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 78 through 83 removed outlier: 4.352A pdb=" N GLY d 78 " --> pdb=" O THR d 52 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR d 52 " --> pdb=" O GLY d 78 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'd' and resid 115 through 119 removed outlier: 5.552A pdb=" N MET d 165 " --> pdb=" O LYS d 116 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE d 118 " --> pdb=" O GLY d 163 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY d 163 " --> pdb=" O PHE d 118 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.078A pdb=" N VAL e 186 " --> pdb=" O ILE e 119 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL e 121 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET e 188 " --> pdb=" O VAL e 121 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'f' and resid 88 through 91 removed outlier: 6.982A pdb=" N THR f 157 " --> pdb=" O GLU f 32 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE f 34 " --> pdb=" O THR f 155 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR f 155 " --> pdb=" O ILE f 34 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU f 36 " --> pdb=" O ASP f 153 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP f 153 " --> pdb=" O LEU f 36 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'g' and resid 16 through 20 removed outlier: 3.969A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'g' and resid 41 through 44 Processing sheet with id= Q, first strand: chain 'g' and resid 161 through 164 Processing sheet with id= R, first strand: chain 'g' and resid 95 through 99 removed outlier: 3.551A pdb=" N VAL g 102 " --> pdb=" O LYS g 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'h' and resid 18 through 20 Processing sheet with id= T, first strand: chain 'i' and resid 15 through 19 removed outlier: 6.505A pdb=" N TYR i 53 " --> pdb=" O TYR i 16 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL i 18 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE i 55 " --> pdb=" O VAL i 18 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'i' and resid 73 through 77 Processing sheet with id= V, first strand: chain 'j' and resid 7 through 9 removed outlier: 6.466A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL j 24 " --> pdb=" O ILE j 38 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ILE j 38 " --> pdb=" O VAL j 24 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS j 59 " --> pdb=" O LEU j 87 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA j 83 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'k' and resid 74 through 78 removed outlier: 6.696A pdb=" N PHE k 107 " --> pdb=" O ALA k 75 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE k 77 " --> pdb=" O PHE k 107 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LYS k 109 " --> pdb=" O ILE k 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'k' and resid 121 through 123 removed outlier: 6.357A pdb=" N LYS k 141 " --> pdb=" O VAL k 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'l' and resid 128 through 132 removed outlier: 3.511A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA l 35 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL l 101 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'l' and resid 39 through 42 removed outlier: 6.980A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TRP l 92 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS l 71 " --> pdb=" O TRP l 92 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'm' and resid 33 through 37 Processing sheet with id= AB, first strand: chain 'n' and resid 91 through 93 removed outlier: 3.646A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'o' and resid 83 through 88 removed outlier: 6.474A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N GLU o 44 " --> pdb=" O ILE o 64 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE o 64 " --> pdb=" O GLU o 44 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE o 50 " --> pdb=" O ALA o 58 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA o 58 " --> pdb=" O ILE o 50 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 11 through 14 removed outlier: 3.530A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN q 6 " --> pdb=" O VAL q 38 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL q 38 " --> pdb=" O GLN q 6 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'q' and resid 19 through 23 Processing sheet with id= AF, first strand: chain 'q' and resid 32 through 35 removed outlier: 6.283A pdb=" N GLU q 62 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE q 98 " --> pdb=" O GLU q 62 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'q' and resid 72 through 78 removed outlier: 4.070A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'r' and resid 2 through 7 removed outlier: 6.735A pdb=" N SER r 108 " --> pdb=" O VAL r 71 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N VAL r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'r' and resid 82 through 87 Processing sheet with id= AJ, first strand: chain 's' and resid 11 through 14 removed outlier: 6.608A pdb=" N LYS s 33 " --> pdb=" O ARG s 12 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL s 31 " --> pdb=" O PRO s 14 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 's' and resid 67 through 69 Processing sheet with id= AL, first strand: chain 't' and resid 22 through 24 removed outlier: 6.068A pdb=" N GLU t 10 " --> pdb=" O PHE t 73 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE t 72 " --> pdb=" O ASP t 81 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 't' and resid 41 through 45 Processing sheet with id= AN, first strand: chain 't' and resid 83 through 87 Processing sheet with id= AO, first strand: chain 't' and resid 25 through 29 removed outlier: 6.650A pdb=" N ILE t 35 " --> pdb=" O LYS t 26 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL t 28 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS t 33 " --> pdb=" O VAL t 28 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'u' and resid 62 through 65 removed outlier: 7.700A pdb=" N ASN u 5 " --> pdb=" O ASP u 43 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP u 43 " --> pdb=" O ASN u 5 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL u 92 " --> pdb=" O ALA u 74 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA u 74 " --> pdb=" O VAL u 92 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'v' and resid 45 through 47 removed outlier: 6.699A pdb=" N LYS v 78 " --> pdb=" O HIS v 46 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'v' and resid 51 through 53 Processing sheet with id= AS, first strand: chain 'w' and resid 13 through 18 Processing sheet with id= AT, first strand: chain 'w' and resid 33 through 40 Processing sheet with id= AU, first strand: chain 'y' and resid 35 through 39 785 hydrogen bonds defined for protein. 2166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2514 hydrogen bonds 3892 hydrogen bond angles 0 basepair planarities 1001 basepair parallelities 1507 stacking parallelities Total time for adding SS restraints: 617.75 Time building geometry restraints manager: 50.81 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: 8666 1.32 - 1.45: 42353 1.45 - 1.58: 36511 1.58 - 1.70: 5740 1.70 - 1.83: 133 Bond restraints: 93403 Sorted by residual: bond pdb=" C4 5MU a 747 " pdb=" C5 5MU a 747 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.11e+02 bond pdb=" C4 5MU a1939 " pdb=" C5 5MU a1939 " ideal model delta sigma weight residual 1.802 1.450 0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" N1 5MU a1939 " pdb=" C6 5MU a1939 " ideal model delta sigma weight residual 1.635 1.387 0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" N1 5MU a 747 " pdb=" C6 5MU a 747 " ideal model delta sigma weight residual 1.635 1.389 0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" N3 5MU a 747 " pdb=" C4 5MU a 747 " ideal model delta sigma weight residual 1.182 1.384 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 93398 not shown) Histogram of bond angle deviations from ideal: 90.47 - 99.28: 895 99.28 - 108.09: 24756 108.09 - 116.90: 58043 116.90 - 125.71: 46052 125.71 - 134.52: 10549 Bond angle restraints: 140295 Sorted by residual: angle pdb=" O3' G a2429 " pdb=" P A a2430 " pdb=" O5' A a2430 " ideal model delta sigma weight residual 104.00 90.47 13.53 1.50e+00 4.44e-01 8.14e+01 angle pdb=" O3' C a1905 " pdb=" P G a1906 " pdb=" O5' G a1906 " ideal model delta sigma weight residual 104.00 90.70 13.30 1.50e+00 4.44e-01 7.86e+01 angle pdb=" O3' A a1373 " pdb=" P G a1374 " pdb=" O5' G a1374 " ideal model delta sigma weight residual 104.00 90.78 13.22 1.50e+00 4.44e-01 7.77e+01 angle pdb=" C UAL E 3 " pdb=" CA UAL E 3 " pdb=" CB UAL E 3 " ideal model delta sigma weight residual 110.50 123.45 -12.95 1.50e+00 4.44e-01 7.45e+01 angle pdb=" C UAL D 3 " pdb=" CA UAL D 3 " pdb=" CB UAL D 3 " ideal model delta sigma weight residual 110.50 123.43 -12.93 1.50e+00 4.44e-01 7.43e+01 ... (remaining 140290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 53141 35.46 - 70.92: 5861 70.92 - 106.38: 748 106.38 - 141.83: 10 141.83 - 177.29: 8 Dihedral angle restraints: 59768 sinusoidal: 51108 harmonic: 8660 Sorted by residual: dihedral pdb=" N KBE V 1 " pdb=" C KBE V 1 " pdb=" CA KBE V 1 " pdb=" CB KBE V 1 " ideal model delta harmonic sigma weight residual 122.80 26.53 96.27 0 2.50e+00 1.60e-01 1.48e+03 dihedral pdb=" N KBE H 1 " pdb=" C KBE H 1 " pdb=" CA KBE H 1 " pdb=" CB KBE H 1 " ideal model delta harmonic sigma weight residual 122.80 28.36 94.44 0 2.50e+00 1.60e-01 1.43e+03 dihedral pdb=" C UAL H 3 " pdb=" N UAL H 3 " pdb=" CA UAL H 3 " pdb=" CB UAL H 3 " ideal model delta harmonic sigma weight residual -122.60 -177.61 55.01 0 2.50e+00 1.60e-01 4.84e+02 ... (remaining 59765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.234: 17954 1.234 - 2.469: 0 2.469 - 3.703: 0 3.703 - 4.938: 0 4.938 - 6.172: 1 Chirality restraints: 17955 Sorted by residual: chirality pdb=" C23 G34 a3001 " pdb=" C24 G34 a3001 " pdb=" C29 G34 a3001 " pdb=" S1 G34 a3001 " both_signs ideal model delta sigma weight residual False -3.11 3.07 -6.17 2.00e-01 2.50e+01 9.52e+02 chirality pdb=" P A a2191 " pdb=" OP1 A a2191 " pdb=" OP2 A a2191 " pdb=" O5' A a2191 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" P G a1177 " pdb=" OP1 G a1177 " pdb=" OP2 G a1177 " pdb=" O5' G a1177 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.10e+00 ... (remaining 17952 not shown) Planarity restraints: 7053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " -0.069 2.00e-02 2.50e+03 6.08e-01 8.31e+03 pdb=" C4' OMC a2498 " -0.425 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " -0.683 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " 0.647 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " 0.640 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " 0.165 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " -0.966 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " -0.223 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " 0.914 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a2445 " 0.085 2.00e-02 2.50e+03 6.08e-01 8.31e+03 pdb=" C4' 2MG a2445 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG a2445 " 0.710 2.00e-02 2.50e+03 pdb=" C3' 2MG a2445 " -0.649 2.00e-02 2.50e+03 pdb=" O3' 2MG a2445 " -0.634 2.00e-02 2.50e+03 pdb=" C2' 2MG a2445 " -0.176 2.00e-02 2.50e+03 pdb=" O2' 2MG a2445 " 0.935 2.00e-02 2.50e+03 pdb=" C1' 2MG a2445 " 0.204 2.00e-02 2.50e+03 pdb=" N9 2MG a2445 " -0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1835 " 0.055 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' 2MG a1835 " 0.434 2.00e-02 2.50e+03 pdb=" O4' 2MG a1835 " 0.742 2.00e-02 2.50e+03 pdb=" C3' 2MG a1835 " -0.633 2.00e-02 2.50e+03 pdb=" O3' 2MG a1835 " -0.573 2.00e-02 2.50e+03 pdb=" C2' 2MG a1835 " -0.206 2.00e-02 2.50e+03 pdb=" O2' 2MG a1835 " 0.896 2.00e-02 2.50e+03 pdb=" C1' 2MG a1835 " 0.192 2.00e-02 2.50e+03 pdb=" N9 2MG a1835 " -0.906 2.00e-02 2.50e+03 ... (remaining 7050 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.49: 1355 2.49 - 3.15: 83068 3.15 - 3.82: 246383 3.82 - 4.48: 355819 4.48 - 5.14: 463570 Nonbonded interactions: 1150195 Sorted by model distance: nonbonded pdb=" OP1 A a2430 " pdb="MG MG a3028 " model vdw 1.830 2.170 nonbonded pdb=" OP2 A a2682 " pdb="MG MG a3030 " model vdw 1.849 2.170 nonbonded pdb=" OP2 A a1678 " pdb="MG MG a3047 " model vdw 1.855 2.170 nonbonded pdb=" OP2 C a2025 " pdb="MG MG a3052 " model vdw 1.861 2.170 nonbonded pdb=" OP1 G a 962 " pdb="MG MG a3032 " model vdw 1.864 2.170 ... (remaining 1150190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 32.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 71.310 Check model and map are aligned: 1.120 Set scattering table: 0.670 Process input model: 829.870 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.480 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 950.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.009 0.353 93403 Z= 0.522 Angle : 1.557 20.522 140295 Z= 0.957 Chirality : 0.113 6.172 17955 Planarity : 0.025 0.608 7053 Dihedral : 22.488 177.293 54180 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 0.65 % Allowed : 4.10 % Favored : 95.25 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 2953 helix: -0.80 (0.16), residues: 796 sheet: -0.86 (0.19), residues: 624 loop : -0.50 (0.14), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP c 248 HIS 0.015 0.003 HIS w 34 PHE 0.042 0.005 PHE p 106 TYR 0.041 0.005 TYR p 32 ARG 0.038 0.004 ARG p 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 561 time to evaluate : 4.276 Fit side-chains revert: symmetry clash REVERT: 0 7 GLU cc_start: 0.7207 (pt0) cc_final: 0.6968 (pt0) REVERT: 0 50 LYS cc_start: 0.7285 (mtmm) cc_final: 0.7080 (mtmt) REVERT: 1 1 MET cc_start: 0.7235 (mtp) cc_final: 0.6732 (mtm) REVERT: 1 2 LYS cc_start: 0.8206 (tttt) cc_final: 0.7954 (ttpt) REVERT: 1 41 ARG cc_start: 0.7668 (mtt90) cc_final: 0.6692 (tmt170) REVERT: 2 15 LYS cc_start: 0.8140 (mptt) cc_final: 0.7885 (mmpt) REVERT: 3 9 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7784 (mtmm) REVERT: 3 12 ARG cc_start: 0.6641 (ptp-170) cc_final: 0.6335 (ptp90) REVERT: 3 15 LYS cc_start: 0.7916 (mttm) cc_final: 0.7383 (mptp) REVERT: c 20 VAL cc_start: 0.7402 (t) cc_final: 0.7164 (p) REVERT: c 97 LYS cc_start: 0.7307 (mttt) cc_final: 0.7059 (tttp) REVERT: c 121 ASP cc_start: 0.5981 (p0) cc_final: 0.5719 (p0) REVERT: c 125 LYS cc_start: 0.7355 (ptmm) cc_final: 0.7106 (pttm) REVERT: c 201 MET cc_start: 0.8306 (ptt) cc_final: 0.8010 (ptp) REVERT: c 269 ARG cc_start: 0.7225 (ttp-170) cc_final: 0.6460 (ttm-80) REVERT: d 7 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8059 (ttmt) REVERT: d 18 ASP cc_start: 0.6897 (p0) cc_final: 0.6697 (p0) REVERT: d 64 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7130 (mt-10) REVERT: d 70 LYS cc_start: 0.7866 (tttt) cc_final: 0.7513 (tmtp) REVERT: d 88 GLU cc_start: 0.6285 (mt-10) cc_final: 0.5829 (mt-10) REVERT: d 89 GLU cc_start: 0.6437 (tp30) cc_final: 0.6150 (mp0) REVERT: d 92 VAL cc_start: 0.7694 (t) cc_final: 0.7369 (p) REVERT: d 128 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7459 (mmt180) REVERT: d 184 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6887 (mtt180) REVERT: e 21 ARG cc_start: 0.6449 (ptm160) cc_final: 0.6190 (ptp-170) REVERT: e 141 MET cc_start: 0.5266 (mtp) cc_final: 0.4919 (mtp) REVERT: e 145 ASP cc_start: 0.7291 (t70) cc_final: 0.7052 (t70) REVERT: e 149 ILE cc_start: 0.8358 (mt) cc_final: 0.8019 (mm) REVERT: e 150 THR cc_start: 0.7447 (m) cc_final: 0.7086 (p) REVERT: e 184 ASP cc_start: 0.7164 (m-30) cc_final: 0.6939 (m-30) REVERT: e 195 GLN cc_start: 0.7032 (mt0) cc_final: 0.6821 (mt0) REVERT: f 17 MET cc_start: 0.3166 (OUTLIER) cc_final: 0.2600 (mmm) REVERT: f 69 LYS cc_start: 0.5941 (mtpp) cc_final: 0.5703 (mmtm) REVERT: f 89 VAL cc_start: 0.7222 (OUTLIER) cc_final: 0.7000 (t) REVERT: g 9 VAL cc_start: 0.5670 (m) cc_final: 0.5376 (t) REVERT: g 10 VAL cc_start: 0.5957 (m) cc_final: 0.5753 (t) REVERT: g 27 LYS cc_start: 0.5597 (ttpp) cc_final: 0.5214 (ptpp) REVERT: g 44 LYS cc_start: 0.4769 (mmtt) cc_final: 0.4506 (mtpt) REVERT: g 74 SER cc_start: 0.7077 (m) cc_final: 0.6450 (p) REVERT: g 88 GLN cc_start: 0.6938 (mt0) cc_final: 0.6724 (mt0) REVERT: g 155 GLU cc_start: 0.7512 (pp20) cc_final: 0.7278 (pp20) REVERT: h 1 MET cc_start: 0.5083 (ttt) cc_final: 0.4568 (tpp) REVERT: i 2 LYS cc_start: 0.7458 (mttt) cc_final: 0.7255 (mttp) REVERT: i 90 GLU cc_start: 0.7741 (pt0) cc_final: 0.7498 (pt0) REVERT: i 95 ARG cc_start: 0.7028 (ttt-90) cc_final: 0.6629 (ttm-80) REVERT: i 96 ARG cc_start: 0.6986 (ptt-90) cc_final: 0.5889 (ttp80) REVERT: i 98 GLU cc_start: 0.7805 (mp0) cc_final: 0.7584 (mp0) REVERT: i 106 LYS cc_start: 0.8317 (tttt) cc_final: 0.7996 (ttmt) REVERT: i 129 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6585 (pt0) REVERT: j 7 MET cc_start: 0.8553 (mmt) cc_final: 0.8338 (mmm) REVERT: j 17 ARG cc_start: 0.7443 (mmt90) cc_final: 0.7002 (mmm160) REVERT: j 53 LYS cc_start: 0.7219 (mmtm) cc_final: 0.7002 (mttp) REVERT: j 88 ASN cc_start: 0.7314 (t0) cc_final: 0.7087 (t0) REVERT: j 98 ARG cc_start: 0.6721 (mmt180) cc_final: 0.6355 (mtp-110) REVERT: j 106 GLU cc_start: 0.7180 (mp0) cc_final: 0.6733 (mp0) REVERT: j 121 GLU cc_start: 0.7735 (pt0) cc_final: 0.6660 (tp30) REVERT: k 84 LYS cc_start: 0.6849 (mttt) cc_final: 0.6574 (mttm) REVERT: k 126 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7140 (mtp180) REVERT: k 129 LYS cc_start: 0.7347 (mmtp) cc_final: 0.6917 (mppt) REVERT: k 141 LYS cc_start: 0.7409 (mtmt) cc_final: 0.7174 (mtmm) REVERT: l 28 PHE cc_start: 0.7908 (m-80) cc_final: 0.7593 (m-80) REVERT: l 30 SER cc_start: 0.8298 (m) cc_final: 0.8061 (p) REVERT: l 106 ASP cc_start: 0.7437 (t70) cc_final: 0.7209 (t70) REVERT: l 115 GLU cc_start: 0.7337 (tp30) cc_final: 0.6514 (mm-30) REVERT: l 126 ILE cc_start: 0.7964 (pt) cc_final: 0.7641 (mt) REVERT: l 127 LYS cc_start: 0.7723 (tppt) cc_final: 0.7472 (ttmm) REVERT: l 132 THR cc_start: 0.7629 (m) cc_final: 0.7368 (p) REVERT: l 136 MET cc_start: 0.5773 (ttm) cc_final: 0.5456 (ttm) REVERT: m 18 GLN cc_start: 0.8432 (tt0) cc_final: 0.8190 (tt0) REVERT: m 110 MET cc_start: 0.8701 (mmm) cc_final: 0.8357 (mmm) REVERT: n 13 ARG cc_start: 0.7185 (tpt170) cc_final: 0.6894 (ttm170) REVERT: n 46 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6109 (mp0) REVERT: n 52 SER cc_start: 0.7762 (m) cc_final: 0.7334 (t) REVERT: n 68 LYS cc_start: 0.6872 (mtmp) cc_final: 0.6443 (mtpp) REVERT: o 6 LYS cc_start: 0.7340 (mttt) cc_final: 0.6713 (mmtt) REVERT: o 7 GLN cc_start: 0.7242 (tt0) cc_final: 0.6868 (tt0) REVERT: o 11 GLU cc_start: 0.7319 (pt0) cc_final: 0.7001 (pt0) REVERT: o 38 LYS cc_start: 0.6509 (ptmt) cc_final: 0.6049 (pttp) REVERT: o 68 GLU cc_start: 0.6659 (mm-30) cc_final: 0.5425 (tp30) REVERT: o 89 ARG cc_start: 0.7674 (mtm180) cc_final: 0.7117 (mmt180) REVERT: o 106 LYS cc_start: 0.7725 (mmtt) cc_final: 0.5844 (pttm) REVERT: o 111 LYS cc_start: 0.7357 (ttmt) cc_final: 0.6766 (mttp) REVERT: p 11 ARG cc_start: 0.7942 (tpm170) cc_final: 0.7287 (ttm110) REVERT: p 89 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7178 (mt-10) REVERT: p 112 LYS cc_start: 0.7683 (ttmm) cc_final: 0.7475 (tptm) REVERT: q 6 GLN cc_start: 0.7938 (mt0) cc_final: 0.7194 (tm-30) REVERT: q 18 GLN cc_start: 0.7046 (mt0) cc_final: 0.6737 (mt0) REVERT: q 73 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7554 (mmtt) REVERT: r 1 MET cc_start: 0.5407 (tpp) cc_final: 0.4384 (tmm) REVERT: r 4 ILE cc_start: 0.8063 (mt) cc_final: 0.7845 (mp) REVERT: r 28 LYS cc_start: 0.7699 (mtpt) cc_final: 0.7332 (mtmp) REVERT: r 31 GLN cc_start: 0.7046 (tp40) cc_final: 0.6820 (tt0) REVERT: r 70 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7503 (mttm) REVERT: r 92 ARG cc_start: 0.7596 (mtt180) cc_final: 0.6757 (ttt180) REVERT: s 3 ARG cc_start: 0.6187 (mtt-85) cc_final: 0.5903 (mtm110) REVERT: s 4 GLU cc_start: 0.6783 (tt0) cc_final: 0.6486 (tt0) REVERT: s 18 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7109 (mp0) REVERT: s 33 LYS cc_start: 0.7590 (tttt) cc_final: 0.7042 (mttm) REVERT: s 54 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6793 (mm-30) REVERT: t 7 ARG cc_start: 0.6914 (ttt90) cc_final: 0.6525 (ttp80) REVERT: t 8 ASP cc_start: 0.7359 (m-30) cc_final: 0.7089 (m-30) REVERT: t 18 ASP cc_start: 0.7611 (m-30) cc_final: 0.7368 (m-30) REVERT: t 26 LYS cc_start: 0.7573 (mmmt) cc_final: 0.7094 (mtmt) REVERT: t 27 ASN cc_start: 0.7862 (p0) cc_final: 0.7548 (m110) REVERT: t 47 LYS cc_start: 0.5941 (mmmt) cc_final: 0.5481 (mptp) REVERT: t 79 LYS cc_start: 0.6331 (pttp) cc_final: 0.5969 (mtpp) REVERT: t 87 PHE cc_start: 0.7610 (m-80) cc_final: 0.7385 (m-80) REVERT: t 101 GLU cc_start: 0.7054 (tp30) cc_final: 0.6410 (mm-30) REVERT: u 7 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6723 (mp0) REVERT: u 10 LYS cc_start: 0.6971 (mttp) cc_final: 0.6670 (mppt) REVERT: u 12 GLN cc_start: 0.7100 (pp30) cc_final: 0.6649 (mt0) REVERT: u 48 MET cc_start: 0.8102 (tpt) cc_final: 0.7790 (tpt) REVERT: u 53 LYS cc_start: 0.5768 (mttm) cc_final: 0.5560 (mttm) REVERT: u 68 LYS cc_start: 0.6391 (mptt) cc_final: 0.6131 (mptt) REVERT: u 75 GLN cc_start: 0.8049 (tp40) cc_final: 0.7694 (tp40) REVERT: v 68 LYS cc_start: 0.8057 (tptp) cc_final: 0.7767 (tttp) REVERT: v 70 GLU cc_start: 0.7371 (pt0) cc_final: 0.7162 (pt0) REVERT: v 75 LYS cc_start: 0.7912 (mttt) cc_final: 0.7708 (mttt) REVERT: v 83 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6527 (mt-10) REVERT: w 20 HIS cc_start: 0.7734 (m170) cc_final: 0.6958 (t70) REVERT: w 65 ASP cc_start: 0.6940 (m-30) cc_final: 0.6660 (m-30) REVERT: x 27 ASN cc_start: 0.7588 (m110) cc_final: 0.7373 (m-40) REVERT: y 6 LYS cc_start: 0.7326 (mtmt) cc_final: 0.7106 (mtpp) REVERT: y 37 GLU cc_start: 0.7332 (tt0) cc_final: 0.6907 (pt0) REVERT: y 41 THR cc_start: 0.7544 (m) cc_final: 0.7203 (p) REVERT: z 31 ASP cc_start: 0.8148 (t70) cc_final: 0.7923 (t70) REVERT: z 36 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6949 (mt-10) REVERT: z 37 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7419 (mmtt) REVERT: z 46 ASP cc_start: 0.6773 (t0) cc_final: 0.6460 (t0) REVERT: z 52 ARG cc_start: 0.7187 (ttm170) cc_final: 0.6515 (ttp80) REVERT: G 6 SER cc_start: 0.6854 (m) cc_final: 0.6413 (p) outliers start: 16 outliers final: 6 residues processed: 573 average time/residue: 2.2984 time to fit residues: 1740.3238 Evaluate side-chains 493 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 485 time to evaluate : 4.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 17 MET Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain v residue 10 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 487 optimal weight: 5.9990 chunk 437 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 295 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 452 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 523 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN f 5 HIS g 38 ASN g 115 HIS i 138 GLN k 104 GLN l 3 GLN m 18 GLN n 19 GLN n 38 GLN n 98 GLN o 66 ASN ** t 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 15 ASN x 58 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.379 179.652 48264 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 1.22 % Allowed : 7.23 % Favored : 91.55 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 476 time to evaluate : 4.424 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7344 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8379 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7212 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5498 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6959 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4907 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6922 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7322 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7168 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7404 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7722 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7537 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5856 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7261 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7343 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7295 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7121 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.6985 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7628 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6988 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5850 (mptt) REVERT: u 75 GLN cc_start: 0.8071 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8039 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7319 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6891 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7065 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 30 outliers final: 14 residues processed: 488 average time/residue: 2.3590 time to fit residues: 1516.4016 Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 291 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 436 optimal weight: 2.9990 chunk 356 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 524 optimal weight: 2.9990 chunk 567 optimal weight: 0.9980 chunk 467 optimal weight: 3.9990 chunk 520 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 421 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN k 104 GLN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.41 % Favored : 90.86 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 464 time to evaluate : 4.272 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7211 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5886 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 473 average time/residue: 2.3922 time to fit residues: 1490.0025 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 518 optimal weight: 4.9990 chunk 394 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 352 optimal weight: 7.9990 chunk 526 optimal weight: 0.9990 chunk 557 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 499 optimal weight: 0.4980 chunk 150 optimal weight: 5.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 5.579 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7210 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5842 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 472 average time/residue: 2.3811 time to fit residues: 1475.7567 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 464 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 415 optimal weight: 0.1980 chunk 230 optimal weight: 6.9990 chunk 475 optimal weight: 4.9990 chunk 385 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 284 optimal weight: 6.9990 chunk 500 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 4.365 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7210 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5838 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 472 average time/residue: 2.3436 time to fit residues: 1450.7251 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 187 optimal weight: 6.9990 chunk 502 optimal weight: 0.0070 chunk 110 optimal weight: 6.9990 chunk 327 optimal weight: 0.1980 chunk 137 optimal weight: 5.9990 chunk 558 optimal weight: 5.9990 chunk 463 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 4.695 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7210 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5848 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 472 average time/residue: 2.3951 time to fit residues: 1490.9164 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 538 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 318 optimal weight: 0.5980 chunk 407 optimal weight: 4.9990 chunk 315 optimal weight: 5.9990 chunk 469 optimal weight: 0.3980 chunk 311 optimal weight: 4.9990 chunk 556 optimal weight: 1.9990 chunk 348 optimal weight: 0.6980 chunk 339 optimal weight: 0.8980 chunk 256 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 4.520 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7210 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5887 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 472 average time/residue: 2.3976 time to fit residues: 1488.5858 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 344 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 332 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 353 optimal weight: 0.8980 chunk 378 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 437 optimal weight: 0.6980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 4.256 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7210 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5843 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 472 average time/residue: 2.2672 time to fit residues: 1403.6218 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 505 optimal weight: 2.9990 chunk 532 optimal weight: 3.9990 chunk 486 optimal weight: 0.9980 chunk 518 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 406 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 468 optimal weight: 3.9990 chunk 490 optimal weight: 0.9980 chunk 516 optimal weight: 0.0970 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 4.351 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6229 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7210 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5884 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 472 average time/residue: 2.3552 time to fit residues: 1460.9094 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 340 optimal weight: 5.9990 chunk 548 optimal weight: 0.9990 chunk 334 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 chunk 380 optimal weight: 0.9990 chunk 574 optimal weight: 6.9990 chunk 529 optimal weight: 4.9990 chunk 457 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 353 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 463 time to evaluate : 4.420 Fit side-chains REVERT: 0 33 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6417 (mmtp) REVERT: 0 50 LYS cc_start: 0.7345 (mtmm) cc_final: 0.7002 (mtmt) REVERT: 1 2 LYS cc_start: 0.8178 (tttt) cc_final: 0.7974 (tttt) REVERT: 2 15 LYS cc_start: 0.8091 (mptt) cc_final: 0.7867 (mmtt) REVERT: 3 9 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7728 (mtmm) REVERT: 3 12 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.6228 (ptp90) REVERT: 3 15 LYS cc_start: 0.7998 (mttm) cc_final: 0.7620 (mmtm) REVERT: c 20 VAL cc_start: 0.7317 (t) cc_final: 0.7083 (p) REVERT: c 97 LYS cc_start: 0.7327 (mttt) cc_final: 0.6906 (mmpt) REVERT: c 121 ASP cc_start: 0.6173 (p0) cc_final: 0.5962 (p0) REVERT: c 125 LYS cc_start: 0.7362 (ptmm) cc_final: 0.7074 (pttm) REVERT: c 201 MET cc_start: 0.8309 (ptt) cc_final: 0.8099 (ptt) REVERT: d 7 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7966 (ttmt) REVERT: d 64 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7066 (mt-10) REVERT: d 88 GLU cc_start: 0.6262 (mt-10) cc_final: 0.5777 (mt-10) REVERT: d 89 GLU cc_start: 0.6428 (tp30) cc_final: 0.6116 (mp0) REVERT: d 91 THR cc_start: 0.7329 (t) cc_final: 0.7089 (m) REVERT: d 128 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7512 (mmt180) REVERT: d 184 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6858 (mtt180) REVERT: e 21 ARG cc_start: 0.6548 (ptm160) cc_final: 0.6215 (ptp-170) REVERT: e 141 MET cc_start: 0.5159 (mtp) cc_final: 0.4706 (mtp) REVERT: e 145 ASP cc_start: 0.7282 (t70) cc_final: 0.7059 (t70) REVERT: e 149 ILE cc_start: 0.8382 (mt) cc_final: 0.7964 (mm) REVERT: e 150 THR cc_start: 0.7210 (m) cc_final: 0.6838 (p) REVERT: e 170 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7383 (mtt90) REVERT: e 184 ASP cc_start: 0.7086 (m-30) cc_final: 0.6819 (m-30) REVERT: e 195 GLN cc_start: 0.7125 (mt0) cc_final: 0.6906 (mt0) REVERT: f 69 LYS cc_start: 0.5928 (mtpp) cc_final: 0.5704 (mmtm) REVERT: g 9 VAL cc_start: 0.5522 (m) cc_final: 0.5284 (t) REVERT: g 27 LYS cc_start: 0.5481 (ttpp) cc_final: 0.5170 (ptpp) REVERT: g 74 SER cc_start: 0.6960 (m) cc_final: 0.6377 (p) REVERT: g 99 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6668 (mtmt) REVERT: g 115 HIS cc_start: 0.6876 (t70) cc_final: 0.6610 (t-90) REVERT: h 1 MET cc_start: 0.4906 (ttt) cc_final: 0.4495 (tpp) REVERT: h 11 ASN cc_start: 0.5963 (m-40) cc_final: 0.5357 (t0) REVERT: i 90 GLU cc_start: 0.7681 (pt0) cc_final: 0.7429 (pt0) REVERT: i 95 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6589 (ttm-80) REVERT: i 96 ARG cc_start: 0.6921 (ptt-90) cc_final: 0.5799 (ttp80) REVERT: i 106 LYS cc_start: 0.8308 (tttt) cc_final: 0.8013 (ttmt) REVERT: i 129 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6626 (pt0) REVERT: j 17 ARG cc_start: 0.7323 (mmt90) cc_final: 0.6948 (mmm160) REVERT: j 53 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6803 (mmpt) REVERT: j 98 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6345 (mtp180) REVERT: j 106 GLU cc_start: 0.7063 (mp0) cc_final: 0.6579 (mp0) REVERT: j 121 GLU cc_start: 0.7719 (pt0) cc_final: 0.6738 (tp30) REVERT: k 84 LYS cc_start: 0.6828 (mttt) cc_final: 0.6567 (mttt) REVERT: k 126 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7115 (mtp180) REVERT: k 129 LYS cc_start: 0.7384 (mmtp) cc_final: 0.6903 (mppt) REVERT: k 141 LYS cc_start: 0.7405 (mtmt) cc_final: 0.7173 (mtmm) REVERT: l 28 PHE cc_start: 0.7969 (m-80) cc_final: 0.7735 (m-80) REVERT: l 115 GLU cc_start: 0.7293 (tp30) cc_final: 0.6384 (mm-30) REVERT: l 127 LYS cc_start: 0.7721 (tppt) cc_final: 0.7259 (mttt) REVERT: l 132 THR cc_start: 0.7543 (m) cc_final: 0.7245 (p) REVERT: l 136 MET cc_start: 0.5851 (ttm) cc_final: 0.5477 (ttm) REVERT: m 110 MET cc_start: 0.8677 (mmm) cc_final: 0.8437 (mmm) REVERT: n 13 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6886 (ttm170) REVERT: n 52 SER cc_start: 0.7699 (m) cc_final: 0.7351 (t) REVERT: n 68 LYS cc_start: 0.6777 (mtmp) cc_final: 0.6377 (mtpp) REVERT: o 6 LYS cc_start: 0.7260 (mttt) cc_final: 0.6636 (mmpt) REVERT: o 11 GLU cc_start: 0.7344 (pt0) cc_final: 0.7088 (mt-10) REVERT: o 68 GLU cc_start: 0.6738 (mm-30) cc_final: 0.5447 (tp30) REVERT: o 89 ARG cc_start: 0.7573 (mtm180) cc_final: 0.7020 (mmt180) REVERT: o 106 LYS cc_start: 0.7767 (mmtt) cc_final: 0.5906 (pttm) REVERT: o 111 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6707 (mttp) REVERT: p 11 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7255 (ttm110) REVERT: p 89 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7299 (mt-10) REVERT: p 112 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7415 (tptm) REVERT: q 18 GLN cc_start: 0.7144 (mt0) cc_final: 0.6902 (mt0) REVERT: q 31 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6321 (mm-30) REVERT: q 60 LYS cc_start: 0.7116 (mtmm) cc_final: 0.6854 (mttm) REVERT: q 62 GLU cc_start: 0.7126 (tt0) cc_final: 0.6792 (tt0) REVERT: q 73 LYS cc_start: 0.7776 (mmtp) cc_final: 0.7567 (mtpt) REVERT: r 1 MET cc_start: 0.5587 (tpp) cc_final: 0.4550 (tmm) REVERT: r 4 ILE cc_start: 0.8059 (mt) cc_final: 0.7846 (mp) REVERT: r 28 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7324 (mtmp) REVERT: r 31 GLN cc_start: 0.6871 (tp40) cc_final: 0.6661 (tt0) REVERT: r 70 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7486 (mttm) REVERT: r 92 ARG cc_start: 0.7537 (mtt180) cc_final: 0.6743 (ttp-170) REVERT: s 3 ARG cc_start: 0.6077 (mtt-85) cc_final: 0.5799 (mtm110) REVERT: s 4 GLU cc_start: 0.6790 (tt0) cc_final: 0.6588 (tt0) REVERT: s 18 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7111 (mp0) REVERT: s 33 LYS cc_start: 0.7587 (tttt) cc_final: 0.7380 (mtpm) REVERT: s 54 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6821 (mm-30) REVERT: t 7 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6556 (ttp80) REVERT: t 26 LYS cc_start: 0.7627 (mmmt) cc_final: 0.7388 (mtmt) REVERT: t 37 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6245 (pp20) REVERT: t 101 GLU cc_start: 0.7017 (tp30) cc_final: 0.6769 (mm-30) REVERT: u 10 LYS cc_start: 0.6987 (mttp) cc_final: 0.6681 (mptt) REVERT: u 12 GLN cc_start: 0.7046 (pp30) cc_final: 0.6656 (mt0) REVERT: u 48 MET cc_start: 0.8032 (tpt) cc_final: 0.7739 (tpt) REVERT: u 68 LYS cc_start: 0.6116 (mptt) cc_final: 0.5839 (mptt) REVERT: u 75 GLN cc_start: 0.8072 (tp40) cc_final: 0.7753 (tp40) REVERT: v 68 LYS cc_start: 0.8055 (tptp) cc_final: 0.7824 (tppp) REVERT: v 75 LYS cc_start: 0.7864 (mttt) cc_final: 0.7653 (mttt) REVERT: w 20 HIS cc_start: 0.7722 (m170) cc_final: 0.6922 (t70) REVERT: x 17 GLU cc_start: 0.6960 (tp30) cc_final: 0.6721 (tp30) REVERT: y 6 LYS cc_start: 0.7314 (mtmt) cc_final: 0.7021 (mmmt) REVERT: z 46 ASP cc_start: 0.6864 (t0) cc_final: 0.6660 (t0) REVERT: z 52 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6230 (ttp-110) REVERT: D 6 SER cc_start: 0.1854 (OUTLIER) cc_final: 0.1622 (p) outliers start: 18 outliers final: 14 residues processed: 472 average time/residue: 2.3771 time to fit residues: 1467.4813 Evaluate side-chains 480 residues out of total 2462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 80 SER Chi-restraints excluded: chain e residue 185 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 152 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 106 SER Chi-restraints excluded: chain j residue 98 ARG Chi-restraints excluded: chain o residue 114 LEU Chi-restraints excluded: chain q residue 31 GLU Chi-restraints excluded: chain q residue 33 VAL Chi-restraints excluded: chain t residue 37 GLU Chi-restraints excluded: chain v residue 10 THR Chi-restraints excluded: chain x residue 11 VAL Chi-restraints excluded: chain x residue 16 THR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain I residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 363 optimal weight: 5.9990 chunk 487 optimal weight: 0.4980 chunk 140 optimal weight: 6.9990 chunk 422 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 458 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 470 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN d 42 ASN j 88 ASN l 3 GLN m 18 GLN n 19 GLN n 38 GLN x 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.122646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096030 restraints weight = 84365.915| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.47 r_work: 0.3145 rms_B_bonded: 0.97 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work: 0.2904 rms_B_bonded: 4.01 restraints_weight: 0.1250 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 93403 Z= 0.345 Angle : 0.918 30.535 140295 Z= 0.473 Chirality : 0.047 0.416 17955 Planarity : 0.009 0.157 7053 Dihedral : 23.377 179.652 48260 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 8.49 % Favored : 90.78 % Cbeta Deviations : 0.57 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.32 (0.14), residues: 2953 helix: 0.23 (0.17), residues: 799 sheet: -0.57 (0.19), residues: 647 loop : -0.14 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 248 HIS 0.008 0.002 HIS q 12 PHE 0.033 0.003 PHE p 106 TYR 0.035 0.003 TYR r 38 ARG 0.010 0.001 ARG r 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29213.25 seconds wall clock time: 513 minutes 16.33 seconds (30796.33 seconds total)