Starting phenix.real_space_refine on Sun Mar 24 09:26:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zka_11242/03_2024/6zka_11242_updated.pdb" } resolution = 2.5 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= 0.010 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 279 5.16 5 C 25981 2.51 5 N 6282 2.21 5 O 8224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "v TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Residue "z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40800 Number of models: 1 Model: "" Number of chains: 74 Chain: "A" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 787 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "H" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2494 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 290} Chain breaks: 1 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1273 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 334 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 7, 'TRANS': 32} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "H" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'3PE': 1, 'DCQ': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 276 Unusual residues: {'3PE': 3, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "M" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 188 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "m" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 26 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "K" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "L" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 156 Classifications: {'water': 156} Link IDs: {None: 155} Chain: "M" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 184 Classifications: {'water': 184} Link IDs: {None: 183} Chain: "N" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 133 Classifications: {'water': 133} Link IDs: {None: 132} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "X" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "k" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "l" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "m" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "n" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "p" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "q" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "r" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "s" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "t" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "w" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "x" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "z" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "4" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 21.70, per 1000 atoms: 0.53 Number of scatterers: 40800 At special positions: 0 Unit cell: (155.5, 144.5, 239, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 279 16.00 P 34 15.00 O 8224 8.00 N 6282 7.00 C 25981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.14 Conformation dependent library (CDL) restraints added in 6.9 seconds 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 201 helices and 4 sheets defined 62.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.73 Creating SS restraints... Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.771A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 30 Proline residue: H 12 - end of helix removed outlier: 3.550A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.784A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.698A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.534A pdb=" N ILE J 5 " --> pdb=" O MET J 2 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 46 Processing helix chain 'J' and resid 50 through 58 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.064A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.871A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 55 through 85 removed outlier: 3.588A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 4.356A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 24 removed outlier: 3.729A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.912A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.569A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.884A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 removed outlier: 3.597A pdb=" N TRP L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 193 removed outlier: 4.016A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.986A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.335A pdb=" N ASN L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.539A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.378A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.626A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.606A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.720A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.656A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 Proline residue: L 530 - end of helix removed outlier: 4.588A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.541A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.098A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.729A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 80 removed outlier: 3.596A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 110 removed outlier: 3.638A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.318A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 171 removed outlier: 3.885A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.507A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 181 removed outlier: 3.914A pdb=" N TYR M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.941A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 removed outlier: 4.451A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 235 through 248 removed outlier: 4.249A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 278 removed outlier: 5.183A pdb=" N ALA M 258 " --> pdb=" O ASP M 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR M 259 " --> pdb=" O PHE M 256 " (cutoff:3.500A) Proline residue: M 260 - end of helix removed outlier: 4.323A pdb=" N TRP M 267 " --> pdb=" O LEU M 264 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N MET M 269 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR M 272 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER M 273 " --> pdb=" O ILE M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 3.913A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.881A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.697A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR M 403 " --> pdb=" O MET M 400 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR M 406 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR M 409 " --> pdb=" O TYR M 406 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET M 410 " --> pdb=" O SER M 407 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.009A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 112 through 121 Proline residue: N 116 - end of helix removed outlier: 3.530A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.044A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.609A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.957A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.626A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.630A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.572A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.669A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 45 removed outlier: 4.246A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.610A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 20 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 69 removed outlier: 4.870A pdb=" N LYS X 69 " --> pdb=" O ILE X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 74 removed outlier: 4.208A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU Y 57 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU Y 58 " --> pdb=" O CYS Y 55 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA Y 66 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU Y 67 " --> pdb=" O GLN Y 64 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU Y 68 " --> pdb=" O CYS Y 65 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG Y 71 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN Y 72 " --> pdb=" O PHE Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.541A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 3.830A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 45 removed outlier: 4.351A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 131 through 141 removed outlier: 4.509A pdb=" N GLU k 136 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG k 140 " --> pdb=" O ALA k 137 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.367A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 217 removed outlier: 4.175A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 263 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 272 through 274 No H-bonds generated for 'chain 'k' and resid 272 through 274' Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 47 through 54 removed outlier: 3.953A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 46 removed outlier: 3.608A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 38 removed outlier: 4.183A pdb=" N ARG n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 45 through 52 removed outlier: 4.659A pdb=" N TRP n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG n 51 " --> pdb=" O ASN n 47 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR n 52 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 87 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 16 through 20 Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.805A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 22 removed outlier: 3.571A pdb=" N TYR p 22 " --> pdb=" O PRO p 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 19 through 22' Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.814A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.515A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 91 Processing helix chain 'p' and resid 95 through 116 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 124 Processing helix chain 'q' and resid 129 through 137 Processing helix chain 'r' and resid 5 through 25 Processing helix chain 'r' and resid 68 through 72 Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 73 Processing helix chain 't' and resid 92 through 96 removed outlier: 4.291A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 140 removed outlier: 3.833A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 45 through 48 No H-bonds generated for 'chain 'u' and resid 45 through 48' Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'u' and resid 61 through 64 No H-bonds generated for 'chain 'u' and resid 61 through 64' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 65 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.003A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP w 88 " --> pdb=" O MET w 85 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 34 removed outlier: 3.648A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU y 15 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL y 16 " --> pdb=" O HIS y 13 " (cutoff:3.500A) Proline residue: y 17 - end of helix removed outlier: 4.295A pdb=" N PHE y 22 " --> pdb=" O GLY y 19 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU y 32 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 30 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.981A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing sheet with id= A, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= B, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= C, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.680A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.451A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 1946 hydrogen bonds defined for protein. 5385 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.68 Time building geometry restraints manager: 17.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6477 1.32 - 1.45: 10773 1.45 - 1.58: 22697 1.58 - 1.70: 67 1.70 - 1.83: 505 Bond restraints: 40519 Sorted by residual: bond pdb=" C GLY A 110 " pdb=" N LEU A 111 " ideal model delta sigma weight residual 1.329 1.203 0.126 1.33e-02 5.65e+03 8.94e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.487 1.339 0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" C10 ZMP X 101 " pdb=" S1 ZMP X 101 " ideal model delta sigma weight residual 1.852 1.706 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.00e-02 1.00e+04 4.83e+01 bond pdb=" OA3 CDL W 201 " pdb=" PA1 CDL W 201 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.00e-02 1.00e+04 4.25e+01 ... (remaining 40514 not shown) Histogram of bond angle deviations from ideal: 94.14 - 102.53: 263 102.53 - 110.93: 13742 110.93 - 119.32: 20485 119.32 - 127.72: 19645 127.72 - 136.11: 546 Bond angle restraints: 54681 Sorted by residual: angle pdb=" CA3 CDL L 704 " pdb=" OA5 CDL L 704 " pdb=" PA1 CDL L 704 " ideal model delta sigma weight residual 121.27 129.38 -8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" CA3 CDL Y 201 " pdb=" OA5 CDL Y 201 " pdb=" PA1 CDL Y 201 " ideal model delta sigma weight residual 121.27 127.77 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" CA3 CDL M 503 " pdb=" OA5 CDL M 503 " pdb=" PA1 CDL M 503 " ideal model delta sigma weight residual 121.27 127.59 -6.32 1.00e+00 1.00e+00 4.00e+01 angle pdb=" CA3 CDL V 203 " pdb=" OA5 CDL V 203 " pdb=" PA1 CDL V 203 " ideal model delta sigma weight residual 121.27 126.33 -5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" N HIS L 230 " pdb=" CA HIS L 230 " pdb=" C HIS L 230 " ideal model delta sigma weight residual 109.81 120.71 -10.90 2.21e+00 2.05e-01 2.43e+01 ... (remaining 54676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.55: 23821 30.55 - 61.10: 779 61.10 - 91.66: 42 91.66 - 122.21: 4 122.21 - 152.76: 4 Dihedral angle restraints: 24650 sinusoidal: 10889 harmonic: 13761 Sorted by residual: dihedral pdb=" C5' AMP k 501 " pdb=" O5' AMP k 501 " pdb=" P AMP k 501 " pdb=" O3P AMP k 501 " ideal model delta sinusoidal sigma weight residual 300.00 147.24 152.76 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C2' AMP k 501 " pdb=" C1' AMP k 501 " pdb=" N9 AMP k 501 " pdb=" C4 AMP k 501 " ideal model delta sinusoidal sigma weight residual 91.55 -52.23 143.78 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" CA ARG l 104 " pdb=" C ARG l 104 " pdb=" N PRO l 105 " pdb=" CA PRO l 105 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 24647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 5909 1.044 - 2.088: 0 2.088 - 3.132: 0 3.132 - 4.175: 0 4.175 - 5.219: 5 Chirality restraints: 5914 Sorted by residual: chirality pdb=" CB4 CDL V 204 " pdb=" CB3 CDL V 204 " pdb=" CB6 CDL V 204 " pdb=" OB6 CDL V 204 " both_signs ideal model delta sigma weight residual False -2.57 2.64 -5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" CB4 CDL Y 201 " pdb=" CB3 CDL Y 201 " pdb=" CB6 CDL Y 201 " pdb=" OB6 CDL Y 201 " both_signs ideal model delta sigma weight residual False -2.57 2.57 -5.14 2.00e-01 2.50e+01 6.61e+02 chirality pdb=" CB4 CDL L 704 " pdb=" CB3 CDL L 704 " pdb=" CB6 CDL L 704 " pdb=" OB6 CDL L 704 " both_signs ideal model delta sigma weight residual False -2.57 2.56 -5.14 2.00e-01 2.50e+01 6.60e+02 ... (remaining 5911 not shown) Planarity restraints: 6668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ H 501 " 0.005 2.00e-02 2.50e+03 8.72e-02 2.28e+02 pdb=" C1M DCQ H 501 " 0.153 2.00e-02 2.50e+03 pdb=" C2 DCQ H 501 " -0.044 2.00e-02 2.50e+03 pdb=" C3 DCQ H 501 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DCQ H 501 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DCQ H 501 " -0.057 2.00e-02 2.50e+03 pdb=" C6 DCQ H 501 " -0.045 2.00e-02 2.50e+03 pdb=" C7 DCQ H 501 " 0.019 2.00e-02 2.50e+03 pdb=" O2 DCQ H 501 " -0.068 2.00e-02 2.50e+03 pdb=" O3 DCQ H 501 " -0.021 2.00e-02 2.50e+03 pdb=" O4 DCQ H 501 " 0.207 2.00e-02 2.50e+03 pdb=" O5 DCQ H 501 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 53 " 0.025 2.00e-02 2.50e+03 3.38e-02 2.00e+01 pdb=" CG PHE K 53 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE K 53 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE K 53 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE K 53 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE K 53 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE K 53 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.035 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP A 106 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.018 2.00e-02 2.50e+03 ... (remaining 6665 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3178 2.73 - 3.27: 40703 3.27 - 3.82: 77345 3.82 - 4.36: 96677 4.36 - 4.90: 154686 Nonbonded interactions: 372589 Sorted by model distance: nonbonded pdb=" OE1 GLU K 70 " pdb=" O HOH K 201 " model vdw 2.189 2.440 nonbonded pdb=" OD1 ASP l 4 " pdb=" O HOH l 201 " model vdw 2.262 2.440 nonbonded pdb=" O PHE u 40 " pdb=" OG SER u 44 " model vdw 2.262 2.440 nonbonded pdb=" O PRO 4 6 " pdb=" O HOH 4 501 " model vdw 2.268 2.440 nonbonded pdb=" O ASN v 87 " pdb=" O HOH v 201 " model vdw 2.272 2.440 ... (remaining 372584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.300 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 102.200 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 0.148 40519 Z= 0.555 Angle : 1.025 15.043 54681 Z= 0.530 Chirality : 0.159 5.219 5914 Planarity : 0.008 0.087 6668 Dihedral : 13.826 152.760 15741 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: -2.18 (0.10), residues: 4621 helix: -1.35 (0.08), residues: 2996 sheet: -1.02 (1.05), residues: 20 loop : -1.31 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP A 106 HIS 0.022 0.003 HIS Z 55 PHE 0.073 0.004 PHE K 53 TYR 0.053 0.004 TYR M 309 ARG 0.030 0.002 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1001 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8777 (tp) cc_final: 0.8572 (mm) REVERT: A 82 THR cc_start: 0.8809 (m) cc_final: 0.8265 (p) REVERT: A 85 ASN cc_start: 0.9182 (m-40) cc_final: 0.8979 (m-40) REVERT: H 227 GLU cc_start: 0.8378 (tt0) cc_final: 0.8172 (tt0) REVERT: H 253 GLU cc_start: 0.8350 (mp0) cc_final: 0.8139 (mp0) REVERT: J 1 MET cc_start: 0.6934 (tmt) cc_final: 0.6628 (tmm) REVERT: J 4 TYR cc_start: 0.8880 (m-80) cc_final: 0.8533 (m-80) REVERT: J 101 PHE cc_start: 0.7392 (m-80) cc_final: 0.6988 (m-80) REVERT: J 118 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7773 (mtmt) REVERT: J 122 MET cc_start: 0.7879 (mtp) cc_final: 0.7331 (mtm) REVERT: J 170 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8357 (mm-30) REVERT: K 7 ASN cc_start: 0.9296 (m-40) cc_final: 0.9069 (m110) REVERT: K 91 GLN cc_start: 0.8713 (pm20) cc_final: 0.8510 (pm20) REVERT: L 27 HIS cc_start: 0.5870 (p-80) cc_final: 0.5417 (p90) REVERT: L 484 HIS cc_start: 0.8369 (m90) cc_final: 0.7762 (t70) REVERT: L 512 LYS cc_start: 0.9010 (mptp) cc_final: 0.8800 (mmtp) REVERT: L 514 ASN cc_start: 0.8387 (m110) cc_final: 0.8049 (m-40) REVERT: L 572 LYS cc_start: 0.8223 (tptt) cc_final: 0.7418 (pttm) REVERT: L 581 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7121 (mmtm) REVERT: M 87 GLU cc_start: 0.8659 (tp30) cc_final: 0.8411 (mm-30) REVERT: M 126 LEU cc_start: 0.8683 (mt) cc_final: 0.8330 (mp) REVERT: N 11 MET cc_start: 0.8427 (mmp) cc_final: 0.8108 (mtp) REVERT: N 263 LYS cc_start: 0.8435 (ptpt) cc_final: 0.7616 (mmtm) REVERT: V 85 ASP cc_start: 0.8170 (t70) cc_final: 0.7335 (t0) REVERT: V 134 VAL cc_start: 0.8051 (p) cc_final: 0.7806 (t) REVERT: W 19 LYS cc_start: 0.9158 (mtpm) cc_final: 0.8796 (mmtm) REVERT: W 107 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8454 (tt0) REVERT: W 111 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8504 (mtm110) REVERT: Y 10 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8581 (mp0) REVERT: Y 101 LYS cc_start: 0.8964 (ptmm) cc_final: 0.8756 (ptmt) REVERT: Z 31 TYR cc_start: 0.8725 (m-80) cc_final: 0.8521 (m-80) REVERT: Z 42 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.8162 (ptt90) REVERT: Z 88 GLU cc_start: 0.8823 (tp30) cc_final: 0.8515 (mm-30) REVERT: Z 121 ARG cc_start: 0.8758 (ttm110) cc_final: 0.7983 (ttm-80) REVERT: k 162 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8537 (mt-10) REVERT: k 178 GLU cc_start: 0.8769 (tp30) cc_final: 0.8513 (tm-30) REVERT: k 297 THR cc_start: 0.8838 (m) cc_final: 0.8282 (p) REVERT: l 27 ARG cc_start: 0.9098 (mmt-90) cc_final: 0.8718 (mmt90) REVERT: l 60 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8623 (mm-30) REVERT: m 9 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8229 (tptt) REVERT: m 14 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8350 (mmpt) REVERT: m 46 ARG cc_start: 0.8572 (ptp-110) cc_final: 0.8194 (mtm-85) REVERT: n 19 LYS cc_start: 0.9108 (mttm) cc_final: 0.8833 (mttm) REVERT: n 22 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8870 (mttm) REVERT: n 41 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8384 (ttm-80) REVERT: n 71 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8560 (ttpp) REVERT: p 112 GLU cc_start: 0.9107 (tp30) cc_final: 0.8887 (tp30) REVERT: q 81 ARG cc_start: 0.8678 (tpt90) cc_final: 0.7970 (ttp80) REVERT: q 105 VAL cc_start: 0.9113 (m) cc_final: 0.8888 (t) REVERT: r 8 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8782 (mtpt) REVERT: t 83 GLU cc_start: 0.8755 (mp0) cc_final: 0.8527 (mm-30) REVERT: t 89 SER cc_start: 0.9114 (t) cc_final: 0.8909 (m) REVERT: t 137 LYS cc_start: 0.8573 (pttp) cc_final: 0.8109 (pptt) REVERT: u 58 GLN cc_start: 0.8917 (mm110) cc_final: 0.8707 (mm110) REVERT: v 103 LYS cc_start: 0.8863 (mttt) cc_final: 0.8434 (tmtt) REVERT: v 145 ASP cc_start: 0.8459 (p0) cc_final: 0.8002 (p0) REVERT: w 49 LYS cc_start: 0.8884 (ptpt) cc_final: 0.8529 (mttt) REVERT: w 117 LYS cc_start: 0.8989 (ptpt) cc_final: 0.8778 (ptmt) REVERT: x 29 ILE cc_start: 0.8763 (pp) cc_final: 0.8535 (mt) REVERT: y 8 ARG cc_start: 0.6920 (tpm170) cc_final: 0.6354 (tpm170) REVERT: y 32 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8429 (mt-10) REVERT: z 25 ARG cc_start: 0.8467 (mtp85) cc_final: 0.7517 (ttt180) REVERT: z 59 ARG cc_start: 0.8703 (mmt-90) cc_final: 0.8491 (mmt90) REVERT: 4 9 GLU cc_start: 0.8568 (tt0) cc_final: 0.7896 (mp0) REVERT: 4 29 LYS cc_start: 0.8178 (pttp) cc_final: 0.7847 (mmmt) outliers start: 3 outliers final: 0 residues processed: 1003 average time/residue: 1.7962 time to fit residues: 2134.5934 Evaluate side-chains 762 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 762 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 266 optimal weight: 0.9990 chunk 414 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 83 ASN H 47 GLN H 138 GLN H 317 GLN K 25 HIS K 52 HIS K 83 ASN L 27 HIS ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 199 GLN L 210 ASN L 446 ASN L 524 ASN M 20 ASN M 81 GLN M 175 ASN N 36 ASN N 134 GLN N 222 ASN N 235 ASN V 88 ASN X 33 ASN Z 90 GLN Z 106 GLN Z 114 GLN Z 123 ASN ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN k 180 GLN k 200 GLN k 239 GLN l 6 GLN l 69 GLN n 32 GLN o 12 GLN o 61 GLN p 32 GLN q 23 ASN s 43 GLN u 16 GLN u 24 GLN v 137 ASN w 86 GLN x 36 ASN y 30 ASN z 58 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 40519 Z= 0.274 Angle : 0.615 12.050 54681 Z= 0.307 Chirality : 0.043 0.275 5914 Planarity : 0.005 0.060 6668 Dihedral : 14.848 142.297 6437 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.29 % Allowed : 8.06 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4621 helix: 0.43 (0.09), residues: 3009 sheet: -0.15 (1.10), residues: 20 loop : -0.66 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 106 HIS 0.010 0.001 HIS Z 55 PHE 0.035 0.002 PHE N 292 TYR 0.025 0.002 TYR Z 95 ARG 0.011 0.001 ARG Z 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 798 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8873 (tp) cc_final: 0.8574 (mm) REVERT: A 82 THR cc_start: 0.8846 (m) cc_final: 0.8542 (p) REVERT: A 98 LEU cc_start: 0.9014 (tt) cc_final: 0.8740 (tp) REVERT: H 259 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8492 (p90) REVERT: J 1 MET cc_start: 0.6893 (tmt) cc_final: 0.6585 (tmm) REVERT: J 4 TYR cc_start: 0.8779 (m-80) cc_final: 0.8484 (m-80) REVERT: J 101 PHE cc_start: 0.7400 (m-80) cc_final: 0.6974 (m-80) REVERT: J 118 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7740 (mtmt) REVERT: J 122 MET cc_start: 0.8043 (mtp) cc_final: 0.7423 (mtm) REVERT: K 7 ASN cc_start: 0.9262 (m-40) cc_final: 0.9032 (m110) REVERT: K 91 GLN cc_start: 0.8703 (pm20) cc_final: 0.8491 (pm20) REVERT: L 2 ASN cc_start: 0.8508 (p0) cc_final: 0.7896 (m-40) REVERT: L 484 HIS cc_start: 0.8477 (m90) cc_final: 0.7969 (t70) REVERT: L 514 ASN cc_start: 0.8323 (m110) cc_final: 0.8047 (m-40) REVERT: L 572 LYS cc_start: 0.8054 (tptt) cc_final: 0.7293 (pttm) REVERT: L 581 LYS cc_start: 0.8145 (mtmm) cc_final: 0.7156 (mmtm) REVERT: M 126 LEU cc_start: 0.8597 (mt) cc_final: 0.8286 (mp) REVERT: N 11 MET cc_start: 0.8443 (mmp) cc_final: 0.8076 (mtp) REVERT: N 268 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7757 (tp40) REVERT: V 85 ASP cc_start: 0.8143 (t70) cc_final: 0.7352 (t0) REVERT: W 19 LYS cc_start: 0.9185 (mtpm) cc_final: 0.8833 (mmtm) REVERT: W 107 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8682 (tt0) REVERT: X 9 GLU cc_start: 0.8810 (tt0) cc_final: 0.8482 (pm20) REVERT: Y 10 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8570 (mp0) REVERT: Y 101 LYS cc_start: 0.9025 (ptmm) cc_final: 0.8707 (ptmt) REVERT: Y 154 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: Z 31 TYR cc_start: 0.8759 (m-80) cc_final: 0.8527 (m-80) REVERT: Z 88 GLU cc_start: 0.8822 (tp30) cc_final: 0.8528 (mm-30) REVERT: Z 121 ARG cc_start: 0.8744 (ttm110) cc_final: 0.7940 (ttm-80) REVERT: k 162 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8541 (mt-10) REVERT: k 297 THR cc_start: 0.8851 (m) cc_final: 0.8344 (p) REVERT: l 27 ARG cc_start: 0.9102 (mmt-90) cc_final: 0.8748 (mpt-90) REVERT: l 60 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8593 (mm-30) REVERT: m 9 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8205 (tptt) REVERT: m 14 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8362 (mmpt) REVERT: n 19 LYS cc_start: 0.9013 (mttm) cc_final: 0.8741 (mttm) REVERT: n 22 LYS cc_start: 0.9081 (mtmm) cc_final: 0.8863 (mttp) REVERT: n 41 ARG cc_start: 0.8629 (ttp80) cc_final: 0.8337 (ttt-90) REVERT: n 71 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8560 (ttpp) REVERT: o 77 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8896 (mtmm) REVERT: p 112 GLU cc_start: 0.9101 (tp30) cc_final: 0.8822 (tp30) REVERT: q 81 ARG cc_start: 0.8655 (tpt90) cc_final: 0.8132 (ttp80) REVERT: r 8 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8687 (mtpt) REVERT: r 121 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: s 83 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: t 134 ARG cc_start: 0.8694 (ttp-110) cc_final: 0.8449 (ttp-110) REVERT: t 137 LYS cc_start: 0.8510 (pttp) cc_final: 0.8043 (pptt) REVERT: u 45 ASP cc_start: 0.8222 (m-30) cc_final: 0.7839 (m-30) REVERT: v 103 LYS cc_start: 0.8776 (mttt) cc_final: 0.8427 (tmtt) REVERT: v 142 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.7409 (mpt180) REVERT: v 145 ASP cc_start: 0.8420 (p0) cc_final: 0.7887 (p0) REVERT: w 49 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8501 (mttt) REVERT: y 8 ARG cc_start: 0.6873 (tpm170) cc_final: 0.6326 (tpm170) REVERT: y 32 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8414 (mt-10) REVERT: z 25 ARG cc_start: 0.8407 (mtp85) cc_final: 0.7551 (tmt170) REVERT: 4 9 GLU cc_start: 0.8673 (tt0) cc_final: 0.7965 (mp0) REVERT: 4 29 LYS cc_start: 0.8184 (pttp) cc_final: 0.7902 (mmmt) outliers start: 95 outliers final: 25 residues processed: 842 average time/residue: 1.7721 time to fit residues: 1774.4584 Evaluate side-chains 777 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 745 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 154 GLU Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 169 THR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 86 SER Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain v residue 18 GLU Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain z residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 281 optimal weight: 0.0270 chunk 114 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 448 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 chunk 411 optimal weight: 0.0980 chunk 141 optimal weight: 6.9990 chunk 332 optimal weight: 30.0000 overall best weight: 2.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN H 47 GLN H 194 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN X 33 ASN Z 129 GLN Z 133 GLN k 89 ASN k 180 GLN l 6 GLN l 69 GLN l 96 HIS n 32 GLN p 32 GLN q 53 ASN q 89 ASN t 17 GLN u 16 GLN u 24 GLN v 56 GLN w 86 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40519 Z= 0.192 Angle : 0.547 11.106 54681 Z= 0.272 Chirality : 0.040 0.188 5914 Planarity : 0.004 0.049 6668 Dihedral : 14.078 141.226 6437 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.51 % Allowed : 8.95 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 4621 helix: 1.12 (0.09), residues: 3008 sheet: 0.74 (1.11), residues: 20 loop : -0.32 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 121 HIS 0.007 0.001 HIS Z 55 PHE 0.032 0.002 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.009 0.000 ARG s 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 785 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8870 (tp) cc_final: 0.8567 (mm) REVERT: A 82 THR cc_start: 0.8782 (m) cc_final: 0.8322 (p) REVERT: A 98 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8695 (tp) REVERT: H 259 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8397 (p90) REVERT: J 1 MET cc_start: 0.6916 (tmt) cc_final: 0.6604 (tmm) REVERT: J 4 TYR cc_start: 0.8761 (m-80) cc_final: 0.8468 (m-80) REVERT: J 99 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5959 (mpp) REVERT: J 101 PHE cc_start: 0.7320 (m-80) cc_final: 0.6898 (m-80) REVERT: J 118 LYS cc_start: 0.8042 (mtpt) cc_final: 0.7697 (mtmt) REVERT: J 122 MET cc_start: 0.8074 (mtp) cc_final: 0.7484 (mtm) REVERT: K 7 ASN cc_start: 0.9230 (m-40) cc_final: 0.9011 (m110) REVERT: L 2 ASN cc_start: 0.8435 (p0) cc_final: 0.7910 (m-40) REVERT: L 27 HIS cc_start: 0.5490 (p90) cc_final: 0.5271 (p90) REVERT: L 484 HIS cc_start: 0.8455 (m90) cc_final: 0.7958 (t70) REVERT: L 503 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7934 (mp0) REVERT: L 514 ASN cc_start: 0.8286 (m110) cc_final: 0.8041 (m-40) REVERT: L 572 LYS cc_start: 0.8092 (tptt) cc_final: 0.7337 (pttm) REVERT: L 581 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7194 (mmtm) REVERT: M 126 LEU cc_start: 0.8558 (mt) cc_final: 0.8259 (mp) REVERT: N 11 MET cc_start: 0.8425 (mmp) cc_final: 0.8078 (mtp) REVERT: N 268 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7640 (tp40) REVERT: V 85 ASP cc_start: 0.8154 (t70) cc_final: 0.7343 (t0) REVERT: W 19 LYS cc_start: 0.9176 (mtpm) cc_final: 0.8830 (mmtm) REVERT: W 107 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8713 (tt0) REVERT: X 9 GLU cc_start: 0.8828 (tt0) cc_final: 0.8474 (pm20) REVERT: Y 10 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8576 (mp0) REVERT: Y 101 LYS cc_start: 0.9010 (ptmm) cc_final: 0.8766 (pttt) REVERT: Z 31 TYR cc_start: 0.8755 (m-80) cc_final: 0.8528 (m-80) REVERT: Z 66 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8652 (mm-30) REVERT: Z 88 GLU cc_start: 0.8786 (tp30) cc_final: 0.8510 (mm-30) REVERT: Z 121 ARG cc_start: 0.8727 (ttm110) cc_final: 0.7936 (ttm-80) REVERT: Z 129 GLN cc_start: 0.8934 (tm130) cc_final: 0.8712 (tm-30) REVERT: k 162 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8500 (mt-10) REVERT: k 185 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8618 (mppt) REVERT: k 297 THR cc_start: 0.8774 (m) cc_final: 0.8261 (p) REVERT: l 27 ARG cc_start: 0.9097 (mmt-90) cc_final: 0.8744 (mpt-90) REVERT: l 60 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8560 (mm-30) REVERT: l 73 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8790 (ttpp) REVERT: m 9 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8152 (tptt) REVERT: m 14 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8366 (mmpt) REVERT: m 15 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8628 (mm-30) REVERT: m 46 ARG cc_start: 0.8799 (ttm110) cc_final: 0.8208 (mtm-85) REVERT: n 41 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8292 (ttt-90) REVERT: n 71 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8565 (ttpp) REVERT: o 77 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8866 (mtmm) REVERT: p 30 LYS cc_start: 0.9016 (mttp) cc_final: 0.8767 (ttpp) REVERT: p 112 GLU cc_start: 0.9034 (tp30) cc_final: 0.8804 (tp30) REVERT: p 113 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8706 (tttm) REVERT: q 81 ARG cc_start: 0.8795 (tpt90) cc_final: 0.8359 (ttp80) REVERT: r 8 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8685 (mtpt) REVERT: r 102 ARG cc_start: 0.8805 (ttm-80) cc_final: 0.8557 (mtt180) REVERT: r 121 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: s 17 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: s 83 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: t 29 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6135 (mmm160) REVERT: t 134 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8448 (ttp-110) REVERT: t 137 LYS cc_start: 0.8513 (pttp) cc_final: 0.8027 (pptt) REVERT: u 45 ASP cc_start: 0.8237 (m-30) cc_final: 0.7847 (m-30) REVERT: v 103 LYS cc_start: 0.8731 (mttt) cc_final: 0.8423 (tmtt) REVERT: v 142 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.7425 (mpt180) REVERT: v 145 ASP cc_start: 0.8432 (p0) cc_final: 0.7891 (p0) REVERT: w 49 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8495 (mttt) REVERT: y 8 ARG cc_start: 0.6836 (tpm170) cc_final: 0.6309 (tpm170) REVERT: y 32 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8396 (mt-10) REVERT: z 25 ARG cc_start: 0.8361 (mtp85) cc_final: 0.7517 (ttt180) REVERT: 4 9 GLU cc_start: 0.8670 (tt0) cc_final: 0.7922 (mp0) REVERT: 4 29 LYS cc_start: 0.8187 (pttp) cc_final: 0.7925 (mmmt) outliers start: 104 outliers final: 30 residues processed: 833 average time/residue: 1.7809 time to fit residues: 1763.8983 Evaluate side-chains 793 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 751 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 73 LYS Chi-restraints excluded: chain l residue 80 ARG Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain m residue 15 GLU Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 29 ARG Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain y residue 29 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 416 optimal weight: 0.7980 chunk 440 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN H 47 GLN H 171 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN L 270 ASN ** L 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 ASN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 130 GLN k 89 ASN k 180 GLN n 32 GLN p 32 GLN u 16 GLN u 58 GLN v 56 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40519 Z= 0.226 Angle : 0.560 11.131 54681 Z= 0.277 Chirality : 0.041 0.189 5914 Planarity : 0.004 0.048 6668 Dihedral : 13.737 142.010 6437 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.75 % Allowed : 9.65 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.12), residues: 4621 helix: 1.40 (0.09), residues: 3005 sheet: 1.32 (1.13), residues: 20 loop : -0.12 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 121 HIS 0.007 0.001 HIS Z 55 PHE 0.031 0.002 PHE N 292 TYR 0.022 0.002 TYR n 85 ARG 0.006 0.000 ARG q 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 764 time to evaluate : 4.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8874 (tp) cc_final: 0.8553 (mm) REVERT: A 82 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8447 (p) REVERT: A 98 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8699 (tp) REVERT: H 259 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8462 (p90) REVERT: J 1 MET cc_start: 0.6932 (tmt) cc_final: 0.6643 (tmm) REVERT: J 4 TYR cc_start: 0.8800 (m-80) cc_final: 0.8528 (m-80) REVERT: J 99 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5940 (mpp) REVERT: J 101 PHE cc_start: 0.7311 (m-80) cc_final: 0.6925 (m-80) REVERT: J 118 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7683 (mtmt) REVERT: J 122 MET cc_start: 0.8048 (mtp) cc_final: 0.7376 (mtm) REVERT: J 124 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: K 7 ASN cc_start: 0.9249 (m-40) cc_final: 0.9004 (m110) REVERT: L 2 ASN cc_start: 0.8371 (p0) cc_final: 0.7860 (m-40) REVERT: L 27 HIS cc_start: 0.5531 (p90) cc_final: 0.5286 (p90) REVERT: L 484 HIS cc_start: 0.8491 (m90) cc_final: 0.7996 (t70) REVERT: L 503 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7925 (mp0) REVERT: L 514 ASN cc_start: 0.8282 (m110) cc_final: 0.8056 (m-40) REVERT: L 572 LYS cc_start: 0.8071 (tptt) cc_final: 0.7346 (pttm) REVERT: L 581 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7246 (mmtm) REVERT: L 601 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7783 (tt) REVERT: M 126 LEU cc_start: 0.8614 (mt) cc_final: 0.8317 (mp) REVERT: M 378 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: N 11 MET cc_start: 0.8428 (mmp) cc_final: 0.8069 (mtp) REVERT: N 268 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7732 (tp40) REVERT: N 321 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8309 (mtpp) REVERT: V 85 ASP cc_start: 0.8145 (t70) cc_final: 0.7271 (t0) REVERT: W 19 LYS cc_start: 0.9190 (mtpm) cc_final: 0.8834 (mmtm) REVERT: W 107 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8755 (tt0) REVERT: X 9 GLU cc_start: 0.8841 (tt0) cc_final: 0.8463 (pm20) REVERT: Y 10 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8578 (mp0) REVERT: Z 27 ASN cc_start: 0.8754 (p0) cc_final: 0.8528 (p0) REVERT: Z 31 TYR cc_start: 0.8768 (m-80) cc_final: 0.8567 (m-80) REVERT: Z 66 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8662 (mm-30) REVERT: Z 88 GLU cc_start: 0.8794 (tp30) cc_final: 0.8520 (mm-30) REVERT: Z 121 ARG cc_start: 0.8725 (ttm110) cc_final: 0.7930 (ttm-80) REVERT: k 162 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8492 (mt-10) REVERT: k 213 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: k 297 THR cc_start: 0.8816 (m) cc_final: 0.8316 (p) REVERT: l 27 ARG cc_start: 0.9094 (mmt-90) cc_final: 0.8748 (mpt-90) REVERT: l 60 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8600 (mm-30) REVERT: l 73 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8796 (ttpp) REVERT: m 9 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8132 (tptt) REVERT: m 14 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8373 (mmpt) REVERT: m 46 ARG cc_start: 0.8808 (ttm110) cc_final: 0.8283 (mtm-85) REVERT: n 34 LYS cc_start: 0.9102 (mttt) cc_final: 0.8719 (tttt) REVERT: n 41 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8251 (ttt-90) REVERT: n 71 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8556 (ttpp) REVERT: o 77 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8865 (mtmm) REVERT: p 30 LYS cc_start: 0.9020 (mttp) cc_final: 0.8775 (ttpp) REVERT: p 112 GLU cc_start: 0.9023 (tp30) cc_final: 0.8791 (tp30) REVERT: p 113 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8787 (tttm) REVERT: q 81 ARG cc_start: 0.8841 (tpt90) cc_final: 0.8378 (ttp80) REVERT: r 8 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8678 (mtpt) REVERT: r 102 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8604 (mtt180) REVERT: r 121 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: s 83 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: t 29 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.6194 (mmm160) REVERT: t 134 ARG cc_start: 0.8692 (ttp-110) cc_final: 0.8486 (ttp-110) REVERT: t 137 LYS cc_start: 0.8542 (pttp) cc_final: 0.8004 (pptt) REVERT: u 45 ASP cc_start: 0.8306 (m-30) cc_final: 0.7827 (m-30) REVERT: u 58 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8691 (mm110) REVERT: v 103 LYS cc_start: 0.8726 (mttt) cc_final: 0.8375 (tmtt) REVERT: v 142 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.7552 (mpt90) REVERT: v 145 ASP cc_start: 0.8433 (p0) cc_final: 0.7873 (p0) REVERT: w 49 LYS cc_start: 0.8910 (ptpt) cc_final: 0.8488 (mttt) REVERT: y 8 ARG cc_start: 0.6833 (tpm170) cc_final: 0.6312 (tpm170) REVERT: y 32 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8411 (mt-10) REVERT: z 25 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7534 (ttt180) REVERT: 4 9 GLU cc_start: 0.8670 (tt0) cc_final: 0.7898 (mp0) REVERT: 4 29 LYS cc_start: 0.8150 (pttp) cc_final: 0.7900 (mmmt) outliers start: 114 outliers final: 42 residues processed: 818 average time/residue: 1.7816 time to fit residues: 1733.0877 Evaluate side-chains 795 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 736 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain N residue 268 GLN Chi-restraints excluded: chain N residue 321 LYS Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 73 LYS Chi-restraints excluded: chain l residue 80 ARG Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 86 SER Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 29 ARG Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 7 ASP Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain y residue 29 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 304 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 225 optimal weight: 0.8980 chunk 395 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN H 171 GLN H 194 ASN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN L 447 ASN M 20 ASN N 63 GLN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN k 180 GLN n 32 GLN p 32 GLN u 16 GLN v 56 GLN x 36 ASN z 58 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 40519 Z= 0.146 Angle : 0.504 9.981 54681 Z= 0.249 Chirality : 0.038 0.179 5914 Planarity : 0.004 0.042 6668 Dihedral : 13.118 139.963 6437 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.15 % Allowed : 10.57 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.59 (0.13), residues: 4621 helix: 1.65 (0.10), residues: 3003 sheet: 1.71 (1.15), residues: 20 loop : 0.00 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 121 HIS 0.006 0.001 HIS M 319 PHE 0.030 0.001 PHE N 292 TYR 0.022 0.001 TYR L 422 ARG 0.011 0.000 ARG s 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 774 time to evaluate : 4.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8875 (tp) cc_final: 0.8558 (mm) REVERT: A 98 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8534 (tp) REVERT: H 259 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8319 (p90) REVERT: J 1 MET cc_start: 0.6945 (tmt) cc_final: 0.6644 (tmm) REVERT: J 4 TYR cc_start: 0.8745 (m-80) cc_final: 0.8435 (m-80) REVERT: J 99 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5958 (mpp) REVERT: J 101 PHE cc_start: 0.7257 (m-80) cc_final: 0.6854 (m-80) REVERT: J 118 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7641 (mtmt) REVERT: J 122 MET cc_start: 0.7966 (mtp) cc_final: 0.7377 (mtm) REVERT: L 2 ASN cc_start: 0.8306 (p0) cc_final: 0.7859 (m-40) REVERT: L 27 HIS cc_start: 0.5534 (p90) cc_final: 0.5238 (p90) REVERT: L 29 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: L 484 HIS cc_start: 0.8469 (m90) cc_final: 0.7984 (t70) REVERT: L 503 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7861 (mp0) REVERT: L 514 ASN cc_start: 0.8249 (m110) cc_final: 0.8022 (m-40) REVERT: L 572 LYS cc_start: 0.8051 (tptt) cc_final: 0.7352 (pttp) REVERT: L 581 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7186 (mmtm) REVERT: L 601 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7761 (tt) REVERT: M 126 LEU cc_start: 0.8543 (mt) cc_final: 0.8243 (mp) REVERT: N 11 MET cc_start: 0.8408 (mmp) cc_final: 0.8059 (mtp) REVERT: N 139 MET cc_start: 0.9133 (mmm) cc_final: 0.8917 (mmt) REVERT: V 85 ASP cc_start: 0.8108 (t70) cc_final: 0.7281 (t0) REVERT: W 19 LYS cc_start: 0.9171 (mtpm) cc_final: 0.8822 (mmtm) REVERT: W 107 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8766 (tt0) REVERT: X 9 GLU cc_start: 0.8844 (tt0) cc_final: 0.8476 (pm20) REVERT: Y 10 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8563 (mp0) REVERT: Z 31 TYR cc_start: 0.8760 (m-80) cc_final: 0.8522 (m-80) REVERT: Z 66 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8668 (mm-30) REVERT: Z 88 GLU cc_start: 0.8712 (tp30) cc_final: 0.8477 (mm-30) REVERT: Z 121 ARG cc_start: 0.8683 (ttm110) cc_final: 0.7929 (ttm-80) REVERT: k 162 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8423 (mt-10) REVERT: k 185 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8625 (mppt) REVERT: k 213 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: l 27 ARG cc_start: 0.9101 (mmt-90) cc_final: 0.8764 (mpt-90) REVERT: l 60 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8602 (mm-30) REVERT: m 9 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8141 (tptt) REVERT: m 14 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8343 (mmpt) REVERT: m 46 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8046 (mtm110) REVERT: n 34 LYS cc_start: 0.9095 (mttt) cc_final: 0.8725 (tttt) REVERT: n 41 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8282 (ttt-90) REVERT: n 71 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8529 (ttpp) REVERT: o 77 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8827 (mtmm) REVERT: p 30 LYS cc_start: 0.9015 (mttp) cc_final: 0.8772 (ttpp) REVERT: p 112 GLU cc_start: 0.8970 (tp30) cc_final: 0.8691 (tp30) REVERT: p 113 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8828 (tttm) REVERT: q 81 ARG cc_start: 0.8800 (tpt90) cc_final: 0.8434 (ttp80) REVERT: r 8 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8667 (mtpt) REVERT: r 102 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8522 (mtt180) REVERT: r 121 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: s 83 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: u 45 ASP cc_start: 0.8226 (m-30) cc_final: 0.7732 (m-30) REVERT: u 58 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8697 (mm110) REVERT: v 103 LYS cc_start: 0.8693 (mttt) cc_final: 0.8390 (tmtt) REVERT: v 142 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.7530 (mpt90) REVERT: v 145 ASP cc_start: 0.8432 (p0) cc_final: 0.7877 (p0) REVERT: w 49 LYS cc_start: 0.8886 (ptpt) cc_final: 0.8495 (mttt) REVERT: w 56 TRP cc_start: 0.8675 (t60) cc_final: 0.8368 (t-100) REVERT: w 70 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8337 (mp) REVERT: y 8 ARG cc_start: 0.6823 (tpm170) cc_final: 0.6303 (tpm170) REVERT: y 32 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8407 (mt-10) REVERT: z 25 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7549 (ttt180) REVERT: 4 9 GLU cc_start: 0.8658 (tt0) cc_final: 0.7893 (mp0) REVERT: 4 29 LYS cc_start: 0.8153 (pttp) cc_final: 0.7912 (mmmt) outliers start: 89 outliers final: 30 residues processed: 818 average time/residue: 1.7655 time to fit residues: 1722.4376 Evaluate side-chains 776 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 735 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 18 THR Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain y residue 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 3.9990 chunk 396 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 441 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 85 ASN H 5 ASN H 47 GLN H 171 GLN ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 ASN L 447 ASN M 20 ASN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN k 180 GLN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 ASN n 32 GLN p 32 GLN p 78 ASN t 140 GLN u 16 GLN v 56 GLN z 58 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40519 Z= 0.213 Angle : 0.548 11.106 54681 Z= 0.270 Chirality : 0.040 0.211 5914 Planarity : 0.004 0.043 6668 Dihedral : 13.061 142.159 6437 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.29 % Allowed : 10.86 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.68 (0.13), residues: 4621 helix: 1.67 (0.10), residues: 3018 sheet: 2.13 (1.20), residues: 20 loop : 0.13 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 121 HIS 0.006 0.001 HIS M 30 PHE 0.030 0.002 PHE N 292 TYR 0.022 0.001 TYR n 85 ARG 0.011 0.000 ARG t 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 740 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8878 (tp) cc_final: 0.8544 (mm) REVERT: A 82 THR cc_start: 0.8834 (m) cc_final: 0.8509 (p) REVERT: A 98 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8606 (tp) REVERT: A 109 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8176 (mtmm) REVERT: H 259 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8379 (p90) REVERT: J 1 MET cc_start: 0.6965 (tmt) cc_final: 0.6661 (tmm) REVERT: J 4 TYR cc_start: 0.8780 (m-80) cc_final: 0.8470 (m-80) REVERT: J 99 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.5931 (mpp) REVERT: J 101 PHE cc_start: 0.7264 (m-80) cc_final: 0.6879 (m-80) REVERT: J 118 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7662 (mtmt) REVERT: J 122 MET cc_start: 0.7950 (mtp) cc_final: 0.7428 (mtm) REVERT: L 2 ASN cc_start: 0.8332 (p0) cc_final: 0.7908 (m-40) REVERT: L 27 HIS cc_start: 0.5597 (p90) cc_final: 0.5303 (p90) REVERT: L 29 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: L 484 HIS cc_start: 0.8486 (m90) cc_final: 0.7992 (t70) REVERT: L 503 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7858 (mp0) REVERT: L 514 ASN cc_start: 0.8248 (m110) cc_final: 0.8032 (m-40) REVERT: L 572 LYS cc_start: 0.8076 (tptt) cc_final: 0.7362 (pttp) REVERT: L 581 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7243 (mmtm) REVERT: L 601 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7784 (tt) REVERT: M 86 LYS cc_start: 0.8626 (mttp) cc_final: 0.8322 (mmtm) REVERT: M 126 LEU cc_start: 0.8611 (mt) cc_final: 0.8293 (mp) REVERT: M 168 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8523 (tp40) REVERT: N 11 MET cc_start: 0.8393 (mmp) cc_final: 0.8037 (mtp) REVERT: N 139 MET cc_start: 0.9195 (mmm) cc_final: 0.8949 (mmt) REVERT: V 85 ASP cc_start: 0.8116 (t70) cc_final: 0.7281 (t0) REVERT: W 19 LYS cc_start: 0.9185 (mtpm) cc_final: 0.8837 (mmtm) REVERT: W 107 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8761 (tt0) REVERT: X 9 GLU cc_start: 0.8856 (tt0) cc_final: 0.8471 (pm20) REVERT: Z 31 TYR cc_start: 0.8768 (m-80) cc_final: 0.8537 (m-80) REVERT: Z 66 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8665 (mm-30) REVERT: Z 88 GLU cc_start: 0.8745 (tp30) cc_final: 0.8505 (mm-30) REVERT: Z 121 ARG cc_start: 0.8692 (ttm110) cc_final: 0.7926 (ttm-80) REVERT: k 162 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8447 (mt-10) REVERT: k 185 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8622 (mppt) REVERT: k 213 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: k 250 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8191 (p0) REVERT: l 27 ARG cc_start: 0.9098 (mmt-90) cc_final: 0.8777 (mpt-90) REVERT: l 56 LYS cc_start: 0.8864 (mtpm) cc_final: 0.8586 (tttp) REVERT: l 60 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8589 (mm-30) REVERT: m 9 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8136 (tptt) REVERT: m 14 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8355 (mmpt) REVERT: m 46 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8025 (mtm110) REVERT: n 34 LYS cc_start: 0.9092 (mttt) cc_final: 0.8720 (tttt) REVERT: n 41 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8249 (ttt-90) REVERT: n 48 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: n 71 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8543 (ttpp) REVERT: o 77 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8858 (mtmm) REVERT: p 30 LYS cc_start: 0.9006 (mttp) cc_final: 0.8771 (ttpp) REVERT: p 112 GLU cc_start: 0.8994 (tp30) cc_final: 0.8709 (tp30) REVERT: p 113 LYS cc_start: 0.9109 (ttpt) cc_final: 0.8858 (tttm) REVERT: q 81 ARG cc_start: 0.8851 (tpt90) cc_final: 0.8425 (ttp80) REVERT: q 84 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: r 8 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8661 (mtpt) REVERT: r 102 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8525 (mtt180) REVERT: r 121 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: s 83 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: s 115 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7880 (mt-10) REVERT: u 18 THR cc_start: 0.8490 (m) cc_final: 0.8035 (p) REVERT: u 45 ASP cc_start: 0.8258 (m-30) cc_final: 0.7762 (m-30) REVERT: u 58 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8695 (mm110) REVERT: v 103 LYS cc_start: 0.8689 (mttt) cc_final: 0.8387 (tmtt) REVERT: v 142 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.7511 (mpt90) REVERT: v 145 ASP cc_start: 0.8450 (p0) cc_final: 0.7890 (p0) REVERT: w 49 LYS cc_start: 0.8900 (ptpt) cc_final: 0.8503 (mttt) REVERT: w 70 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8360 (mp) REVERT: y 8 ARG cc_start: 0.6830 (tpm170) cc_final: 0.6306 (tpm170) REVERT: y 32 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8420 (mt-10) REVERT: z 25 ARG cc_start: 0.8346 (mtp85) cc_final: 0.7570 (ttt180) REVERT: 4 9 GLU cc_start: 0.8691 (tt0) cc_final: 0.8411 (tt0) REVERT: 4 29 LYS cc_start: 0.8127 (pttp) cc_final: 0.7895 (mmmt) outliers start: 95 outliers final: 40 residues processed: 788 average time/residue: 1.7985 time to fit residues: 1687.9881 Evaluate side-chains 780 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 725 time to evaluate : 4.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 168 GLN Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 126 LYS Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 48 GLU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 84 GLN Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 7 ASP Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 0.0270 chunk 49 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 439 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 194 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 91 ASN Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 143 HIS k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 GLN p 32 GLN t 123 GLN u 16 GLN v 56 GLN z 58 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40519 Z= 0.280 Angle : 0.587 11.743 54681 Z= 0.290 Chirality : 0.043 0.228 5914 Planarity : 0.004 0.046 6668 Dihedral : 13.254 145.986 6437 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.44 % Allowed : 10.98 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.63 (0.13), residues: 4621 helix: 1.61 (0.09), residues: 3010 sheet: 2.24 (1.23), residues: 20 loop : 0.18 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP H 121 HIS 0.007 0.001 HIS M 30 PHE 0.027 0.002 PHE N 292 TYR 0.024 0.002 TYR n 85 ARG 0.013 0.001 ARG t 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 741 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8878 (tp) cc_final: 0.8532 (mm) REVERT: A 82 THR cc_start: 0.8834 (m) cc_final: 0.8519 (p) REVERT: A 98 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8650 (tp) REVERT: A 109 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8199 (mtmm) REVERT: H 259 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8467 (p90) REVERT: J 1 MET cc_start: 0.7042 (tmt) cc_final: 0.6724 (tmm) REVERT: J 4 TYR cc_start: 0.8829 (m-80) cc_final: 0.8550 (m-80) REVERT: J 99 MET cc_start: 0.6541 (OUTLIER) cc_final: 0.5994 (mpp) REVERT: J 101 PHE cc_start: 0.7291 (m-80) cc_final: 0.6922 (m-80) REVERT: J 118 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7674 (mtmt) REVERT: J 122 MET cc_start: 0.7980 (mtp) cc_final: 0.7414 (mtm) REVERT: L 2 ASN cc_start: 0.8405 (p0) cc_final: 0.7952 (m-40) REVERT: L 27 HIS cc_start: 0.5667 (p90) cc_final: 0.5223 (p90) REVERT: L 29 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: L 484 HIS cc_start: 0.8457 (m90) cc_final: 0.7951 (t70) REVERT: L 503 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7863 (mp0) REVERT: L 514 ASN cc_start: 0.8264 (m110) cc_final: 0.8038 (m-40) REVERT: L 572 LYS cc_start: 0.8087 (tptt) cc_final: 0.7363 (pttm) REVERT: L 581 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7302 (mmtm) REVERT: L 601 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7834 (tt) REVERT: M 86 LYS cc_start: 0.8615 (mttp) cc_final: 0.8308 (mmtm) REVERT: M 126 LEU cc_start: 0.8633 (mt) cc_final: 0.8308 (mp) REVERT: N 11 MET cc_start: 0.8412 (mmp) cc_final: 0.8048 (mtp) REVERT: V 85 ASP cc_start: 0.8136 (t70) cc_final: 0.7859 (t0) REVERT: W 19 LYS cc_start: 0.9194 (mtpm) cc_final: 0.8911 (mppt) REVERT: W 107 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8758 (tt0) REVERT: X 9 GLU cc_start: 0.8871 (tt0) cc_final: 0.8457 (pm20) REVERT: Z 66 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8657 (mm-30) REVERT: Z 88 GLU cc_start: 0.8785 (tp30) cc_final: 0.8519 (mm-30) REVERT: Z 121 ARG cc_start: 0.8722 (ttm110) cc_final: 0.7919 (ttm-80) REVERT: k 162 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8463 (mt-10) REVERT: k 185 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8589 (mppt) REVERT: k 213 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8291 (pt0) REVERT: k 250 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8214 (p0) REVERT: l 27 ARG cc_start: 0.9101 (mmt-90) cc_final: 0.8782 (mpt-90) REVERT: l 56 LYS cc_start: 0.8880 (mtpm) cc_final: 0.8631 (tttp) REVERT: l 60 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8624 (mm-30) REVERT: m 9 LYS cc_start: 0.9048 (ttpp) cc_final: 0.8117 (tptt) REVERT: m 14 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8335 (mmpt) REVERT: m 30 ILE cc_start: 0.8668 (pt) cc_final: 0.8266 (mt) REVERT: m 46 ARG cc_start: 0.8749 (ttm110) cc_final: 0.8052 (mtm110) REVERT: n 34 LYS cc_start: 0.9094 (mttt) cc_final: 0.8709 (tttt) REVERT: n 41 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8153 (ttt-90) REVERT: n 48 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8128 (mm-30) REVERT: n 71 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8571 (ttpp) REVERT: o 77 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8867 (mtmm) REVERT: p 30 LYS cc_start: 0.9000 (mttp) cc_final: 0.8781 (ttpp) REVERT: p 56 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8320 (tmm-80) REVERT: p 112 GLU cc_start: 0.9022 (tp30) cc_final: 0.8737 (tp30) REVERT: p 113 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8863 (tttm) REVERT: q 81 ARG cc_start: 0.8884 (tpt90) cc_final: 0.8412 (ttp80) REVERT: q 84 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: r 8 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8657 (mtpt) REVERT: r 102 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8590 (mtt180) REVERT: r 121 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: s 17 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: s 83 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: u 18 THR cc_start: 0.8516 (m) cc_final: 0.8084 (p) REVERT: u 45 ASP cc_start: 0.8334 (m-30) cc_final: 0.7822 (m-30) REVERT: u 58 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8696 (mm110) REVERT: v 35 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: v 103 LYS cc_start: 0.8695 (mttt) cc_final: 0.8388 (tmtt) REVERT: v 142 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7412 (mpt180) REVERT: v 145 ASP cc_start: 0.8445 (p0) cc_final: 0.7902 (p0) REVERT: w 49 LYS cc_start: 0.8905 (ptpt) cc_final: 0.8520 (mttt) REVERT: w 70 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8379 (mp) REVERT: y 8 ARG cc_start: 0.6846 (tpm170) cc_final: 0.6327 (tpm170) REVERT: y 32 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8437 (mt-10) REVERT: z 25 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7579 (ttt180) REVERT: 4 9 GLU cc_start: 0.8691 (tt0) cc_final: 0.8395 (tt0) REVERT: 4 29 LYS cc_start: 0.8118 (pttp) cc_final: 0.7870 (mmmt) outliers start: 101 outliers final: 48 residues processed: 794 average time/residue: 1.7872 time to fit residues: 1687.6550 Evaluate side-chains 787 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 721 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 52 GLU Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 48 GLU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 86 SER Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 84 GLN Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 35 GLU Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 299 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN H 47 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 32 GLN p 32 GLN t 123 GLN u 16 GLN v 56 GLN w 86 GLN z 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40519 Z= 0.244 Angle : 0.568 11.538 54681 Z= 0.280 Chirality : 0.041 0.201 5914 Planarity : 0.004 0.052 6668 Dihedral : 13.115 146.111 6437 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.07 % Allowed : 11.75 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.69 (0.13), residues: 4621 helix: 1.64 (0.09), residues: 3009 sheet: 2.30 (1.23), residues: 20 loop : 0.23 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP H 121 HIS 0.006 0.001 HIS M 30 PHE 0.026 0.002 PHE N 292 TYR 0.023 0.001 TYR n 85 ARG 0.013 0.000 ARG t 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 722 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8873 (tp) cc_final: 0.8537 (mm) REVERT: A 82 THR cc_start: 0.8817 (m) cc_final: 0.8506 (p) REVERT: A 98 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8639 (tp) REVERT: A 109 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8210 (mtmm) REVERT: H 259 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8452 (p90) REVERT: J 1 MET cc_start: 0.7020 (tmt) cc_final: 0.6710 (tmm) REVERT: J 4 TYR cc_start: 0.8807 (m-80) cc_final: 0.8525 (m-80) REVERT: J 99 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6010 (mpp) REVERT: J 101 PHE cc_start: 0.7284 (m-80) cc_final: 0.6923 (m-80) REVERT: J 118 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7657 (mtmt) REVERT: J 122 MET cc_start: 0.7953 (mtp) cc_final: 0.7419 (mtm) REVERT: L 2 ASN cc_start: 0.8395 (p0) cc_final: 0.7931 (m-40) REVERT: L 27 HIS cc_start: 0.5660 (p90) cc_final: 0.5456 (p90) REVERT: L 484 HIS cc_start: 0.8457 (m90) cc_final: 0.7928 (t70) REVERT: L 503 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7840 (mp0) REVERT: L 514 ASN cc_start: 0.8276 (m110) cc_final: 0.8044 (m-40) REVERT: L 572 LYS cc_start: 0.8077 (tptt) cc_final: 0.7355 (pttm) REVERT: L 581 LYS cc_start: 0.8246 (mtmm) cc_final: 0.7296 (mmtm) REVERT: L 601 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7840 (tt) REVERT: M 86 LYS cc_start: 0.8618 (mttp) cc_final: 0.8313 (mmtm) REVERT: M 126 LEU cc_start: 0.8621 (mt) cc_final: 0.8282 (mp) REVERT: N 11 MET cc_start: 0.8413 (mmp) cc_final: 0.8053 (mtp) REVERT: V 85 ASP cc_start: 0.8144 (t70) cc_final: 0.7865 (t0) REVERT: W 19 LYS cc_start: 0.9190 (mtpm) cc_final: 0.8903 (mppt) REVERT: W 107 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8757 (tt0) REVERT: X 9 GLU cc_start: 0.8874 (tt0) cc_final: 0.8462 (pm20) REVERT: Z 66 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8662 (mm-30) REVERT: Z 88 GLU cc_start: 0.8776 (tp30) cc_final: 0.8526 (mm-30) REVERT: Z 121 ARG cc_start: 0.8694 (ttm110) cc_final: 0.7895 (ttm-80) REVERT: k 162 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8461 (mt-10) REVERT: k 213 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: k 250 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8176 (p0) REVERT: l 27 ARG cc_start: 0.9097 (mmt-90) cc_final: 0.8795 (mpt-90) REVERT: l 56 LYS cc_start: 0.8860 (mtpm) cc_final: 0.8610 (tttp) REVERT: l 60 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8608 (mm-30) REVERT: m 9 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8116 (tptt) REVERT: m 14 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8347 (mmpt) REVERT: m 30 ILE cc_start: 0.8649 (pt) cc_final: 0.8262 (mt) REVERT: m 46 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8064 (mtm110) REVERT: n 34 LYS cc_start: 0.9093 (mttt) cc_final: 0.8707 (tttt) REVERT: n 41 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8159 (ttt-90) REVERT: n 48 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: n 71 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8558 (ttpp) REVERT: o 77 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8850 (mtmm) REVERT: p 24 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8325 (mm) REVERT: p 30 LYS cc_start: 0.8993 (mttp) cc_final: 0.8776 (ttpp) REVERT: p 56 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8322 (tmm-80) REVERT: p 112 GLU cc_start: 0.9008 (tp30) cc_final: 0.8735 (tp30) REVERT: p 113 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8868 (tttp) REVERT: q 81 ARG cc_start: 0.8864 (tpt90) cc_final: 0.8409 (ttp80) REVERT: q 84 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: r 8 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8666 (mtpt) REVERT: r 102 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8583 (mtt180) REVERT: r 121 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: s 17 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: s 83 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: u 18 THR cc_start: 0.8498 (m) cc_final: 0.8082 (p) REVERT: u 45 ASP cc_start: 0.8303 (m-30) cc_final: 0.7910 (m-30) REVERT: u 58 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8708 (mm110) REVERT: v 103 LYS cc_start: 0.8687 (mttt) cc_final: 0.8384 (tmtt) REVERT: v 142 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.7447 (mpt90) REVERT: w 49 LYS cc_start: 0.8906 (ptpt) cc_final: 0.8518 (mttt) REVERT: w 70 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8370 (mp) REVERT: y 8 ARG cc_start: 0.6843 (tpm170) cc_final: 0.6327 (tpm170) REVERT: y 32 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8425 (mt-10) REVERT: z 25 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7588 (ttt180) REVERT: 4 9 GLU cc_start: 0.8706 (tt0) cc_final: 0.8412 (tt0) REVERT: 4 29 LYS cc_start: 0.8130 (pttp) cc_final: 0.7866 (mmmt) outliers start: 86 outliers final: 47 residues processed: 770 average time/residue: 1.7879 time to fit residues: 1641.2231 Evaluate side-chains 782 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 718 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 48 GLU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 86 SER Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 84 GLN Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 6.9990 chunk 421 optimal weight: 3.9990 chunk 384 optimal weight: 9.9990 chunk 409 optimal weight: 10.0000 chunk 420 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 321 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 370 optimal weight: 0.0370 chunk 387 optimal weight: 20.0000 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 171 GLN H 194 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS n 32 GLN p 32 GLN t 123 GLN t 168 HIS u 16 GLN v 56 GLN z 58 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 40519 Z= 0.258 Angle : 0.581 11.693 54681 Z= 0.286 Chirality : 0.042 0.206 5914 Planarity : 0.004 0.072 6668 Dihedral : 13.108 146.928 6437 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.20 % Allowed : 11.92 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.67 (0.13), residues: 4621 helix: 1.61 (0.09), residues: 3015 sheet: 2.36 (1.24), residues: 20 loop : 0.26 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP H 121 HIS 0.006 0.001 HIS M 30 PHE 0.027 0.002 PHE M 122 TYR 0.023 0.002 TYR n 85 ARG 0.018 0.000 ARG s 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 726 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8874 (tp) cc_final: 0.8537 (mm) REVERT: A 82 THR cc_start: 0.8811 (m) cc_final: 0.8505 (p) REVERT: A 98 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8641 (tp) REVERT: A 109 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8211 (mtmm) REVERT: H 259 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8462 (p90) REVERT: J 1 MET cc_start: 0.7052 (tmt) cc_final: 0.6744 (tmm) REVERT: J 4 TYR cc_start: 0.8801 (m-80) cc_final: 0.8507 (m-80) REVERT: J 99 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6004 (mpp) REVERT: J 101 PHE cc_start: 0.7257 (m-80) cc_final: 0.6890 (m-80) REVERT: J 118 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7681 (mtmt) REVERT: J 122 MET cc_start: 0.7968 (mtp) cc_final: 0.7423 (mtm) REVERT: L 2 ASN cc_start: 0.8408 (p0) cc_final: 0.7938 (m-40) REVERT: L 484 HIS cc_start: 0.8451 (m90) cc_final: 0.7950 (t70) REVERT: L 503 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7859 (mp0) REVERT: L 514 ASN cc_start: 0.8284 (m110) cc_final: 0.8048 (m-40) REVERT: L 572 LYS cc_start: 0.8086 (tptt) cc_final: 0.7363 (pttm) REVERT: L 581 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7301 (mmtm) REVERT: L 601 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7850 (tt) REVERT: M 86 LYS cc_start: 0.8619 (mttp) cc_final: 0.8314 (mmtm) REVERT: M 126 LEU cc_start: 0.8621 (mt) cc_final: 0.8317 (mp) REVERT: N 11 MET cc_start: 0.8410 (mmp) cc_final: 0.8050 (mtp) REVERT: V 85 ASP cc_start: 0.8157 (t70) cc_final: 0.7878 (t0) REVERT: W 19 LYS cc_start: 0.9189 (mtpm) cc_final: 0.8903 (mppt) REVERT: W 107 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8754 (tt0) REVERT: X 9 GLU cc_start: 0.8881 (tt0) cc_final: 0.8466 (pm20) REVERT: Z 66 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8655 (mm-30) REVERT: Z 88 GLU cc_start: 0.8778 (tp30) cc_final: 0.8526 (mm-30) REVERT: Z 121 ARG cc_start: 0.8691 (ttm110) cc_final: 0.7894 (ttm-80) REVERT: k 162 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8459 (mt-10) REVERT: k 185 LYS cc_start: 0.8963 (mppt) cc_final: 0.8610 (mppt) REVERT: k 213 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: k 250 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8208 (p0) REVERT: l 27 ARG cc_start: 0.9096 (mmt-90) cc_final: 0.8798 (mpt-90) REVERT: l 56 LYS cc_start: 0.8862 (mtpm) cc_final: 0.8617 (tttp) REVERT: l 60 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8618 (mm-30) REVERT: m 9 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8113 (tptt) REVERT: m 14 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8354 (mmpt) REVERT: m 30 ILE cc_start: 0.8656 (pt) cc_final: 0.8266 (mt) REVERT: m 46 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8061 (mtm110) REVERT: n 34 LYS cc_start: 0.9094 (mttt) cc_final: 0.8702 (tttt) REVERT: n 41 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8168 (ttt-90) REVERT: n 48 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: n 71 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8560 (ttpp) REVERT: o 77 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8855 (mtmm) REVERT: p 24 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8312 (mm) REVERT: p 30 LYS cc_start: 0.8995 (mttp) cc_final: 0.8780 (ttpp) REVERT: p 56 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8314 (tmm-80) REVERT: p 112 GLU cc_start: 0.9012 (tp30) cc_final: 0.8740 (tp30) REVERT: p 113 LYS cc_start: 0.9116 (ttpt) cc_final: 0.8870 (tttp) REVERT: q 81 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8407 (ttp80) REVERT: q 84 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: r 8 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8668 (mtpt) REVERT: r 102 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8589 (mtt180) REVERT: r 121 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: s 17 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: s 83 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: u 18 THR cc_start: 0.8484 (m) cc_final: 0.8069 (p) REVERT: u 45 ASP cc_start: 0.8355 (m-30) cc_final: 0.7958 (m-30) REVERT: u 58 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8715 (mm110) REVERT: v 103 LYS cc_start: 0.8690 (mttt) cc_final: 0.8390 (tmtt) REVERT: v 142 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.7457 (mpt90) REVERT: w 49 LYS cc_start: 0.8903 (ptpt) cc_final: 0.8518 (mttt) REVERT: w 70 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8372 (mp) REVERT: y 8 ARG cc_start: 0.6838 (tpm170) cc_final: 0.6317 (tpm170) REVERT: y 32 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8426 (mt-10) REVERT: z 25 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7587 (ptt90) REVERT: 4 9 GLU cc_start: 0.8707 (tt0) cc_final: 0.8471 (tt0) REVERT: 4 29 LYS cc_start: 0.8122 (pttp) cc_final: 0.7853 (mmmt) outliers start: 91 outliers final: 54 residues processed: 778 average time/residue: 1.7514 time to fit residues: 1624.5380 Evaluate side-chains 791 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 719 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 99 MET Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 197 ASP Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 400 MET Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain Z residue 163 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 52 GLU Chi-restraints excluded: chain l residue 82 ARG Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 48 GLU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 86 SER Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 81 ARG Chi-restraints excluded: chain q residue 84 GLN Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 121 GLU Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 70 LEU Chi-restraints excluded: chain 4 residue 35 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 433 optimal weight: 0.3980 chunk 264 optimal weight: 5.9990 chunk 205 optimal weight: 50.0000 chunk 301 optimal weight: 7.9990 chunk 454 optimal weight: 0.0770 chunk 418 optimal weight: 10.0000 chunk 361 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 overall best weight: 2.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN H 47 GLN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS n 32 GLN t 123 GLN u 16 GLN z 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40519 Z= 0.190 Angle : 0.548 10.990 54681 Z= 0.270 Chirality : 0.040 0.191 5914 Planarity : 0.004 0.062 6668 Dihedral : 12.827 145.686 6437 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.66 % Allowed : 12.62 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.79 (0.13), residues: 4621 helix: 1.72 (0.10), residues: 3009 sheet: 2.52 (1.26), residues: 20 loop : 0.27 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP H 121 HIS 0.005 0.001 HIS M 30 PHE 0.028 0.001 PHE N 292 TYR 0.023 0.001 TYR n 85 ARG 0.015 0.000 ARG t 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9242 Ramachandran restraints generated. 4621 Oldfield, 0 Emsley, 4621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 724 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8871 (tp) cc_final: 0.8546 (mm) REVERT: A 82 THR cc_start: 0.8790 (m) cc_final: 0.8450 (p) REVERT: A 98 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8640 (tp) REVERT: A 109 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8207 (mtmm) REVERT: H 259 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8402 (p90) REVERT: J 1 MET cc_start: 0.7020 (tmt) cc_final: 0.6699 (tmm) REVERT: J 4 TYR cc_start: 0.8765 (m-80) cc_final: 0.8509 (m-80) REVERT: J 101 PHE cc_start: 0.7230 (m-80) cc_final: 0.6853 (m-80) REVERT: J 118 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7629 (mtmt) REVERT: J 122 MET cc_start: 0.7978 (mtp) cc_final: 0.7470 (mtm) REVERT: L 2 ASN cc_start: 0.8354 (p0) cc_final: 0.7910 (m-40) REVERT: L 484 HIS cc_start: 0.8441 (m90) cc_final: 0.7894 (t70) REVERT: L 503 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7837 (mp0) REVERT: L 514 ASN cc_start: 0.8282 (m110) cc_final: 0.8060 (m-40) REVERT: L 572 LYS cc_start: 0.8077 (tptt) cc_final: 0.7360 (pttp) REVERT: L 581 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7261 (mmtm) REVERT: L 601 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7835 (tt) REVERT: M 86 LYS cc_start: 0.8624 (mttp) cc_final: 0.8317 (mmtm) REVERT: M 126 LEU cc_start: 0.8584 (mt) cc_final: 0.8247 (mp) REVERT: N 11 MET cc_start: 0.8402 (mmp) cc_final: 0.8064 (mtp) REVERT: N 139 MET cc_start: 0.9154 (mmm) cc_final: 0.8889 (mmt) REVERT: V 85 ASP cc_start: 0.8156 (t70) cc_final: 0.7881 (t0) REVERT: W 19 LYS cc_start: 0.9175 (mtpm) cc_final: 0.8829 (mmtm) REVERT: W 107 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8759 (tt0) REVERT: X 9 GLU cc_start: 0.8877 (tt0) cc_final: 0.8470 (pm20) REVERT: Z 66 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8663 (mm-30) REVERT: Z 88 GLU cc_start: 0.8733 (tp30) cc_final: 0.8500 (mm-30) REVERT: Z 121 ARG cc_start: 0.8679 (ttm110) cc_final: 0.7891 (ttm-80) REVERT: k 162 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8441 (mt-10) REVERT: k 185 LYS cc_start: 0.8966 (mppt) cc_final: 0.8611 (mppt) REVERT: k 213 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: k 250 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8148 (p0) REVERT: l 27 ARG cc_start: 0.9092 (mmt-90) cc_final: 0.8794 (mpt-90) REVERT: l 56 LYS cc_start: 0.8842 (mtpm) cc_final: 0.8589 (tptp) REVERT: l 60 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8599 (mm-30) REVERT: m 9 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8109 (tptt) REVERT: m 14 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8334 (mmpt) REVERT: m 30 ILE cc_start: 0.8633 (pt) cc_final: 0.8277 (mt) REVERT: m 39 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8406 (ptmm) REVERT: m 46 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8024 (mtm110) REVERT: n 34 LYS cc_start: 0.9092 (mttt) cc_final: 0.8711 (tttt) REVERT: n 41 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8176 (ttt-90) REVERT: n 48 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: n 71 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8543 (ttpp) REVERT: o 77 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8825 (mtmm) REVERT: p 24 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8301 (mm) REVERT: p 30 LYS cc_start: 0.8991 (mttp) cc_final: 0.8774 (ttpp) REVERT: p 112 GLU cc_start: 0.8986 (tp30) cc_final: 0.8699 (tp30) REVERT: p 113 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8869 (tttp) REVERT: q 81 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8413 (ttp80) REVERT: q 84 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: r 8 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8668 (mtpt) REVERT: r 102 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8564 (mtt180) REVERT: s 17 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: s 83 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: u 18 THR cc_start: 0.8470 (m) cc_final: 0.8065 (p) REVERT: u 45 ASP cc_start: 0.8275 (m-30) cc_final: 0.7887 (m-30) REVERT: u 58 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8709 (mm110) REVERT: v 103 LYS cc_start: 0.8676 (mttt) cc_final: 0.8394 (tmtt) REVERT: v 142 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.7396 (mpt180) REVERT: w 49 LYS cc_start: 0.8897 (ptpt) cc_final: 0.8520 (mttt) REVERT: w 70 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8360 (mp) REVERT: y 8 ARG cc_start: 0.6841 (tpm170) cc_final: 0.6321 (tpm170) REVERT: y 32 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8416 (mt-10) REVERT: z 25 ARG cc_start: 0.8289 (mtp85) cc_final: 0.7591 (ptt90) REVERT: 4 9 GLU cc_start: 0.8707 (tt0) cc_final: 0.8476 (tt0) REVERT: 4 29 LYS cc_start: 0.8111 (pttp) cc_final: 0.7849 (mmmt) outliers start: 69 outliers final: 40 residues processed: 762 average time/residue: 1.8280 time to fit residues: 1672.8976 Evaluate side-chains 766 residues out of total 4145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 710 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 331 THR Chi-restraints excluded: chain L residue 410 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain N residue 200 MET Chi-restraints excluded: chain V residue 36 SER Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain Y residue 13 LYS Chi-restraints excluded: chain Y residue 15 GLN Chi-restraints excluded: chain Y residue 77 CYS Chi-restraints excluded: chain Y residue 99 CYS Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 160 VAL Chi-restraints excluded: chain k residue 213 GLU Chi-restraints excluded: chain k residue 250 ASP Chi-restraints excluded: chain l residue 5 VAL Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 52 GLU Chi-restraints excluded: chain m residue 39 LYS Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 48 GLU Chi-restraints excluded: chain o residue 67 SER Chi-restraints excluded: chain o residue 77 LYS Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain q residue 48 SER Chi-restraints excluded: chain q residue 81 ARG Chi-restraints excluded: chain q residue 84 GLN Chi-restraints excluded: chain r residue 16 GLU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain s residue 17 GLU Chi-restraints excluded: chain s residue 58 CYS Chi-restraints excluded: chain s residue 83 GLN Chi-restraints excluded: chain t residue 120 LYS Chi-restraints excluded: chain v residue 142 ARG Chi-restraints excluded: chain w residue 34 ASP Chi-restraints excluded: chain w residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 7.9990 chunk 287 optimal weight: 8.9990 chunk 385 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 333 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 372 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 171 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 89 ASN ** l 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS n 32 GLN t 123 GLN u 16 GLN z 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.089264 restraints weight = 51178.306| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.30 r_work: 0.2881 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40519 Z= 0.202 Angle : 0.557 11.668 54681 Z= 0.274 Chirality : 0.040 0.190 5914 Planarity : 0.004 0.079 6668 Dihedral : 12.724 145.930 6437 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.74 % Allowed : 12.86 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.81 (0.13), residues: 4621 helix: 1.73 (0.09), residues: 3007 sheet: 2.56 (1.26), residues: 20 loop : 0.30 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP H 121 HIS 0.005 0.001 HIS N 112 PHE 0.027 0.001 PHE N 292 TYR 0.024 0.001 TYR n 85 ARG 0.019 0.000 ARG s 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27036.00 seconds wall clock time: 473 minutes 35.43 seconds (28415.43 seconds total)