Starting phenix.real_space_refine on Tue Mar 12 08:47:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2q_13780/03_2024/7q2q_13780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2q_13780/03_2024/7q2q_13780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2q_13780/03_2024/7q2q_13780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2q_13780/03_2024/7q2q_13780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2q_13780/03_2024/7q2q_13780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2q_13780/03_2024/7q2q_13780.pdb" } resolution = 4.3 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 147 5.49 5 S 49 5.16 5 C 38661 2.51 5 N 11025 2.21 5 O 12495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 62377 Number of models: 1 Model: "" Number of chains: 98 Chain: "A" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "C" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "E" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "G" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "I" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "K" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "M" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "O" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "P" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "Q" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "S" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "T" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "U" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "V" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "W" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "Y" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "0" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "1" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "2" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "3" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "4" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "5" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "6" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "7" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "8" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "9" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "a" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "c" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "d" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "e" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "f" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "g" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "h" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "i" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "j" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "k" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "l" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "m" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "n" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "o" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "p" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "q" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "r" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "s" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "t" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "u" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "v" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "w" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "x" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "y" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AA" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AB" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AC" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AD" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AE" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AF" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AG" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AH" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AI" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AJ" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AK" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AL" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AM" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AN" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AO" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AP" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AQ" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AR" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AS" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AT" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AU" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AV" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AW" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AX" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "AY" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "AZ" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "A0" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "A1" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "A2" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "A3" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "A4" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "A5" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "A6" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "A7" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "A8" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1206 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "A9" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 25.04, per 1000 atoms: 0.40 Number of scatterers: 62377 At special positions: 0 Unit cell: (193.06, 193.06, 117.6, 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 49 16.00 P 147 15.00 O 12495 8.00 N 11025 7.00 C 38661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.02 Conformation dependent library (CDL) restraints added in 8.4 seconds 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14504 Finding SS restraints... Secondary structure from input PDB file: 392 helices and 49 sheets defined 58.8% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.56 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU C 79 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 131 " --> pdb=" O ASN C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 19 through 29 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU E 79 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG E 112 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL E 119 " --> pdb=" O ASP E 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU E 131 " --> pdb=" O ASN E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER E 146 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 14 Processing helix chain 'G' and resid 19 through 29 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU G 79 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARG G 112 " --> pdb=" O LEU G 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL G 119 " --> pdb=" O ASP G 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU G 131 " --> pdb=" O ASN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER G 146 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 14 Processing helix chain 'I' and resid 19 through 29 Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.297A pdb=" N LEU I 79 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE I 87 " --> pdb=" O LEU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'I' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL I 119 " --> pdb=" O ASP I 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 131 " --> pdb=" O ASN I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER I 146 " --> pdb=" O SER I 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 14 Processing helix chain 'K' and resid 19 through 29 Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU K 79 " --> pdb=" O VAL K 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE K 87 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 97 Processing helix chain 'K' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG K 112 " --> pdb=" O LEU K 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU K 131 " --> pdb=" O ASN K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 14 Processing helix chain 'M' and resid 19 through 29 Processing helix chain 'M' and resid 30 through 32 No H-bonds generated for 'chain 'M' and resid 30 through 32' Processing helix chain 'M' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU M 79 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE M 87 " --> pdb=" O LEU M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 97 Processing helix chain 'M' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARG M 112 " --> pdb=" O LEU M 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL M 119 " --> pdb=" O ASP M 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU M 131 " --> pdb=" O ASN M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER M 146 " --> pdb=" O SER M 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 14 Processing helix chain 'O' and resid 19 through 29 Processing helix chain 'O' and resid 30 through 32 No H-bonds generated for 'chain 'O' and resid 30 through 32' Processing helix chain 'O' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU O 79 " --> pdb=" O VAL O 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG O 112 " --> pdb=" O LEU O 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR O 118 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL O 119 " --> pdb=" O ASP O 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU O 131 " --> pdb=" O ASN O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER O 146 " --> pdb=" O SER O 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 14 Processing helix chain 'Q' and resid 19 through 29 Processing helix chain 'Q' and resid 30 through 32 No H-bonds generated for 'chain 'Q' and resid 30 through 32' Processing helix chain 'Q' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL Q 44 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 97 Processing helix chain 'Q' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR Q 118 " --> pdb=" O VAL Q 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL Q 119 " --> pdb=" O ASP Q 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU Q 131 " --> pdb=" O ASN Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER Q 146 " --> pdb=" O SER Q 142 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 14 Processing helix chain 'S' and resid 19 through 29 Processing helix chain 'S' and resid 30 through 32 No H-bonds generated for 'chain 'S' and resid 30 through 32' Processing helix chain 'S' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU S 79 " --> pdb=" O VAL S 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE S 87 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'S' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG S 112 " --> pdb=" O LEU S 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR S 118 " --> pdb=" O VAL S 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL S 119 " --> pdb=" O ASP S 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU S 131 " --> pdb=" O ASN S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER S 146 " --> pdb=" O SER S 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 14 Processing helix chain 'U' and resid 19 through 29 Processing helix chain 'U' and resid 30 through 32 No H-bonds generated for 'chain 'U' and resid 30 through 32' Processing helix chain 'U' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU U 79 " --> pdb=" O VAL U 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 97 Processing helix chain 'U' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARG U 112 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR U 118 " --> pdb=" O VAL U 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL U 119 " --> pdb=" O ASP U 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU U 131 " --> pdb=" O ASN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER U 146 " --> pdb=" O SER U 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 14 Processing helix chain 'W' and resid 19 through 29 Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU W 79 " --> pdb=" O VAL W 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 92 through 97 Processing helix chain 'W' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG W 112 " --> pdb=" O LEU W 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR W 118 " --> pdb=" O VAL W 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU W 131 " --> pdb=" O ASN W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER W 146 " --> pdb=" O SER W 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 14 Processing helix chain 'Y' and resid 19 through 29 Processing helix chain 'Y' and resid 30 through 32 No H-bonds generated for 'chain 'Y' and resid 30 through 32' Processing helix chain 'Y' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL Y 44 " --> pdb=" O ALA Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU Y 79 " --> pdb=" O VAL Y 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE Y 87 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 97 Processing helix chain 'Y' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG Y 112 " --> pdb=" O LEU Y 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR Y 118 " --> pdb=" O VAL Y 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL Y 119 " --> pdb=" O ASP Y 115 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU Y 131 " --> pdb=" O ASN Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER Y 146 " --> pdb=" O SER Y 142 " (cutoff:3.500A) Processing helix chain '0' and resid 10 through 14 Processing helix chain '0' and resid 19 through 29 Processing helix chain '0' and resid 30 through 32 No H-bonds generated for 'chain '0' and resid 30 through 32' Processing helix chain '0' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL 0 44 " --> pdb=" O ALA 0 40 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU 0 79 " --> pdb=" O VAL 0 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE 0 87 " --> pdb=" O LEU 0 83 " (cutoff:3.500A) Processing helix chain '0' and resid 92 through 97 Processing helix chain '0' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARG 0 112 " --> pdb=" O LEU 0 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR 0 118 " --> pdb=" O VAL 0 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL 0 119 " --> pdb=" O ASP 0 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU 0 131 " --> pdb=" O ASN 0 127 " (cutoff:3.500A) Processing helix chain '0' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER 0 146 " --> pdb=" O SER 0 142 " (cutoff:3.500A) Processing helix chain '2' and resid 10 through 14 Processing helix chain '2' and resid 19 through 29 Processing helix chain '2' and resid 30 through 32 No H-bonds generated for 'chain '2' and resid 30 through 32' Processing helix chain '2' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL 2 44 " --> pdb=" O ALA 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU 2 79 " --> pdb=" O VAL 2 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE 2 87 " --> pdb=" O LEU 2 83 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 97 Processing helix chain '2' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG 2 112 " --> pdb=" O LEU 2 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR 2 118 " --> pdb=" O VAL 2 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL 2 119 " --> pdb=" O ASP 2 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU 2 131 " --> pdb=" O ASN 2 127 " (cutoff:3.500A) Processing helix chain '2' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER 2 146 " --> pdb=" O SER 2 142 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 14 Processing helix chain '4' and resid 19 through 29 Processing helix chain '4' and resid 30 through 32 No H-bonds generated for 'chain '4' and resid 30 through 32' Processing helix chain '4' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL 4 44 " --> pdb=" O ALA 4 40 " (cutoff:3.500A) Processing helix chain '4' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU 4 79 " --> pdb=" O VAL 4 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE 4 87 " --> pdb=" O LEU 4 83 " (cutoff:3.500A) Processing helix chain '4' and resid 92 through 97 Processing helix chain '4' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG 4 112 " --> pdb=" O LEU 4 108 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR 4 118 " --> pdb=" O VAL 4 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL 4 119 " --> pdb=" O ASP 4 115 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU 4 131 " --> pdb=" O ASN 4 127 " (cutoff:3.500A) Processing helix chain '4' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER 4 146 " --> pdb=" O SER 4 142 " (cutoff:3.500A) Processing helix chain '6' and resid 10 through 14 Processing helix chain '6' and resid 19 through 29 Processing helix chain '6' and resid 30 through 32 No H-bonds generated for 'chain '6' and resid 30 through 32' Processing helix chain '6' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL 6 44 " --> pdb=" O ALA 6 40 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU 6 79 " --> pdb=" O VAL 6 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE 6 87 " --> pdb=" O LEU 6 83 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 97 Processing helix chain '6' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR 6 118 " --> pdb=" O VAL 6 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL 6 119 " --> pdb=" O ASP 6 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU 6 131 " --> pdb=" O ASN 6 127 " (cutoff:3.500A) Processing helix chain '6' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER 6 146 " --> pdb=" O SER 6 142 " (cutoff:3.500A) Processing helix chain '8' and resid 10 through 14 Processing helix chain '8' and resid 19 through 29 Processing helix chain '8' and resid 30 through 32 No H-bonds generated for 'chain '8' and resid 30 through 32' Processing helix chain '8' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL 8 44 " --> pdb=" O ALA 8 40 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU 8 79 " --> pdb=" O VAL 8 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE 8 87 " --> pdb=" O LEU 8 83 " (cutoff:3.500A) Processing helix chain '8' and resid 92 through 97 Processing helix chain '8' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG 8 112 " --> pdb=" O LEU 8 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR 8 118 " --> pdb=" O VAL 8 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL 8 119 " --> pdb=" O ASP 8 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU 8 131 " --> pdb=" O ASN 8 127 " (cutoff:3.500A) Processing helix chain '8' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER 8 146 " --> pdb=" O SER 8 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 14 Processing helix chain 'a' and resid 19 through 29 Processing helix chain 'a' and resid 30 through 32 No H-bonds generated for 'chain 'a' and resid 30 through 32' Processing helix chain 'a' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL a 44 " --> pdb=" O ALA a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU a 79 " --> pdb=" O VAL a 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE a 87 " --> pdb=" O LEU a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 92 through 97 Processing helix chain 'a' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR a 118 " --> pdb=" O VAL a 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL a 119 " --> pdb=" O ASP a 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU a 131 " --> pdb=" O ASN a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER a 146 " --> pdb=" O SER a 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 14 Processing helix chain 'c' and resid 19 through 29 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL c 44 " --> pdb=" O ALA c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU c 79 " --> pdb=" O VAL c 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE c 87 " --> pdb=" O LEU c 83 " (cutoff:3.500A) Processing helix chain 'c' and resid 92 through 97 Processing helix chain 'c' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG c 112 " --> pdb=" O LEU c 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR c 118 " --> pdb=" O VAL c 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL c 119 " --> pdb=" O ASP c 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU c 131 " --> pdb=" O ASN c 127 " (cutoff:3.500A) Processing helix chain 'c' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER c 146 " --> pdb=" O SER c 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 14 Processing helix chain 'e' and resid 19 through 29 Processing helix chain 'e' and resid 30 through 32 No H-bonds generated for 'chain 'e' and resid 30 through 32' Processing helix chain 'e' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL e 44 " --> pdb=" O ALA e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU e 79 " --> pdb=" O VAL e 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE e 87 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 97 Processing helix chain 'e' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG e 112 " --> pdb=" O LEU e 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR e 118 " --> pdb=" O VAL e 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL e 119 " --> pdb=" O ASP e 115 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU e 131 " --> pdb=" O ASN e 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER e 146 " --> pdb=" O SER e 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 14 Processing helix chain 'g' and resid 19 through 29 Processing helix chain 'g' and resid 30 through 32 No H-bonds generated for 'chain 'g' and resid 30 through 32' Processing helix chain 'g' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL g 44 " --> pdb=" O ALA g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU g 79 " --> pdb=" O VAL g 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE g 87 " --> pdb=" O LEU g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 97 Processing helix chain 'g' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG g 112 " --> pdb=" O LEU g 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR g 118 " --> pdb=" O VAL g 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL g 119 " --> pdb=" O ASP g 115 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU g 131 " --> pdb=" O ASN g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER g 146 " --> pdb=" O SER g 142 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 14 Processing helix chain 'i' and resid 19 through 29 Processing helix chain 'i' and resid 30 through 32 No H-bonds generated for 'chain 'i' and resid 30 through 32' Processing helix chain 'i' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL i 44 " --> pdb=" O ALA i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 87 removed outlier: 4.299A pdb=" N LEU i 79 " --> pdb=" O VAL i 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE i 87 " --> pdb=" O LEU i 83 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 97 Processing helix chain 'i' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG i 112 " --> pdb=" O LEU i 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR i 118 " --> pdb=" O VAL i 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL i 119 " --> pdb=" O ASP i 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU i 131 " --> pdb=" O ASN i 127 " (cutoff:3.500A) Processing helix chain 'i' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER i 146 " --> pdb=" O SER i 142 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 14 Processing helix chain 'k' and resid 19 through 29 Processing helix chain 'k' and resid 30 through 32 No H-bonds generated for 'chain 'k' and resid 30 through 32' Processing helix chain 'k' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL k 44 " --> pdb=" O ALA k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU k 79 " --> pdb=" O VAL k 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE k 87 " --> pdb=" O LEU k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 97 Processing helix chain 'k' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG k 112 " --> pdb=" O LEU k 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR k 118 " --> pdb=" O VAL k 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL k 119 " --> pdb=" O ASP k 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU k 131 " --> pdb=" O ASN k 127 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER k 146 " --> pdb=" O SER k 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 14 Processing helix chain 'm' and resid 19 through 29 Processing helix chain 'm' and resid 30 through 32 No H-bonds generated for 'chain 'm' and resid 30 through 32' Processing helix chain 'm' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL m 44 " --> pdb=" O ALA m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 75 through 87 removed outlier: 4.297A pdb=" N LEU m 79 " --> pdb=" O VAL m 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE m 87 " --> pdb=" O LEU m 83 " (cutoff:3.500A) Processing helix chain 'm' and resid 92 through 97 Processing helix chain 'm' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARG m 112 " --> pdb=" O LEU m 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR m 118 " --> pdb=" O VAL m 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL m 119 " --> pdb=" O ASP m 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU m 131 " --> pdb=" O ASN m 127 " (cutoff:3.500A) Processing helix chain 'm' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER m 146 " --> pdb=" O SER m 142 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 14 Processing helix chain 'o' and resid 19 through 29 Processing helix chain 'o' and resid 30 through 32 No H-bonds generated for 'chain 'o' and resid 30 through 32' Processing helix chain 'o' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL o 44 " --> pdb=" O ALA o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU o 79 " --> pdb=" O VAL o 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE o 87 " --> pdb=" O LEU o 83 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 97 Processing helix chain 'o' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG o 112 " --> pdb=" O LEU o 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR o 118 " --> pdb=" O VAL o 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL o 119 " --> pdb=" O ASP o 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU o 131 " --> pdb=" O ASN o 127 " (cutoff:3.500A) Processing helix chain 'o' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER o 146 " --> pdb=" O SER o 142 " (cutoff:3.500A) Processing helix chain 'q' and resid 10 through 14 Processing helix chain 'q' and resid 19 through 29 Processing helix chain 'q' and resid 30 through 32 No H-bonds generated for 'chain 'q' and resid 30 through 32' Processing helix chain 'q' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL q 44 " --> pdb=" O ALA q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU q 79 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE q 87 " --> pdb=" O LEU q 83 " (cutoff:3.500A) Processing helix chain 'q' and resid 92 through 97 Processing helix chain 'q' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG q 112 " --> pdb=" O LEU q 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR q 118 " --> pdb=" O VAL q 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL q 119 " --> pdb=" O ASP q 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU q 131 " --> pdb=" O ASN q 127 " (cutoff:3.500A) Processing helix chain 'q' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER q 146 " --> pdb=" O SER q 142 " (cutoff:3.500A) Processing helix chain 's' and resid 10 through 14 Processing helix chain 's' and resid 19 through 29 Processing helix chain 's' and resid 30 through 32 No H-bonds generated for 'chain 's' and resid 30 through 32' Processing helix chain 's' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL s 44 " --> pdb=" O ALA s 40 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU s 79 " --> pdb=" O VAL s 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE s 87 " --> pdb=" O LEU s 83 " (cutoff:3.500A) Processing helix chain 's' and resid 92 through 97 Processing helix chain 's' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG s 112 " --> pdb=" O LEU s 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR s 118 " --> pdb=" O VAL s 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL s 119 " --> pdb=" O ASP s 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU s 131 " --> pdb=" O ASN s 127 " (cutoff:3.500A) Processing helix chain 's' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER s 146 " --> pdb=" O SER s 142 " (cutoff:3.500A) Processing helix chain 'u' and resid 10 through 14 Processing helix chain 'u' and resid 19 through 29 Processing helix chain 'u' and resid 30 through 32 No H-bonds generated for 'chain 'u' and resid 30 through 32' Processing helix chain 'u' and resid 37 through 49 removed outlier: 3.678A pdb=" N VAL u 44 " --> pdb=" O ALA u 40 " (cutoff:3.500A) Processing helix chain 'u' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU u 79 " --> pdb=" O VAL u 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE u 87 " --> pdb=" O LEU u 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 92 through 97 Processing helix chain 'u' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG u 112 " --> pdb=" O LEU u 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR u 118 " --> pdb=" O VAL u 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL u 119 " --> pdb=" O ASP u 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU u 131 " --> pdb=" O ASN u 127 " (cutoff:3.500A) Processing helix chain 'u' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER u 146 " --> pdb=" O SER u 142 " (cutoff:3.500A) Processing helix chain 'w' and resid 10 through 14 Processing helix chain 'w' and resid 19 through 29 Processing helix chain 'w' and resid 30 through 32 No H-bonds generated for 'chain 'w' and resid 30 through 32' Processing helix chain 'w' and resid 37 through 49 removed outlier: 3.680A pdb=" N VAL w 44 " --> pdb=" O ALA w 40 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU w 79 " --> pdb=" O VAL w 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE w 87 " --> pdb=" O LEU w 83 " (cutoff:3.500A) Processing helix chain 'w' and resid 92 through 97 Processing helix chain 'w' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG w 112 " --> pdb=" O LEU w 108 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR w 118 " --> pdb=" O VAL w 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL w 119 " --> pdb=" O ASP w 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU w 131 " --> pdb=" O ASN w 127 " (cutoff:3.500A) Processing helix chain 'w' and resid 142 through 149 removed outlier: 3.663A pdb=" N SER w 146 " --> pdb=" O SER w 142 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 14 Processing helix chain 'y' and resid 19 through 29 Processing helix chain 'y' and resid 30 through 32 No H-bonds generated for 'chain 'y' and resid 30 through 32' Processing helix chain 'y' and resid 37 through 49 removed outlier: 3.679A pdb=" N VAL y 44 " --> pdb=" O ALA y 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEU y 79 " --> pdb=" O VAL y 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE y 87 " --> pdb=" O LEU y 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 92 through 97 Processing helix chain 'y' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARG y 112 " --> pdb=" O LEU y 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR y 118 " --> pdb=" O VAL y 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL y 119 " --> pdb=" O ASP y 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU y 131 " --> pdb=" O ASN y 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 142 through 149 removed outlier: 3.664A pdb=" N SER y 146 " --> pdb=" O SER y 142 " (cutoff:3.500A) Processing helix chain 'AA' and resid 10 through 14 Processing helix chain 'AA' and resid 19 through 29 Processing helix chain 'AA' and resid 30 through 32 No H-bonds generated for 'chain 'AA' and resid 30 through 32' Processing helix chain 'AA' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAA 44 " --> pdb=" O ALAAA 40 " (cutoff:3.500A) Processing helix chain 'AA' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAA 79 " --> pdb=" O VALAA 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAA 87 " --> pdb=" O LEUAA 83 " (cutoff:3.500A) Processing helix chain 'AA' and resid 92 through 97 Processing helix chain 'AA' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGAA 112 " --> pdb=" O LEUAA 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAA 118 " --> pdb=" O VALAA 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAA 119 " --> pdb=" O ASPAA 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAA 131 " --> pdb=" O ASNAA 127 " (cutoff:3.500A) Processing helix chain 'AA' and resid 142 through 149 removed outlier: 3.664A pdb=" N SERAA 146 " --> pdb=" O SERAA 142 " (cutoff:3.500A) Processing helix chain 'AC' and resid 10 through 14 Processing helix chain 'AC' and resid 19 through 29 Processing helix chain 'AC' and resid 30 through 32 No H-bonds generated for 'chain 'AC' and resid 30 through 32' Processing helix chain 'AC' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAC 44 " --> pdb=" O ALAAC 40 " (cutoff:3.500A) Processing helix chain 'AC' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAC 79 " --> pdb=" O VALAC 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHEAC 87 " --> pdb=" O LEUAC 83 " (cutoff:3.500A) Processing helix chain 'AC' and resid 92 through 97 Processing helix chain 'AC' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAC 112 " --> pdb=" O LEUAC 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THRAC 118 " --> pdb=" O VALAC 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAC 119 " --> pdb=" O ASPAC 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAC 131 " --> pdb=" O ASNAC 127 " (cutoff:3.500A) Processing helix chain 'AC' and resid 142 through 149 removed outlier: 3.664A pdb=" N SERAC 146 " --> pdb=" O SERAC 142 " (cutoff:3.500A) Processing helix chain 'AE' and resid 10 through 14 Processing helix chain 'AE' and resid 19 through 29 Processing helix chain 'AE' and resid 30 through 32 No H-bonds generated for 'chain 'AE' and resid 30 through 32' Processing helix chain 'AE' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAE 44 " --> pdb=" O ALAAE 40 " (cutoff:3.500A) Processing helix chain 'AE' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAE 79 " --> pdb=" O VALAE 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAE 87 " --> pdb=" O LEUAE 83 " (cutoff:3.500A) Processing helix chain 'AE' and resid 92 through 97 Processing helix chain 'AE' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGAE 112 " --> pdb=" O LEUAE 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAE 118 " --> pdb=" O VALAE 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAE 119 " --> pdb=" O ASPAE 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAE 131 " --> pdb=" O ASNAE 127 " (cutoff:3.500A) Processing helix chain 'AE' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAE 146 " --> pdb=" O SERAE 142 " (cutoff:3.500A) Processing helix chain 'AG' and resid 10 through 14 Processing helix chain 'AG' and resid 19 through 29 Processing helix chain 'AG' and resid 30 through 32 No H-bonds generated for 'chain 'AG' and resid 30 through 32' Processing helix chain 'AG' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAG 44 " --> pdb=" O ALAAG 40 " (cutoff:3.500A) Processing helix chain 'AG' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAG 79 " --> pdb=" O VALAG 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAG 87 " --> pdb=" O LEUAG 83 " (cutoff:3.500A) Processing helix chain 'AG' and resid 92 through 97 Processing helix chain 'AG' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAG 112 " --> pdb=" O LEUAG 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAG 118 " --> pdb=" O VALAG 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAG 119 " --> pdb=" O ASPAG 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAG 131 " --> pdb=" O ASNAG 127 " (cutoff:3.500A) Processing helix chain 'AG' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAG 146 " --> pdb=" O SERAG 142 " (cutoff:3.500A) Processing helix chain 'AI' and resid 10 through 14 Processing helix chain 'AI' and resid 19 through 29 Processing helix chain 'AI' and resid 30 through 32 No H-bonds generated for 'chain 'AI' and resid 30 through 32' Processing helix chain 'AI' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAI 44 " --> pdb=" O ALAAI 40 " (cutoff:3.500A) Processing helix chain 'AI' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAI 79 " --> pdb=" O VALAI 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHEAI 87 " --> pdb=" O LEUAI 83 " (cutoff:3.500A) Processing helix chain 'AI' and resid 92 through 97 Processing helix chain 'AI' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAI 112 " --> pdb=" O LEUAI 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THRAI 118 " --> pdb=" O VALAI 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VALAI 119 " --> pdb=" O ASPAI 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAI 131 " --> pdb=" O ASNAI 127 " (cutoff:3.500A) Processing helix chain 'AI' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAI 146 " --> pdb=" O SERAI 142 " (cutoff:3.500A) Processing helix chain 'AK' and resid 10 through 14 Processing helix chain 'AK' and resid 19 through 29 Processing helix chain 'AK' and resid 30 through 32 No H-bonds generated for 'chain 'AK' and resid 30 through 32' Processing helix chain 'AK' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAK 44 " --> pdb=" O ALAAK 40 " (cutoff:3.500A) Processing helix chain 'AK' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAK 79 " --> pdb=" O VALAK 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAK 87 " --> pdb=" O LEUAK 83 " (cutoff:3.500A) Processing helix chain 'AK' and resid 92 through 97 Processing helix chain 'AK' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAK 112 " --> pdb=" O LEUAK 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAK 118 " --> pdb=" O VALAK 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAK 119 " --> pdb=" O ASPAK 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAK 131 " --> pdb=" O ASNAK 127 " (cutoff:3.500A) Processing helix chain 'AK' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAK 146 " --> pdb=" O SERAK 142 " (cutoff:3.500A) Processing helix chain 'AM' and resid 10 through 14 Processing helix chain 'AM' and resid 19 through 29 Processing helix chain 'AM' and resid 30 through 32 No H-bonds generated for 'chain 'AM' and resid 30 through 32' Processing helix chain 'AM' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAM 44 " --> pdb=" O ALAAM 40 " (cutoff:3.500A) Processing helix chain 'AM' and resid 75 through 87 removed outlier: 4.297A pdb=" N LEUAM 79 " --> pdb=" O VALAM 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAM 87 " --> pdb=" O LEUAM 83 " (cutoff:3.500A) Processing helix chain 'AM' and resid 92 through 97 Processing helix chain 'AM' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAM 112 " --> pdb=" O LEUAM 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAM 118 " --> pdb=" O VALAM 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAM 119 " --> pdb=" O ASPAM 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAM 131 " --> pdb=" O ASNAM 127 " (cutoff:3.500A) Processing helix chain 'AM' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAM 146 " --> pdb=" O SERAM 142 " (cutoff:3.500A) Processing helix chain 'AO' and resid 10 through 14 Processing helix chain 'AO' and resid 19 through 29 Processing helix chain 'AO' and resid 30 through 32 No H-bonds generated for 'chain 'AO' and resid 30 through 32' Processing helix chain 'AO' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAO 44 " --> pdb=" O ALAAO 40 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAO 79 " --> pdb=" O VALAO 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAO 87 " --> pdb=" O LEUAO 83 " (cutoff:3.500A) Processing helix chain 'AO' and resid 92 through 97 Processing helix chain 'AO' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAO 112 " --> pdb=" O LEUAO 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAO 118 " --> pdb=" O VALAO 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAO 119 " --> pdb=" O ASPAO 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAO 131 " --> pdb=" O ASNAO 127 " (cutoff:3.500A) Processing helix chain 'AO' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAO 146 " --> pdb=" O SERAO 142 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 10 through 14 Processing helix chain 'AQ' and resid 19 through 29 Processing helix chain 'AQ' and resid 30 through 32 No H-bonds generated for 'chain 'AQ' and resid 30 through 32' Processing helix chain 'AQ' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAQ 44 " --> pdb=" O ALAAQ 40 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAQ 79 " --> pdb=" O VALAQ 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAQ 87 " --> pdb=" O LEUAQ 83 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 92 through 97 Processing helix chain 'AQ' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGAQ 112 " --> pdb=" O LEUAQ 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAQ 118 " --> pdb=" O VALAQ 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VALAQ 119 " --> pdb=" O ASPAQ 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLUAQ 131 " --> pdb=" O ASNAQ 127 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 142 through 149 removed outlier: 3.664A pdb=" N SERAQ 146 " --> pdb=" O SERAQ 142 " (cutoff:3.500A) Processing helix chain 'AS' and resid 10 through 14 Processing helix chain 'AS' and resid 19 through 29 Processing helix chain 'AS' and resid 30 through 32 No H-bonds generated for 'chain 'AS' and resid 30 through 32' Processing helix chain 'AS' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAS 44 " --> pdb=" O ALAAS 40 " (cutoff:3.500A) Processing helix chain 'AS' and resid 75 through 87 removed outlier: 4.299A pdb=" N LEUAS 79 " --> pdb=" O VALAS 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAS 87 " --> pdb=" O LEUAS 83 " (cutoff:3.500A) Processing helix chain 'AS' and resid 92 through 97 Processing helix chain 'AS' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAS 112 " --> pdb=" O LEUAS 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAS 118 " --> pdb=" O VALAS 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAS 119 " --> pdb=" O ASPAS 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAS 131 " --> pdb=" O ASNAS 127 " (cutoff:3.500A) Processing helix chain 'AS' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAS 146 " --> pdb=" O SERAS 142 " (cutoff:3.500A) Processing helix chain 'AU' and resid 10 through 14 Processing helix chain 'AU' and resid 19 through 29 Processing helix chain 'AU' and resid 30 through 32 No H-bonds generated for 'chain 'AU' and resid 30 through 32' Processing helix chain 'AU' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAU 44 " --> pdb=" O ALAAU 40 " (cutoff:3.500A) Processing helix chain 'AU' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAU 79 " --> pdb=" O VALAU 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEAU 87 " --> pdb=" O LEUAU 83 " (cutoff:3.500A) Processing helix chain 'AU' and resid 92 through 97 Processing helix chain 'AU' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAU 112 " --> pdb=" O LEUAU 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRAU 118 " --> pdb=" O VALAU 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VALAU 119 " --> pdb=" O ASPAU 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAU 131 " --> pdb=" O ASNAU 127 " (cutoff:3.500A) Processing helix chain 'AU' and resid 142 through 149 removed outlier: 3.664A pdb=" N SERAU 146 " --> pdb=" O SERAU 142 " (cutoff:3.500A) Processing helix chain 'AW' and resid 10 through 14 Processing helix chain 'AW' and resid 19 through 29 Processing helix chain 'AW' and resid 30 through 32 No H-bonds generated for 'chain 'AW' and resid 30 through 32' Processing helix chain 'AW' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALAW 44 " --> pdb=" O ALAAW 40 " (cutoff:3.500A) Processing helix chain 'AW' and resid 75 through 87 removed outlier: 4.297A pdb=" N LEUAW 79 " --> pdb=" O VALAW 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHEAW 87 " --> pdb=" O LEUAW 83 " (cutoff:3.500A) Processing helix chain 'AW' and resid 92 through 97 Processing helix chain 'AW' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGAW 112 " --> pdb=" O LEUAW 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THRAW 118 " --> pdb=" O VALAW 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAW 119 " --> pdb=" O ASPAW 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAW 131 " --> pdb=" O ASNAW 127 " (cutoff:3.500A) Processing helix chain 'AW' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERAW 146 " --> pdb=" O SERAW 142 " (cutoff:3.500A) Processing helix chain 'AY' and resid 10 through 14 Processing helix chain 'AY' and resid 19 through 29 Processing helix chain 'AY' and resid 30 through 32 No H-bonds generated for 'chain 'AY' and resid 30 through 32' Processing helix chain 'AY' and resid 37 through 49 removed outlier: 3.678A pdb=" N VALAY 44 " --> pdb=" O ALAAY 40 " (cutoff:3.500A) Processing helix chain 'AY' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUAY 79 " --> pdb=" O VALAY 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHEAY 87 " --> pdb=" O LEUAY 83 " (cutoff:3.500A) Processing helix chain 'AY' and resid 92 through 97 Processing helix chain 'AY' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGAY 112 " --> pdb=" O LEUAY 108 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THRAY 118 " --> pdb=" O VALAY 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALAY 119 " --> pdb=" O ASPAY 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUAY 131 " --> pdb=" O ASNAY 127 " (cutoff:3.500A) Processing helix chain 'AY' and resid 142 through 149 removed outlier: 3.664A pdb=" N SERAY 146 " --> pdb=" O SERAY 142 " (cutoff:3.500A) Processing helix chain 'A0' and resid 10 through 14 Processing helix chain 'A0' and resid 19 through 29 Processing helix chain 'A0' and resid 30 through 32 No H-bonds generated for 'chain 'A0' and resid 30 through 32' Processing helix chain 'A0' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALA0 44 " --> pdb=" O ALAA0 40 " (cutoff:3.500A) Processing helix chain 'A0' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUA0 79 " --> pdb=" O VALA0 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHEA0 87 " --> pdb=" O LEUA0 83 " (cutoff:3.500A) Processing helix chain 'A0' and resid 92 through 97 Processing helix chain 'A0' and resid 103 through 133 removed outlier: 3.627A pdb=" N ARGA0 112 " --> pdb=" O LEUA0 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRA0 118 " --> pdb=" O VALA0 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALA0 119 " --> pdb=" O ASPA0 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUA0 131 " --> pdb=" O ASNA0 127 " (cutoff:3.500A) Processing helix chain 'A0' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERA0 146 " --> pdb=" O SERA0 142 " (cutoff:3.500A) Processing helix chain 'A2' and resid 10 through 14 Processing helix chain 'A2' and resid 19 through 29 Processing helix chain 'A2' and resid 30 through 32 No H-bonds generated for 'chain 'A2' and resid 30 through 32' Processing helix chain 'A2' and resid 37 through 49 removed outlier: 3.678A pdb=" N VALA2 44 " --> pdb=" O ALAA2 40 " (cutoff:3.500A) Processing helix chain 'A2' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUA2 79 " --> pdb=" O VALA2 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEA2 87 " --> pdb=" O LEUA2 83 " (cutoff:3.500A) Processing helix chain 'A2' and resid 92 through 97 Processing helix chain 'A2' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGA2 112 " --> pdb=" O LEUA2 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRA2 118 " --> pdb=" O VALA2 114 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VALA2 119 " --> pdb=" O ASPA2 115 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLUA2 131 " --> pdb=" O ASNA2 127 " (cutoff:3.500A) Processing helix chain 'A2' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERA2 146 " --> pdb=" O SERA2 142 " (cutoff:3.500A) Processing helix chain 'A4' and resid 10 through 14 Processing helix chain 'A4' and resid 19 through 29 Processing helix chain 'A4' and resid 30 through 32 No H-bonds generated for 'chain 'A4' and resid 30 through 32' Processing helix chain 'A4' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALA4 44 " --> pdb=" O ALAA4 40 " (cutoff:3.500A) Processing helix chain 'A4' and resid 75 through 87 removed outlier: 4.298A pdb=" N LEUA4 79 " --> pdb=" O VALA4 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHEA4 87 " --> pdb=" O LEUA4 83 " (cutoff:3.500A) Processing helix chain 'A4' and resid 92 through 97 Processing helix chain 'A4' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGA4 112 " --> pdb=" O LEUA4 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRA4 118 " --> pdb=" O VALA4 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALA4 119 " --> pdb=" O ASPA4 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUA4 131 " --> pdb=" O ASNA4 127 " (cutoff:3.500A) Processing helix chain 'A4' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERA4 146 " --> pdb=" O SERA4 142 " (cutoff:3.500A) Processing helix chain 'A6' and resid 10 through 14 Processing helix chain 'A6' and resid 19 through 29 Processing helix chain 'A6' and resid 30 through 32 No H-bonds generated for 'chain 'A6' and resid 30 through 32' Processing helix chain 'A6' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALA6 44 " --> pdb=" O ALAA6 40 " (cutoff:3.500A) Processing helix chain 'A6' and resid 75 through 87 removed outlier: 4.297A pdb=" N LEUA6 79 " --> pdb=" O VALA6 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEA6 87 " --> pdb=" O LEUA6 83 " (cutoff:3.500A) Processing helix chain 'A6' and resid 92 through 97 Processing helix chain 'A6' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGA6 112 " --> pdb=" O LEUA6 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRA6 118 " --> pdb=" O VALA6 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALA6 119 " --> pdb=" O ASPA6 115 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLUA6 131 " --> pdb=" O ASNA6 127 " (cutoff:3.500A) Processing helix chain 'A6' and resid 142 through 149 removed outlier: 3.663A pdb=" N SERA6 146 " --> pdb=" O SERA6 142 " (cutoff:3.500A) Processing helix chain 'A8' and resid 10 through 14 Processing helix chain 'A8' and resid 19 through 29 Processing helix chain 'A8' and resid 30 through 32 No H-bonds generated for 'chain 'A8' and resid 30 through 32' Processing helix chain 'A8' and resid 37 through 49 removed outlier: 3.679A pdb=" N VALA8 44 " --> pdb=" O ALAA8 40 " (cutoff:3.500A) Processing helix chain 'A8' and resid 75 through 87 removed outlier: 4.297A pdb=" N LEUA8 79 " --> pdb=" O VALA8 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHEA8 87 " --> pdb=" O LEUA8 83 " (cutoff:3.500A) Processing helix chain 'A8' and resid 92 through 97 Processing helix chain 'A8' and resid 103 through 133 removed outlier: 3.628A pdb=" N ARGA8 112 " --> pdb=" O LEUA8 108 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THRA8 118 " --> pdb=" O VALA8 114 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VALA8 119 " --> pdb=" O ASPA8 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLUA8 131 " --> pdb=" O ASNA8 127 " (cutoff:3.500A) Processing helix chain 'A8' and resid 142 through 149 removed outlier: 3.664A pdb=" N SERA8 146 " --> pdb=" O SERA8 142 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id= 2, first strand: chain 'C' and resid 17 through 18 Processing sheet with id= 3, first strand: chain 'E' and resid 17 through 18 Processing sheet with id= 4, first strand: chain 'G' and resid 17 through 18 Processing sheet with id= 5, first strand: chain 'I' and resid 17 through 18 Processing sheet with id= 6, first strand: chain 'K' and resid 17 through 18 Processing sheet with id= 7, first strand: chain 'M' and resid 17 through 18 Processing sheet with id= 8, first strand: chain 'O' and resid 17 through 18 Processing sheet with id= 9, first strand: chain 'Q' and resid 17 through 18 Processing sheet with id= 10, first strand: chain 'S' and resid 17 through 18 Processing sheet with id= 11, first strand: chain 'U' and resid 17 through 18 Processing sheet with id= 12, first strand: chain 'W' and resid 17 through 18 Processing sheet with id= 13, first strand: chain 'Y' and resid 17 through 18 Processing sheet with id= 14, first strand: chain '0' and resid 17 through 18 Processing sheet with id= 15, first strand: chain '2' and resid 17 through 18 Processing sheet with id= 16, first strand: chain '4' and resid 17 through 18 Processing sheet with id= 17, first strand: chain '6' and resid 17 through 18 Processing sheet with id= 18, first strand: chain '8' and resid 17 through 18 Processing sheet with id= 19, first strand: chain 'a' and resid 17 through 18 Processing sheet with id= 20, first strand: chain 'c' and resid 17 through 18 Processing sheet with id= 21, first strand: chain 'e' and resid 17 through 18 Processing sheet with id= 22, first strand: chain 'g' and resid 17 through 18 Processing sheet with id= 23, first strand: chain 'i' and resid 17 through 18 Processing sheet with id= 24, first strand: chain 'k' and resid 17 through 18 Processing sheet with id= 25, first strand: chain 'm' and resid 17 through 18 Processing sheet with id= 26, first strand: chain 'o' and resid 17 through 18 Processing sheet with id= 27, first strand: chain 'q' and resid 17 through 18 Processing sheet with id= 28, first strand: chain 's' and resid 17 through 18 Processing sheet with id= 29, first strand: chain 'u' and resid 17 through 18 Processing sheet with id= 30, first strand: chain 'w' and resid 17 through 18 Processing sheet with id= 31, first strand: chain 'y' and resid 17 through 18 Processing sheet with id= 32, first strand: chain 'AA' and resid 17 through 18 Processing sheet with id= 33, first strand: chain 'AC' and resid 17 through 18 Processing sheet with id= 34, first strand: chain 'AE' and resid 17 through 18 Processing sheet with id= 35, first strand: chain 'AG' and resid 17 through 18 Processing sheet with id= 36, first strand: chain 'AI' and resid 17 through 18 Processing sheet with id= 37, first strand: chain 'AK' and resid 17 through 18 Processing sheet with id= 38, first strand: chain 'AM' and resid 17 through 18 Processing sheet with id= 39, first strand: chain 'AO' and resid 17 through 18 Processing sheet with id= 40, first strand: chain 'AQ' and resid 17 through 18 Processing sheet with id= 41, first strand: chain 'AS' and resid 17 through 18 Processing sheet with id= 42, first strand: chain 'AU' and resid 17 through 18 Processing sheet with id= 43, first strand: chain 'AW' and resid 17 through 18 Processing sheet with id= 44, first strand: chain 'AY' and resid 17 through 18 Processing sheet with id= 45, first strand: chain 'A0' and resid 17 through 18 Processing sheet with id= 46, first strand: chain 'A2' and resid 17 through 18 Processing sheet with id= 47, first strand: chain 'A4' and resid 17 through 18 Processing sheet with id= 48, first strand: chain 'A6' and resid 17 through 18 Processing sheet with id= 49, first strand: chain 'A8' and resid 17 through 18 2744 hydrogen bonds defined for protein. 7791 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: 19.35 Time building geometry restraints manager: 22.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10584 1.31 - 1.44: 18068 1.44 - 1.56: 35048 1.56 - 1.68: 196 1.68 - 1.80: 49 Bond restraints: 63945 Sorted by residual: bond pdb=" O3' AAX 2 " pdb=" P AAX 3 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.07e+01 bond pdb=" O3' A r 2 " pdb=" P A r 3 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.07e+01 bond pdb=" O3' A P 2 " pdb=" P A P 3 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.06e+01 bond pdb=" O3' A f 2 " pdb=" P A f 3 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.06e+01 bond pdb=" O3' AAN 2 " pdb=" P AAN 3 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.06e+01 ... (remaining 63940 not shown) Histogram of bond angle deviations from ideal: 101.39 - 108.09: 4377 108.09 - 114.79: 36318 114.79 - 121.49: 31222 121.49 - 128.19: 15352 128.19 - 134.88: 735 Bond angle restraints: 88004 Sorted by residual: angle pdb=" N SERAC 142 " pdb=" CA SERAC 142 " pdb=" C SERAC 142 " ideal model delta sigma weight residual 114.56 101.39 13.17 1.27e+00 6.20e-01 1.08e+02 angle pdb=" N SERAM 142 " pdb=" CA SERAM 142 " pdb=" C SERAM 142 " ideal model delta sigma weight residual 114.56 101.39 13.17 1.27e+00 6.20e-01 1.08e+02 angle pdb=" N SERAA 142 " pdb=" CA SERAA 142 " pdb=" C SERAA 142 " ideal model delta sigma weight residual 114.56 101.39 13.17 1.27e+00 6.20e-01 1.07e+02 angle pdb=" N SER k 142 " pdb=" CA SER k 142 " pdb=" C SER k 142 " ideal model delta sigma weight residual 114.56 101.40 13.16 1.27e+00 6.20e-01 1.07e+02 angle pdb=" N SER i 142 " pdb=" CA SER i 142 " pdb=" C SER i 142 " ideal model delta sigma weight residual 114.56 101.40 13.16 1.27e+00 6.20e-01 1.07e+02 ... (remaining 87999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 35378 16.40 - 32.80: 1568 32.80 - 49.20: 833 49.20 - 65.60: 196 65.60 - 82.00: 49 Dihedral angle restraints: 38024 sinusoidal: 15876 harmonic: 22148 Sorted by residual: dihedral pdb=" CA GLU K 97 " pdb=" C GLU K 97 " pdb=" N ASN K 98 " pdb=" CA ASN K 98 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA GLU e 97 " pdb=" C GLU e 97 " pdb=" N ASN e 98 " pdb=" CA ASN e 98 " ideal model delta harmonic sigma weight residual 180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU 4 97 " pdb=" C GLU 4 97 " pdb=" N ASN 4 98 " pdb=" CA ASN 4 98 " ideal model delta harmonic sigma weight residual -180.00 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 38021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 9121 0.084 - 0.169: 826 0.169 - 0.253: 245 0.253 - 0.338: 196 0.338 - 0.422: 49 Chirality restraints: 10437 Sorted by residual: chirality pdb=" CA ASP 0 64 " pdb=" N ASP 0 64 " pdb=" C ASP 0 64 " pdb=" CB ASP 0 64 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA ASPAY 64 " pdb=" N ASPAY 64 " pdb=" C ASPAY 64 " pdb=" CB ASPAY 64 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA ASP 6 64 " pdb=" N ASP 6 64 " pdb=" C ASP 6 64 " pdb=" CB ASP 6 64 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 10434 not shown) Planarity restraints: 10878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILEAO 133 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C ILEAO 133 " 0.049 2.00e-02 2.50e+03 pdb=" O ILEAO 133 " -0.019 2.00e-02 2.50e+03 pdb=" N ARGAO 134 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE g 133 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C ILE g 133 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE g 133 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG g 134 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILEAW 133 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C ILEAW 133 " 0.049 2.00e-02 2.50e+03 pdb=" O ILEAW 133 " -0.019 2.00e-02 2.50e+03 pdb=" N ARGAW 134 " -0.017 2.00e-02 2.50e+03 ... (remaining 10875 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.91: 96 1.91 - 2.66: 2147 2.66 - 3.41: 90205 3.41 - 4.15: 153838 4.15 - 4.90: 284997 Nonbonded interactions: 531283 Sorted by model distance: nonbonded pdb=" O3' A J 3 " pdb=" P G L 1 " model vdw 1.166 3.400 nonbonded pdb=" O3' A V 3 " pdb=" P G X 1 " model vdw 1.166 3.400 nonbonded pdb=" O3' A b 3 " pdb=" P G d 1 " model vdw 1.166 3.400 nonbonded pdb=" O3' A 7 3 " pdb=" P G 9 1 " model vdw 1.166 3.400 nonbonded pdb=" O3' A l 3 " pdb=" P G n 1 " model vdw 1.166 3.400 ... (remaining 531278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A' selection = chain 'A0' selection = chain 'A2' selection = chain 'A4' selection = chain 'A6' selection = chain 'A8' selection = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AG' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AO' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AU' selection = chain 'AW' selection = chain 'AY' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A1' selection = chain 'A3' selection = chain 'A5' selection = chain 'A7' selection = chain 'A9' selection = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'AT' selection = chain 'AV' selection = chain 'AX' selection = chain 'AZ' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'x' selection = chain 'z' } 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 group one per residue 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 5.720 Check model and map are aligned: 0.730 Set scattering table: 0.450 Process input model: 137.350 Find NCS groups from input model: 3.400 Set up NCS constraints: 1.170 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.010 0.068 63945 Z= 0.653 Angle : 1.397 13.173 88004 Z= 0.980 Chirality : 0.076 0.422 10437 Planarity : 0.006 0.030 10878 Dihedral : 12.765 82.004 23520 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.51 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.23 (0.08), residues: 7399 helix: -3.20 (0.06), residues: 4214 sheet: None (None), residues: 0 loop : -2.02 (0.10), residues: 3185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAG 152 PHE 0.014 0.002 PHEA8 12 TYR 0.014 0.002 TYRAM 70 ARG 0.008 0.001 ARGA2 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2894 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2894 time to evaluate : 5.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.8523 (mp) cc_final: 0.8312 (mm) REVERT: A 64 ASP cc_start: 0.7301 (t70) cc_final: 0.6874 (p0) REVERT: A 87 PHE cc_start: 0.8209 (m-80) cc_final: 0.7811 (m-80) REVERT: A 93 ILE cc_start: 0.8034 (mt) cc_final: 0.7533 (mt) REVERT: A 94 ILE cc_start: 0.8325 (mm) cc_final: 0.7843 (mp) REVERT: A 127 ASN cc_start: 0.8063 (m-40) cc_final: 0.7697 (m110) REVERT: A 128 LEU cc_start: 0.8578 (tp) cc_final: 0.8080 (tp) REVERT: C 64 ASP cc_start: 0.7444 (t70) cc_final: 0.6613 (p0) REVERT: E 64 ASP cc_start: 0.7693 (t70) cc_final: 0.6864 (p0) REVERT: E 139 TYR cc_start: 0.7308 (m-10) cc_final: 0.6798 (m-10) REVERT: E 150 LEU cc_start: 0.7642 (mt) cc_final: 0.7245 (mt) REVERT: G 64 ASP cc_start: 0.7789 (t70) cc_final: 0.7051 (p0) REVERT: G 91 ASN cc_start: 0.6698 (t0) cc_final: 0.6440 (t0) REVERT: G 125 ILE cc_start: 0.8536 (mt) cc_final: 0.8188 (mm) REVERT: G 131 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6903 (mm-30) REVERT: G 139 TYR cc_start: 0.7785 (m-10) cc_final: 0.7450 (m-10) REVERT: G 150 LEU cc_start: 0.7670 (mt) cc_final: 0.7400 (mp) REVERT: I 64 ASP cc_start: 0.7614 (t70) cc_final: 0.6874 (p0) REVERT: I 72 TYR cc_start: 0.7663 (m-80) cc_final: 0.7423 (m-10) REVERT: I 148 SER cc_start: 0.7001 (t) cc_final: 0.6630 (t) REVERT: I 150 LEU cc_start: 0.7691 (mt) cc_final: 0.7473 (mt) REVERT: K 131 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6971 (mm-30) REVERT: K 145 GLU cc_start: 0.5769 (mt-10) cc_final: 0.5087 (mt-10) REVERT: K 148 SER cc_start: 0.6758 (t) cc_final: 0.6264 (p) REVERT: M 31 LEU cc_start: 0.8300 (mt) cc_final: 0.8043 (mp) REVERT: M 64 ASP cc_start: 0.8149 (t70) cc_final: 0.7022 (p0) REVERT: M 90 ARG cc_start: 0.6252 (ttm-80) cc_final: 0.5685 (mtp-110) REVERT: M 93 ILE cc_start: 0.7511 (mt) cc_final: 0.6874 (tt) REVERT: M 132 LEU cc_start: 0.8746 (tp) cc_final: 0.8509 (tt) REVERT: M 148 SER cc_start: 0.6556 (t) cc_final: 0.6194 (p) REVERT: M 150 LEU cc_start: 0.7989 (mt) cc_final: 0.7539 (mp) REVERT: O 4 ILE cc_start: 0.6444 (mp) cc_final: 0.5980 (mt) REVERT: O 31 LEU cc_start: 0.8397 (mt) cc_final: 0.8158 (mp) REVERT: O 64 ASP cc_start: 0.8074 (t70) cc_final: 0.7239 (p0) REVERT: O 84 LEU cc_start: 0.8133 (mp) cc_final: 0.7876 (mt) REVERT: O 87 PHE cc_start: 0.8111 (m-80) cc_final: 0.7694 (m-80) REVERT: O 150 LEU cc_start: 0.7875 (mt) cc_final: 0.7637 (mt) REVERT: Q 4 ILE cc_start: 0.6060 (mp) cc_final: 0.5782 (mt) REVERT: Q 31 LEU cc_start: 0.8341 (mt) cc_final: 0.8090 (mp) REVERT: Q 87 PHE cc_start: 0.7997 (m-80) cc_final: 0.7416 (m-80) REVERT: Q 109 ASP cc_start: 0.6991 (t70) cc_final: 0.6632 (t70) REVERT: Q 145 GLU cc_start: 0.5923 (mt-10) cc_final: 0.5656 (mm-30) REVERT: Q 148 SER cc_start: 0.6593 (t) cc_final: 0.6237 (t) REVERT: Q 150 LEU cc_start: 0.7943 (mt) cc_final: 0.7472 (mt) REVERT: S 31 LEU cc_start: 0.8228 (mt) cc_final: 0.7998 (mp) REVERT: S 59 THR cc_start: 0.8549 (m) cc_final: 0.8274 (t) REVERT: S 64 ASP cc_start: 0.7971 (t70) cc_final: 0.6954 (p0) REVERT: S 150 LEU cc_start: 0.7928 (mt) cc_final: 0.7646 (mt) REVERT: S 152 TRP cc_start: 0.5759 (t-100) cc_final: 0.5547 (t60) REVERT: U 25 ASN cc_start: 0.8572 (m-40) cc_final: 0.8367 (m-40) REVERT: U 31 LEU cc_start: 0.8218 (mt) cc_final: 0.7946 (mm) REVERT: U 87 PHE cc_start: 0.7644 (m-80) cc_final: 0.7292 (m-80) REVERT: U 91 ASN cc_start: 0.6747 (t0) cc_final: 0.6006 (t0) REVERT: W 4 ILE cc_start: 0.6982 (mp) cc_final: 0.6584 (mt) REVERT: W 93 ILE cc_start: 0.7607 (mt) cc_final: 0.7385 (tp) REVERT: W 109 ASP cc_start: 0.7104 (t70) cc_final: 0.6617 (t70) REVERT: Y 4 ILE cc_start: 0.6701 (mp) cc_final: 0.6288 (mt) REVERT: Y 87 PHE cc_start: 0.8001 (m-80) cc_final: 0.7675 (m-80) REVERT: Y 93 ILE cc_start: 0.7661 (mt) cc_final: 0.7408 (tp) REVERT: Y 125 ILE cc_start: 0.8757 (mt) cc_final: 0.8423 (mm) REVERT: 0 4 ILE cc_start: 0.7009 (mp) cc_final: 0.6701 (mt) REVERT: 0 50 GLU cc_start: 0.7418 (tp30) cc_final: 0.7042 (tp30) REVERT: 0 87 PHE cc_start: 0.7856 (m-80) cc_final: 0.7202 (m-80) REVERT: 0 93 ILE cc_start: 0.8038 (mt) cc_final: 0.7312 (tp) REVERT: 0 125 ILE cc_start: 0.8728 (mt) cc_final: 0.8354 (mm) REVERT: 0 131 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7053 (mm-30) REVERT: 0 151 VAL cc_start: 0.8617 (p) cc_final: 0.8369 (t) REVERT: 2 4 ILE cc_start: 0.7103 (mp) cc_final: 0.6685 (mt) REVERT: 2 24 ILE cc_start: 0.8255 (mp) cc_final: 0.8045 (mt) REVERT: 2 25 ASN cc_start: 0.8419 (m-40) cc_final: 0.8200 (m-40) REVERT: 2 31 LEU cc_start: 0.8275 (mt) cc_final: 0.7875 (mm) REVERT: 2 38 GLN cc_start: 0.7318 (tp40) cc_final: 0.6900 (tp-100) REVERT: 2 87 PHE cc_start: 0.8006 (m-80) cc_final: 0.7390 (m-80) REVERT: 2 93 ILE cc_start: 0.7994 (mt) cc_final: 0.7705 (tp) REVERT: 2 109 ASP cc_start: 0.6849 (t70) cc_final: 0.6443 (t70) REVERT: 2 125 ILE cc_start: 0.8969 (mt) cc_final: 0.8734 (mm) REVERT: 2 148 SER cc_start: 0.6722 (t) cc_final: 0.6408 (t) REVERT: 4 4 ILE cc_start: 0.7187 (mp) cc_final: 0.6790 (mt) REVERT: 4 23 LEU cc_start: 0.8178 (tp) cc_final: 0.7917 (tt) REVERT: 4 87 PHE cc_start: 0.8194 (m-80) cc_final: 0.7561 (m-80) REVERT: 4 94 ILE cc_start: 0.8575 (mm) cc_final: 0.8297 (mm) REVERT: 4 125 ILE cc_start: 0.8869 (mt) cc_final: 0.8534 (mm) REVERT: 6 4 ILE cc_start: 0.6961 (mp) cc_final: 0.6614 (mt) REVERT: 6 62 PHE cc_start: 0.6972 (t80) cc_final: 0.6725 (t80) REVERT: 6 84 LEU cc_start: 0.8376 (mp) cc_final: 0.8113 (mt) REVERT: 6 87 PHE cc_start: 0.8090 (m-80) cc_final: 0.7743 (m-80) REVERT: 6 90 ARG cc_start: 0.6186 (ttm-80) cc_final: 0.5742 (mtp-110) REVERT: 6 93 ILE cc_start: 0.8110 (mt) cc_final: 0.7143 (tp) REVERT: 6 94 ILE cc_start: 0.8283 (mm) cc_final: 0.8060 (mp) REVERT: 6 125 ILE cc_start: 0.8888 (mt) cc_final: 0.8639 (mm) REVERT: 6 127 ASN cc_start: 0.8034 (m-40) cc_final: 0.7608 (m-40) REVERT: 6 152 TRP cc_start: 0.5359 (t-100) cc_final: 0.4937 (t-100) REVERT: 8 4 ILE cc_start: 0.6932 (mp) cc_final: 0.6654 (mt) REVERT: 8 31 LEU cc_start: 0.8042 (mt) cc_final: 0.7731 (mm) REVERT: 8 50 GLU cc_start: 0.7373 (tp30) cc_final: 0.7171 (tp30) REVERT: 8 59 THR cc_start: 0.8512 (m) cc_final: 0.8285 (t) REVERT: 8 64 ASP cc_start: 0.6997 (t70) cc_final: 0.5997 (p0) REVERT: 8 87 PHE cc_start: 0.8015 (m-80) cc_final: 0.7714 (m-80) REVERT: 8 94 ILE cc_start: 0.8516 (mm) cc_final: 0.8203 (tp) REVERT: 8 127 ASN cc_start: 0.7908 (m-40) cc_final: 0.7521 (m110) REVERT: a 19 ASP cc_start: 0.7846 (t0) cc_final: 0.7644 (t0) REVERT: a 24 ILE cc_start: 0.8185 (mp) cc_final: 0.7957 (mm) REVERT: a 31 LEU cc_start: 0.8051 (mt) cc_final: 0.7510 (mm) REVERT: a 87 PHE cc_start: 0.8247 (m-80) cc_final: 0.7902 (m-80) REVERT: a 112 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.8009 (tpp80) REVERT: a 127 ASN cc_start: 0.7997 (m-40) cc_final: 0.7764 (m-40) REVERT: c 31 LEU cc_start: 0.8119 (mt) cc_final: 0.7866 (mm) REVERT: c 53 LYS cc_start: 0.7830 (mttm) cc_final: 0.7623 (pptt) REVERT: c 64 ASP cc_start: 0.7042 (t70) cc_final: 0.6702 (p0) REVERT: c 87 PHE cc_start: 0.8337 (m-80) cc_final: 0.7876 (m-80) REVERT: c 93 ILE cc_start: 0.8199 (mt) cc_final: 0.7842 (tp) REVERT: c 131 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7231 (mm-30) REVERT: c 150 LEU cc_start: 0.7153 (mt) cc_final: 0.6776 (mt) REVERT: e 4 ILE cc_start: 0.7066 (mp) cc_final: 0.6770 (mt) REVERT: e 50 GLU cc_start: 0.7066 (tp30) cc_final: 0.6741 (tp30) REVERT: e 53 LYS cc_start: 0.7626 (mttm) cc_final: 0.7418 (ptmt) REVERT: e 64 ASP cc_start: 0.7087 (t70) cc_final: 0.6652 (p0) REVERT: e 83 LEU cc_start: 0.8347 (tp) cc_final: 0.8118 (tp) REVERT: e 91 ASN cc_start: 0.7303 (t0) cc_final: 0.6979 (m-40) REVERT: e 94 ILE cc_start: 0.8380 (mm) cc_final: 0.7834 (mm) REVERT: e 127 ASN cc_start: 0.7991 (m-40) cc_final: 0.7654 (m110) REVERT: e 132 LEU cc_start: 0.7990 (tp) cc_final: 0.7677 (tt) REVERT: g 31 LEU cc_start: 0.8086 (mt) cc_final: 0.7859 (mp) REVERT: g 39 GLN cc_start: 0.7886 (tt0) cc_final: 0.7589 (tt0) REVERT: g 64 ASP cc_start: 0.7067 (t70) cc_final: 0.6740 (p0) REVERT: g 128 LEU cc_start: 0.8722 (tp) cc_final: 0.8272 (tp) REVERT: i 94 ILE cc_start: 0.8427 (mm) cc_final: 0.7969 (mp) REVERT: i 127 ASN cc_start: 0.8128 (m-40) cc_final: 0.7414 (m110) REVERT: i 128 LEU cc_start: 0.8684 (tp) cc_final: 0.8407 (tp) REVERT: k 19 ASP cc_start: 0.8182 (t0) cc_final: 0.7921 (t0) REVERT: k 39 GLN cc_start: 0.8046 (tt0) cc_final: 0.7825 (tt0) REVERT: k 50 GLU cc_start: 0.7278 (tp30) cc_final: 0.6850 (tp30) REVERT: m 127 ASN cc_start: 0.8297 (m-40) cc_final: 0.8081 (m110) REVERT: o 127 ASN cc_start: 0.8166 (m-40) cc_final: 0.7932 (m-40) REVERT: o 131 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7713 (mm-30) REVERT: q 152 TRP cc_start: 0.6142 (t-100) cc_final: 0.5083 (t-100) REVERT: s 42 THR cc_start: 0.7060 (p) cc_final: 0.6596 (p) REVERT: s 50 GLU cc_start: 0.7814 (tp30) cc_final: 0.7504 (tp30) REVERT: s 127 ASN cc_start: 0.8348 (m-40) cc_final: 0.7947 (m-40) REVERT: u 4 ILE cc_start: 0.7546 (mp) cc_final: 0.7284 (mt) REVERT: u 93 ILE cc_start: 0.8271 (mt) cc_final: 0.7971 (tt) REVERT: u 127 ASN cc_start: 0.8392 (m-40) cc_final: 0.8125 (m110) REVERT: w 127 ASN cc_start: 0.8210 (m-40) cc_final: 0.7819 (m110) REVERT: w 152 TRP cc_start: 0.6567 (t-100) cc_final: 0.5815 (t-100) REVERT: y 75 VAL cc_start: 0.8115 (t) cc_final: 0.7809 (t) REVERT: y 139 TYR cc_start: 0.8235 (m-10) cc_final: 0.7883 (m-10) REVERT: AA 88 ASP cc_start: 0.6962 (t0) cc_final: 0.6672 (t0) REVERT: AA 93 ILE cc_start: 0.8253 (mt) cc_final: 0.8001 (tt) REVERT: AA 127 ASN cc_start: 0.8339 (m-40) cc_final: 0.7844 (m-40) REVERT: AA 131 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7613 (mm-30) REVERT: AC 46 ARG cc_start: 0.7656 (mtt180) cc_final: 0.6859 (mmm-85) REVERT: AC 90 ARG cc_start: 0.6576 (ttm-80) cc_final: 0.6215 (mtt180) REVERT: AC 92 ARG cc_start: 0.5777 (ttt180) cc_final: 0.4068 (ttm170) REVERT: AC 127 ASN cc_start: 0.8291 (m-40) cc_final: 0.8050 (m110) REVERT: AE 23 LEU cc_start: 0.8041 (tp) cc_final: 0.7745 (tt) REVERT: AE 39 GLN cc_start: 0.7999 (tt0) cc_final: 0.7568 (mp10) REVERT: AE 46 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6904 (mmm-85) REVERT: AE 62 PHE cc_start: 0.7226 (t80) cc_final: 0.6561 (t80) REVERT: AE 80 VAL cc_start: 0.8492 (m) cc_final: 0.8265 (p) REVERT: AE 90 ARG cc_start: 0.6262 (ttm-80) cc_final: 0.5719 (mtt180) REVERT: AE 92 ARG cc_start: 0.6235 (ttt180) cc_final: 0.4485 (ttm170) REVERT: AE 93 ILE cc_start: 0.8473 (mt) cc_final: 0.8201 (tt) REVERT: AE 94 ILE cc_start: 0.8308 (mm) cc_final: 0.7959 (tp) REVERT: AE 139 TYR cc_start: 0.8356 (m-10) cc_final: 0.8022 (m-80) REVERT: AE 150 LEU cc_start: 0.6478 (mt) cc_final: 0.6167 (mt) REVERT: AE 151 VAL cc_start: 0.8609 (p) cc_final: 0.8253 (m) REVERT: AG 39 GLN cc_start: 0.8130 (tt0) cc_final: 0.7591 (mp10) REVERT: AG 46 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7185 (mmm-85) REVERT: AG 92 ARG cc_start: 0.6422 (ttt180) cc_final: 0.4016 (ttm170) REVERT: AG 94 ILE cc_start: 0.8236 (mm) cc_final: 0.7847 (mm) REVERT: AG 151 VAL cc_start: 0.8494 (p) cc_final: 0.8285 (m) REVERT: AI 39 GLN cc_start: 0.8094 (tt0) cc_final: 0.7557 (mp10) REVERT: AI 46 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7291 (mmm-85) REVERT: AI 92 ARG cc_start: 0.6130 (ttt180) cc_final: 0.4021 (ttm170) REVERT: AI 94 ILE cc_start: 0.8168 (mm) cc_final: 0.7944 (tp) REVERT: AI 139 TYR cc_start: 0.8445 (m-10) cc_final: 0.8236 (m-80) REVERT: AI 150 LEU cc_start: 0.5700 (mt) cc_final: 0.5483 (mt) REVERT: AK 39 GLN cc_start: 0.8180 (tt0) cc_final: 0.7414 (mp10) REVERT: AK 46 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7268 (mmm-85) REVERT: AK 51 VAL cc_start: 0.7431 (p) cc_final: 0.6980 (m) REVERT: AK 62 PHE cc_start: 0.7321 (t80) cc_final: 0.7099 (t80) REVERT: AK 88 ASP cc_start: 0.6887 (t0) cc_final: 0.6357 (t0) REVERT: AK 92 ARG cc_start: 0.5681 (ttt180) cc_final: 0.3936 (ttm170) REVERT: AK 131 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7727 (mm-30) REVERT: AM 39 GLN cc_start: 0.8048 (tt0) cc_final: 0.7742 (mp10) REVERT: AM 51 VAL cc_start: 0.7533 (p) cc_final: 0.7197 (m) REVERT: AM 88 ASP cc_start: 0.6994 (t0) cc_final: 0.6630 (t0) REVERT: AM 90 ARG cc_start: 0.6598 (ttm-80) cc_final: 0.5883 (mtt180) REVERT: AM 92 ARG cc_start: 0.6007 (ttt180) cc_final: 0.4078 (ttm170) REVERT: AM 139 TYR cc_start: 0.8109 (m-10) cc_final: 0.7842 (m-80) REVERT: AM 140 ASN cc_start: 0.8089 (p0) cc_final: 0.7624 (p0) REVERT: AM 151 VAL cc_start: 0.8141 (p) cc_final: 0.7934 (t) REVERT: AO 23 LEU cc_start: 0.8161 (tp) cc_final: 0.7838 (tt) REVERT: AO 46 ARG cc_start: 0.7949 (mtt180) cc_final: 0.6808 (tmm160) REVERT: AO 75 VAL cc_start: 0.8249 (t) cc_final: 0.7999 (t) REVERT: AO 88 ASP cc_start: 0.6774 (t0) cc_final: 0.6248 (t0) REVERT: AO 92 ARG cc_start: 0.6083 (ttt180) cc_final: 0.4232 (ttm-80) REVERT: AO 94 ILE cc_start: 0.8290 (mm) cc_final: 0.7941 (tp) REVERT: AO 113 ARG cc_start: 0.7649 (mtp-110) cc_final: 0.7292 (mtp85) REVERT: AO 151 VAL cc_start: 0.7990 (p) cc_final: 0.7776 (t) REVERT: AQ 46 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7182 (mmm-85) REVERT: AQ 62 PHE cc_start: 0.7169 (t80) cc_final: 0.6835 (t80) REVERT: AQ 90 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.6134 (mtt180) REVERT: AQ 92 ARG cc_start: 0.6357 (ttt180) cc_final: 0.4716 (ttm170) REVERT: AQ 109 ASP cc_start: 0.7579 (t70) cc_final: 0.7130 (t70) REVERT: AQ 121 ILE cc_start: 0.7988 (mt) cc_final: 0.7722 (mt) REVERT: AQ 151 VAL cc_start: 0.7831 (p) cc_final: 0.7557 (t) REVERT: AS 46 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7114 (mmm-85) REVERT: AS 90 ARG cc_start: 0.6754 (ttm-80) cc_final: 0.5840 (mtt180) REVERT: AS 92 ARG cc_start: 0.6147 (ttt180) cc_final: 0.4302 (ttm170) REVERT: AS 112 ARG cc_start: 0.8336 (tpp-160) cc_final: 0.8111 (tpp-160) REVERT: AS 131 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7776 (mm-30) REVERT: AS 140 ASN cc_start: 0.8194 (p0) cc_final: 0.7942 (p0) REVERT: AU 23 LEU cc_start: 0.8259 (tp) cc_final: 0.8020 (tt) REVERT: AU 39 GLN cc_start: 0.8077 (tt0) cc_final: 0.7502 (mp10) REVERT: AU 46 ARG cc_start: 0.7882 (mtt180) cc_final: 0.6760 (tmm160) REVERT: AU 88 ASP cc_start: 0.6690 (t0) cc_final: 0.6205 (t0) REVERT: AU 90 ARG cc_start: 0.6647 (ttm-80) cc_final: 0.6141 (mtt180) REVERT: AU 92 ARG cc_start: 0.6180 (ttt180) cc_final: 0.4447 (ttm170) REVERT: AU 112 ARG cc_start: 0.8196 (tpp-160) cc_final: 0.7934 (mmt180) REVERT: AU 139 TYR cc_start: 0.7862 (m-10) cc_final: 0.7653 (m-80) REVERT: AW 34 GLN cc_start: 0.7436 (mt0) cc_final: 0.7216 (mt0) REVERT: AW 38 GLN cc_start: 0.7163 (tp40) cc_final: 0.6692 (mm-40) REVERT: AW 39 GLN cc_start: 0.7930 (tt0) cc_final: 0.7604 (mp10) REVERT: AW 45 GLN cc_start: 0.6944 (tt0) cc_final: 0.6605 (tt0) REVERT: AW 46 ARG cc_start: 0.7726 (mtt180) cc_final: 0.6832 (tmm160) REVERT: AW 92 ARG cc_start: 0.5736 (ttt180) cc_final: 0.4062 (ttm170) REVERT: AW 112 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8021 (mmt180) REVERT: AW 139 TYR cc_start: 0.7644 (m-10) cc_final: 0.7432 (m-80) REVERT: AW 140 ASN cc_start: 0.8328 (p0) cc_final: 0.8088 (p0) REVERT: AW 150 LEU cc_start: 0.6067 (mt) cc_final: 0.5784 (mt) REVERT: AW 151 VAL cc_start: 0.7843 (p) cc_final: 0.7581 (t) REVERT: AY 33 ASN cc_start: 0.7648 (t0) cc_final: 0.7441 (t0) REVERT: AY 39 GLN cc_start: 0.8022 (tt0) cc_final: 0.7681 (mp10) REVERT: AY 46 ARG cc_start: 0.7812 (mtt180) cc_final: 0.6695 (tmm160) REVERT: AY 65 SER cc_start: 0.6896 (p) cc_final: 0.6664 (m) REVERT: AY 91 ASN cc_start: 0.7940 (t0) cc_final: 0.7733 (t0) REVERT: AY 92 ARG cc_start: 0.5861 (ttt180) cc_final: 0.4341 (ttm170) REVERT: AY 130 VAL cc_start: 0.8734 (m) cc_final: 0.8493 (t) REVERT: AY 151 VAL cc_start: 0.7962 (p) cc_final: 0.7718 (t) REVERT: A0 33 ASN cc_start: 0.7911 (t0) cc_final: 0.7691 (t0) REVERT: A0 39 GLN cc_start: 0.7970 (tt0) cc_final: 0.7439 (mp10) REVERT: A0 90 ARG cc_start: 0.6853 (ttm-80) cc_final: 0.6462 (mtt180) REVERT: A0 91 ASN cc_start: 0.7977 (t0) cc_final: 0.7506 (t0) REVERT: A0 92 ARG cc_start: 0.6107 (ttt180) cc_final: 0.4414 (ttm170) REVERT: A0 152 TRP cc_start: 0.6048 (t-100) cc_final: 0.5568 (t-100) REVERT: A2 38 GLN cc_start: 0.7017 (tp40) cc_final: 0.5598 (mp10) REVERT: A2 39 GLN cc_start: 0.7622 (tt0) cc_final: 0.7139 (mp10) REVERT: A2 65 SER cc_start: 0.7581 (p) cc_final: 0.7325 (m) REVERT: A2 88 ASP cc_start: 0.7213 (t0) cc_final: 0.6702 (t0) REVERT: A2 92 ARG cc_start: 0.5865 (ttt180) cc_final: 0.4485 (ttm170) REVERT: A2 112 ARG cc_start: 0.8391 (tpp-160) cc_final: 0.8102 (tpt170) REVERT: A2 130 VAL cc_start: 0.8942 (m) cc_final: 0.8537 (p) REVERT: A4 33 ASN cc_start: 0.7561 (t0) cc_final: 0.6719 (m110) REVERT: A4 38 GLN cc_start: 0.6746 (tp40) cc_final: 0.5317 (mp10) REVERT: A4 39 GLN cc_start: 0.7571 (tt0) cc_final: 0.7108 (mp10) REVERT: A4 65 SER cc_start: 0.7808 (p) cc_final: 0.7529 (m) REVERT: A4 88 ASP cc_start: 0.7379 (t0) cc_final: 0.7159 (t0) REVERT: A4 92 ARG cc_start: 0.5422 (ttt180) cc_final: 0.4324 (ttm170) REVERT: A4 130 VAL cc_start: 0.8952 (m) cc_final: 0.8747 (p) REVERT: A4 151 VAL cc_start: 0.7766 (p) cc_final: 0.7560 (t) REVERT: A6 27 CYS cc_start: 0.7714 (p) cc_final: 0.7507 (p) REVERT: A6 33 ASN cc_start: 0.7989 (t0) cc_final: 0.7212 (m110) REVERT: A6 38 GLN cc_start: 0.6809 (tp40) cc_final: 0.5219 (pm20) REVERT: A6 65 SER cc_start: 0.7490 (p) cc_final: 0.7232 (m) REVERT: A6 88 ASP cc_start: 0.7135 (t0) cc_final: 0.6517 (t0) REVERT: A6 112 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.7910 (tpt170) REVERT: A6 139 TYR cc_start: 0.8292 (m-10) cc_final: 0.8029 (m-80) REVERT: A6 151 VAL cc_start: 0.7717 (p) cc_final: 0.7105 (t) REVERT: A8 33 ASN cc_start: 0.7838 (t0) cc_final: 0.7291 (m-40) REVERT: A8 38 GLN cc_start: 0.7001 (tp40) cc_final: 0.5338 (pm20) REVERT: A8 45 GLN cc_start: 0.8140 (tt0) cc_final: 0.7899 (tt0) REVERT: A8 87 PHE cc_start: 0.8090 (m-80) cc_final: 0.7757 (m-80) REVERT: A8 90 ARG cc_start: 0.6897 (ttm-80) cc_final: 0.6629 (mtt180) outliers start: 0 outliers final: 0 residues processed: 2894 average time/residue: 0.6882 time to fit residues: 3162.0188 Evaluate side-chains 1699 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1699 time to evaluate : 5.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 6.9990 chunk 557 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 375 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 576 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 428 optimal weight: 6.9990 chunk 667 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN C 39 GLN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 47 GLN G 39 GLN G 57 GLN ** G 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 57 GLN K 39 GLN K 47 GLN ** K 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 GLN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 57 GLN U 73 ASN ** U 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN W 45 GLN W 73 ASN ** W 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN Y 39 GLN ** Y 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 39 GLN 0 73 ASN 0 91 ASN 2 39 GLN 2 73 ASN 4 39 GLN ** 4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 39 GLN 6 73 ASN 8 39 GLN 8 73 ASN c 25 ASN g 29 ASN g 39 GLN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 ASN g 127 ASN i 39 GLN ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 39 GLN m 29 ASN ** m 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 98 ASN o 91 ASN o 98 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 39 GLN s 45 GLN ** s 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 98 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 98 ASN w 57 GLN ** w 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 57 GLN y 98 ASN y 127 ASN AA 29 ASN AA 47 GLN ** AA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 73 ASN ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 91 ASN ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 91 ASN AI 98 ASN ** AI 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 91 ASN ** AK 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 98 ASN ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 91 ASN ** AO 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 45 GLN AQ 91 ASN AQ 126 ASN ** AS 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 127 ASN AU 57 GLN ** AU 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 127 ASN ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 34 GLN A2 36 GLN A2 45 GLN A2 91 ASN A4 45 GLN ** A4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 101 ASN A6 39 GLN ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 126 ASN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 36 GLN A8 39 GLN ** A8 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 126 ASN A8 127 ASN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 63945 Z= 0.328 Angle : 0.716 6.202 88004 Z= 0.393 Chirality : 0.046 0.179 10437 Planarity : 0.006 0.054 10878 Dihedral : 12.094 66.883 10094 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.42 % Allowed : 3.16 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.02 (0.08), residues: 7399 helix: -1.57 (0.07), residues: 4116 sheet: None (None), residues: 0 loop : -2.53 (0.09), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 152 PHE 0.030 0.003 PHE e 67 TYR 0.021 0.002 TYR W 70 ARG 0.013 0.001 ARG 6 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2104 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 2076 time to evaluate : 5.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 CYS cc_start: 0.8050 (p) cc_final: 0.7663 (p) REVERT: A 50 GLU cc_start: 0.7918 (tp30) cc_final: 0.7535 (tp30) REVERT: A 53 LYS cc_start: 0.7604 (ptmt) cc_final: 0.7363 (ptpp) REVERT: A 62 PHE cc_start: 0.7202 (t80) cc_final: 0.6877 (t80) REVERT: A 141 ARG cc_start: 0.6613 (ttt90) cc_final: 0.6208 (ttm-80) REVERT: C 19 ASP cc_start: 0.7813 (t0) cc_final: 0.7319 (m-30) REVERT: C 64 ASP cc_start: 0.7306 (t70) cc_final: 0.6981 (p0) REVERT: C 77 ASP cc_start: 0.7816 (t70) cc_final: 0.7612 (t70) REVERT: C 127 ASN cc_start: 0.7878 (m-40) cc_final: 0.7540 (m-40) REVERT: E 19 ASP cc_start: 0.7663 (t0) cc_final: 0.7131 (m-30) REVERT: E 64 ASP cc_start: 0.7764 (t70) cc_final: 0.7157 (p0) REVERT: E 84 LEU cc_start: 0.8507 (mt) cc_final: 0.8301 (mt) REVERT: E 139 TYR cc_start: 0.7905 (m-10) cc_final: 0.7293 (m-10) REVERT: G 19 ASP cc_start: 0.7844 (t0) cc_final: 0.7492 (t0) REVERT: G 64 ASP cc_start: 0.7495 (t70) cc_final: 0.7150 (p0) REVERT: I 47 GLN cc_start: 0.8260 (mt0) cc_final: 0.7966 (mt0) REVERT: K 64 ASP cc_start: 0.8122 (t70) cc_final: 0.7340 (p0) REVERT: K 141 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7315 (ttm-80) REVERT: M 19 ASP cc_start: 0.7456 (t0) cc_final: 0.7182 (t0) REVERT: M 29 ASN cc_start: 0.7179 (m110) cc_final: 0.6886 (t0) REVERT: M 31 LEU cc_start: 0.8367 (mt) cc_final: 0.8095 (mm) REVERT: M 64 ASP cc_start: 0.7976 (t70) cc_final: 0.7288 (p0) REVERT: M 131 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6997 (mm-30) REVERT: O 19 ASP cc_start: 0.7943 (t0) cc_final: 0.7622 (t0) REVERT: O 62 PHE cc_start: 0.7913 (t80) cc_final: 0.7685 (t80) REVERT: O 89 THR cc_start: 0.7624 (m) cc_final: 0.7017 (p) REVERT: O 134 ARG cc_start: 0.7172 (mtp85) cc_final: 0.6841 (mtt-85) REVERT: Q 62 PHE cc_start: 0.7889 (t80) cc_final: 0.7669 (t80) REVERT: Q 68 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7405 (mmmm) REVERT: S 59 THR cc_start: 0.8679 (m) cc_final: 0.8419 (t) REVERT: S 62 PHE cc_start: 0.7700 (t80) cc_final: 0.7468 (t80) REVERT: S 109 ASP cc_start: 0.6821 (t70) cc_final: 0.6590 (t70) REVERT: U 25 ASN cc_start: 0.8725 (m-40) cc_final: 0.8241 (m-40) REVERT: U 31 LEU cc_start: 0.8104 (mt) cc_final: 0.7873 (mm) REVERT: U 43 VAL cc_start: 0.8113 (p) cc_final: 0.7865 (m) REVERT: U 62 PHE cc_start: 0.7674 (t80) cc_final: 0.7307 (t80) REVERT: U 68 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7421 (mmmm) REVERT: U 89 THR cc_start: 0.7429 (m) cc_final: 0.6937 (p) REVERT: W 62 PHE cc_start: 0.7398 (t80) cc_final: 0.6984 (t80) REVERT: W 93 ILE cc_start: 0.7743 (mt) cc_final: 0.7094 (tp) REVERT: W 141 ARG cc_start: 0.7295 (ttt90) cc_final: 0.6412 (ttt90) REVERT: Y 38 GLN cc_start: 0.7184 (tp40) cc_final: 0.6728 (tp40) REVERT: Y 59 THR cc_start: 0.8624 (m) cc_final: 0.8408 (t) REVERT: Y 93 ILE cc_start: 0.7803 (mt) cc_final: 0.7517 (tp) REVERT: Y 112 ARG cc_start: 0.8103 (tpp-160) cc_final: 0.7728 (tpt170) REVERT: Y 127 ASN cc_start: 0.8475 (m-40) cc_final: 0.8241 (m-40) REVERT: Y 131 GLU cc_start: 0.7634 (mp0) cc_final: 0.7312 (mp0) REVERT: 0 50 GLU cc_start: 0.7440 (tp30) cc_final: 0.7154 (tp30) REVERT: 0 62 PHE cc_start: 0.7423 (t80) cc_final: 0.6841 (t80) REVERT: 0 89 THR cc_start: 0.7409 (m) cc_final: 0.6600 (p) REVERT: 0 93 ILE cc_start: 0.8056 (mt) cc_final: 0.7174 (tp) REVERT: 0 127 ASN cc_start: 0.8526 (m-40) cc_final: 0.8132 (m110) REVERT: 2 38 GLN cc_start: 0.6827 (tp40) cc_final: 0.6302 (tp-100) REVERT: 2 89 THR cc_start: 0.7742 (m) cc_final: 0.7104 (p) REVERT: 2 93 ILE cc_start: 0.7955 (mt) cc_final: 0.7408 (tp) REVERT: 2 127 ASN cc_start: 0.8347 (m-40) cc_final: 0.8129 (m110) REVERT: 4 21 ILE cc_start: 0.8267 (mp) cc_final: 0.8045 (mp) REVERT: 4 62 PHE cc_start: 0.6990 (t80) cc_final: 0.6758 (t80) REVERT: 4 150 LEU cc_start: 0.8073 (mt) cc_final: 0.7565 (mt) REVERT: 6 24 ILE cc_start: 0.8282 (mm) cc_final: 0.7933 (mm) REVERT: 6 25 ASN cc_start: 0.8436 (m-40) cc_final: 0.7993 (m-40) REVERT: 6 27 CYS cc_start: 0.8324 (p) cc_final: 0.8012 (p) REVERT: 6 50 GLU cc_start: 0.7436 (tp30) cc_final: 0.7230 (tp30) REVERT: 6 59 THR cc_start: 0.8682 (m) cc_final: 0.8411 (t) REVERT: 6 127 ASN cc_start: 0.8460 (m-40) cc_final: 0.8195 (m110) REVERT: 6 131 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7017 (mm-30) REVERT: 8 64 ASP cc_start: 0.6989 (t70) cc_final: 0.6256 (p0) REVERT: 8 94 ILE cc_start: 0.8283 (mm) cc_final: 0.7714 (mm) REVERT: 8 127 ASN cc_start: 0.8126 (m-40) cc_final: 0.7854 (m110) REVERT: a 25 ASN cc_start: 0.8750 (m-40) cc_final: 0.8326 (m-40) REVERT: a 38 GLN cc_start: 0.7173 (tp40) cc_final: 0.6957 (tp40) REVERT: a 59 THR cc_start: 0.8533 (m) cc_final: 0.8328 (t) REVERT: a 109 ASP cc_start: 0.7256 (t70) cc_final: 0.6982 (t70) REVERT: a 112 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.8105 (tpp-160) REVERT: a 127 ASN cc_start: 0.8299 (m-40) cc_final: 0.8044 (m110) REVERT: c 25 ASN cc_start: 0.8857 (m-40) cc_final: 0.8501 (m110) REVERT: c 27 CYS cc_start: 0.8624 (p) cc_final: 0.8305 (p) REVERT: c 62 PHE cc_start: 0.6935 (t80) cc_final: 0.6693 (t80) REVERT: c 93 ILE cc_start: 0.8211 (mt) cc_final: 0.7451 (tp) REVERT: c 141 ARG cc_start: 0.6820 (ttt90) cc_final: 0.5814 (ttt90) REVERT: c 150 LEU cc_start: 0.8019 (mt) cc_final: 0.7389 (mt) REVERT: e 25 ASN cc_start: 0.8743 (m-40) cc_final: 0.8527 (m110) REVERT: e 50 GLU cc_start: 0.7333 (tp30) cc_final: 0.6780 (tp30) REVERT: e 91 ASN cc_start: 0.7048 (t0) cc_final: 0.6754 (m-40) REVERT: e 129 ILE cc_start: 0.8003 (tp) cc_final: 0.7711 (tp) REVERT: e 141 ARG cc_start: 0.6435 (ttt90) cc_final: 0.5750 (ttm-80) REVERT: g 24 ILE cc_start: 0.8790 (mm) cc_final: 0.8386 (mm) REVERT: g 38 GLN cc_start: 0.7147 (tp40) cc_final: 0.6912 (tp40) REVERT: g 62 PHE cc_start: 0.6939 (t80) cc_final: 0.6480 (t80) REVERT: g 141 ARG cc_start: 0.7179 (ttt90) cc_final: 0.6632 (ttt90) REVERT: i 27 CYS cc_start: 0.7921 (p) cc_final: 0.7697 (t) REVERT: i 53 LYS cc_start: 0.7807 (pttp) cc_final: 0.7566 (ptpp) REVERT: i 62 PHE cc_start: 0.6765 (t80) cc_final: 0.6470 (t80) REVERT: i 68 LYS cc_start: 0.7765 (mmmm) cc_final: 0.7250 (mmtp) REVERT: i 95 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7839 (mm-30) REVERT: i 126 ASN cc_start: 0.7583 (t0) cc_final: 0.7177 (t0) REVERT: k 19 ASP cc_start: 0.8357 (t0) cc_final: 0.8045 (t0) REVERT: k 39 GLN cc_start: 0.8224 (tt0) cc_final: 0.7943 (tt0) REVERT: k 50 GLU cc_start: 0.7589 (tp30) cc_final: 0.7122 (tp30) REVERT: k 62 PHE cc_start: 0.7026 (t80) cc_final: 0.6812 (t80) REVERT: m 129 ILE cc_start: 0.8023 (tp) cc_final: 0.7790 (tp) REVERT: o 80 VAL cc_start: 0.8342 (m) cc_final: 0.8054 (p) REVERT: o 84 LEU cc_start: 0.8726 (mt) cc_final: 0.8440 (mm) REVERT: o 129 ILE cc_start: 0.7962 (tp) cc_final: 0.7661 (tp) REVERT: q 29 ASN cc_start: 0.7686 (m-40) cc_final: 0.7405 (m110) REVERT: q 129 ILE cc_start: 0.8038 (tp) cc_final: 0.7788 (tp) REVERT: s 50 GLU cc_start: 0.7911 (tp30) cc_final: 0.7680 (tp30) REVERT: s 152 TRP cc_start: 0.6383 (t-100) cc_final: 0.5476 (t-100) REVERT: u 62 PHE cc_start: 0.6965 (t80) cc_final: 0.6327 (t80) REVERT: u 113 ARG cc_start: 0.7125 (mtp85) cc_final: 0.6825 (mtp85) REVERT: u 141 ARG cc_start: 0.7089 (ttt90) cc_final: 0.6585 (ttt180) REVERT: w 19 ASP cc_start: 0.8168 (t0) cc_final: 0.7070 (m-30) REVERT: w 22 GLU cc_start: 0.8249 (pp20) cc_final: 0.7867 (pp20) REVERT: w 127 ASN cc_start: 0.8310 (m-40) cc_final: 0.8088 (m110) REVERT: y 19 ASP cc_start: 0.8048 (t0) cc_final: 0.7647 (t0) REVERT: y 22 GLU cc_start: 0.8330 (pp20) cc_final: 0.8104 (pp20) REVERT: y 53 LYS cc_start: 0.8235 (mtmm) cc_final: 0.8012 (mtmm) REVERT: AA 19 ASP cc_start: 0.8096 (t0) cc_final: 0.7746 (t0) REVERT: AA 29 ASN cc_start: 0.8313 (m-40) cc_final: 0.8017 (m110) REVERT: AA 95 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7199 (mm-30) REVERT: AA 127 ASN cc_start: 0.8353 (m-40) cc_final: 0.8121 (m-40) REVERT: AC 19 ASP cc_start: 0.8015 (t0) cc_final: 0.7577 (m-30) REVERT: AC 46 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7539 (mmm-85) REVERT: AC 55 SER cc_start: 0.9196 (m) cc_final: 0.8677 (t) REVERT: AC 57 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7363 (mp10) REVERT: AC 62 PHE cc_start: 0.7118 (t80) cc_final: 0.6798 (t80) REVERT: AC 90 ARG cc_start: 0.6532 (ttm-80) cc_final: 0.5827 (mtt180) REVERT: AC 92 ARG cc_start: 0.6106 (ttt180) cc_final: 0.4231 (ttm170) REVERT: AC 129 ILE cc_start: 0.8042 (tp) cc_final: 0.7754 (tp) REVERT: AE 39 GLN cc_start: 0.8199 (tt0) cc_final: 0.7680 (mp10) REVERT: AE 46 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7388 (mmm-85) REVERT: AE 62 PHE cc_start: 0.7427 (t80) cc_final: 0.7183 (t80) REVERT: AE 76 LEU cc_start: 0.8414 (mp) cc_final: 0.7738 (mp) REVERT: AE 92 ARG cc_start: 0.5884 (ttt180) cc_final: 0.4418 (ttm170) REVERT: AE 129 ILE cc_start: 0.8029 (tp) cc_final: 0.7763 (tp) REVERT: AG 19 ASP cc_start: 0.7923 (t0) cc_final: 0.7417 (m-30) REVERT: AG 39 GLN cc_start: 0.8134 (tt0) cc_final: 0.7502 (mp10) REVERT: AG 46 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7541 (mtp180) REVERT: AG 92 ARG cc_start: 0.6138 (ttt180) cc_final: 0.4090 (ttm170) REVERT: AG 129 ILE cc_start: 0.8089 (tp) cc_final: 0.7871 (tp) REVERT: AI 39 GLN cc_start: 0.8490 (tt0) cc_final: 0.7701 (mp10) REVERT: AI 46 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7708 (mmm-85) REVERT: AI 62 PHE cc_start: 0.7335 (t80) cc_final: 0.6834 (t80) REVERT: AI 92 ARG cc_start: 0.5601 (ttt180) cc_final: 0.4127 (ttm170) REVERT: AI 129 ILE cc_start: 0.8205 (tp) cc_final: 0.7962 (tp) REVERT: AK 39 GLN cc_start: 0.8352 (tt0) cc_final: 0.7429 (mp10) REVERT: AK 46 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7667 (mmm-85) REVERT: AK 62 PHE cc_start: 0.7438 (t80) cc_final: 0.7184 (t80) REVERT: AK 88 ASP cc_start: 0.6980 (t0) cc_final: 0.6630 (t0) REVERT: AK 92 ARG cc_start: 0.4948 (ttt180) cc_final: 0.3555 (ttm170) REVERT: AM 19 ASP cc_start: 0.7607 (t0) cc_final: 0.7397 (t0) REVERT: AM 39 GLN cc_start: 0.8415 (tt0) cc_final: 0.7795 (mp10) REVERT: AM 53 LYS cc_start: 0.7348 (mmpt) cc_final: 0.7027 (mtmm) REVERT: AM 57 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7549 (mm-40) REVERT: AM 62 PHE cc_start: 0.7248 (t80) cc_final: 0.7010 (t80) REVERT: AM 88 ASP cc_start: 0.7465 (t0) cc_final: 0.7157 (t0) REVERT: AM 92 ARG cc_start: 0.5234 (ttt180) cc_final: 0.3875 (ttm170) REVERT: AO 46 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7652 (mtp180) REVERT: AO 88 ASP cc_start: 0.7144 (t0) cc_final: 0.6909 (t0) REVERT: AO 92 ARG cc_start: 0.5429 (ttt180) cc_final: 0.3480 (ttm-80) REVERT: AO 140 ASN cc_start: 0.7610 (p0) cc_final: 0.7295 (p0) REVERT: AQ 46 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7634 (mtp180) REVERT: AQ 50 GLU cc_start: 0.8182 (tp30) cc_final: 0.7894 (tp30) REVERT: AQ 62 PHE cc_start: 0.7403 (t80) cc_final: 0.7097 (t80) REVERT: AQ 92 ARG cc_start: 0.5446 (ttt180) cc_final: 0.4195 (ttm170) REVERT: AQ 109 ASP cc_start: 0.7607 (t70) cc_final: 0.7293 (t70) REVERT: AS 29 ASN cc_start: 0.8227 (m110) cc_final: 0.7644 (m110) REVERT: AS 46 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7575 (mtp180) REVERT: AS 88 ASP cc_start: 0.6872 (t0) cc_final: 0.6366 (t0) REVERT: AS 90 ARG cc_start: 0.6824 (ttm-80) cc_final: 0.5897 (mtt180) REVERT: AS 91 ASN cc_start: 0.6802 (t0) cc_final: 0.6449 (t0) REVERT: AS 92 ARG cc_start: 0.4693 (ttt180) cc_final: 0.3393 (ttm170) REVERT: AS 129 ILE cc_start: 0.8533 (tp) cc_final: 0.8332 (tp) REVERT: AS 140 ASN cc_start: 0.7956 (p0) cc_final: 0.7104 (p0) REVERT: AU 33 ASN cc_start: 0.7778 (m-40) cc_final: 0.7176 (m-40) REVERT: AU 34 GLN cc_start: 0.7039 (mt0) cc_final: 0.6498 (mt0) REVERT: AU 39 GLN cc_start: 0.8243 (tt0) cc_final: 0.7512 (mp10) REVERT: AU 46 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7336 (tmm160) REVERT: AU 84 LEU cc_start: 0.8799 (mt) cc_final: 0.8506 (mm) REVERT: AU 88 ASP cc_start: 0.7089 (t0) cc_final: 0.6550 (t0) REVERT: AU 90 ARG cc_start: 0.6494 (ttm-80) cc_final: 0.6119 (mtt180) REVERT: AU 91 ASN cc_start: 0.6964 (t0) cc_final: 0.6471 (t0) REVERT: AU 92 ARG cc_start: 0.4874 (ttt180) cc_final: 0.4300 (ttm170) REVERT: AU 112 ARG cc_start: 0.8231 (tpp-160) cc_final: 0.7966 (mmt180) REVERT: AU 127 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8110 (m-40) REVERT: AU 129 ILE cc_start: 0.8463 (tp) cc_final: 0.8170 (tp) REVERT: AU 140 ASN cc_start: 0.7876 (p0) cc_final: 0.7669 (p0) REVERT: AW 31 LEU cc_start: 0.8469 (mt) cc_final: 0.8206 (mt) REVERT: AW 34 GLN cc_start: 0.7076 (mt0) cc_final: 0.6670 (mt0) REVERT: AW 39 GLN cc_start: 0.8193 (tt0) cc_final: 0.7810 (mp10) REVERT: AW 46 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7460 (tmt170) REVERT: AW 55 SER cc_start: 0.8928 (m) cc_final: 0.8679 (t) REVERT: AW 92 ARG cc_start: 0.4716 (ttt180) cc_final: 0.4387 (ttm170) REVERT: AW 140 ASN cc_start: 0.7874 (p0) cc_final: 0.7491 (p0) REVERT: AY 23 LEU cc_start: 0.8144 (tp) cc_final: 0.7787 (tt) REVERT: AY 29 ASN cc_start: 0.8425 (m110) cc_final: 0.8031 (m-40) REVERT: AY 34 GLN cc_start: 0.7783 (tt0) cc_final: 0.7281 (tt0) REVERT: AY 39 GLN cc_start: 0.8182 (tt0) cc_final: 0.7719 (mp10) REVERT: AY 46 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7332 (tmt170) REVERT: AY 64 ASP cc_start: 0.5895 (t70) cc_final: 0.5646 (t70) REVERT: AY 88 ASP cc_start: 0.7411 (t0) cc_final: 0.5447 (p0) REVERT: AY 92 ARG cc_start: 0.5389 (ttt180) cc_final: 0.4221 (ttm170) REVERT: AY 139 TYR cc_start: 0.7629 (m-80) cc_final: 0.7425 (m-80) REVERT: AY 140 ASN cc_start: 0.7539 (p0) cc_final: 0.7100 (p0) REVERT: AY 151 VAL cc_start: 0.7809 (p) cc_final: 0.7604 (t) REVERT: A0 19 ASP cc_start: 0.7986 (t0) cc_final: 0.7785 (t0) REVERT: A0 23 LEU cc_start: 0.8388 (tp) cc_final: 0.7954 (tp) REVERT: A0 39 GLN cc_start: 0.8160 (tt0) cc_final: 0.7334 (mp10) REVERT: A0 92 ARG cc_start: 0.5009 (ttt180) cc_final: 0.4069 (ttm170) REVERT: A0 139 TYR cc_start: 0.7616 (m-80) cc_final: 0.7410 (m-80) REVERT: A2 33 ASN cc_start: 0.7288 (t0) cc_final: 0.7029 (m-40) REVERT: A2 39 GLN cc_start: 0.7776 (tt0) cc_final: 0.7089 (mp10) REVERT: A2 92 ARG cc_start: 0.4708 (ttt180) cc_final: 0.4347 (ttm170) REVERT: A2 112 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.8143 (tpt170) REVERT: A2 132 LEU cc_start: 0.8263 (tp) cc_final: 0.8047 (tp) REVERT: A2 140 ASN cc_start: 0.7833 (p0) cc_final: 0.7339 (p0) REVERT: A4 39 GLN cc_start: 0.7855 (tt0) cc_final: 0.7212 (mp10) REVERT: A4 53 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8104 (mtmm) REVERT: A4 88 ASP cc_start: 0.7835 (t0) cc_final: 0.7561 (t0) REVERT: A4 92 ARG cc_start: 0.4780 (ttt180) cc_final: 0.3918 (ttm170) REVERT: A6 29 ASN cc_start: 0.7995 (m110) cc_final: 0.7523 (m110) REVERT: A6 38 GLN cc_start: 0.6710 (tp40) cc_final: 0.5450 (mp10) REVERT: A6 46 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7366 (ppt170) REVERT: A6 92 ARG cc_start: 0.5196 (ttt180) cc_final: 0.4413 (ttm170) REVERT: A6 93 ILE cc_start: 0.8104 (tp) cc_final: 0.7899 (tp) REVERT: A6 112 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.8029 (tpt170) REVERT: A8 38 GLN cc_start: 0.6891 (tp40) cc_final: 0.5316 (pm20) REVERT: A8 87 PHE cc_start: 0.8002 (m-80) cc_final: 0.7759 (m-80) REVERT: A8 90 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7239 (mtp-110) outliers start: 28 outliers final: 6 residues processed: 2085 average time/residue: 0.6266 time to fit residues: 2182.5954 Evaluate side-chains 1541 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1534 time to evaluate : 5.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 555 optimal weight: 30.0000 chunk 454 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 668 optimal weight: 5.9990 chunk 722 optimal weight: 5.9990 chunk 595 optimal weight: 10.0000 chunk 663 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 536 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN G 57 GLN I 91 ASN K 39 GLN M 29 ASN M 39 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN O 91 ASN Q 45 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 ASN Q 98 ASN S 57 GLN S 91 ASN W 57 GLN W 73 ASN ** W 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 ASN Y 33 ASN ** Y 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 45 GLN 0 98 ASN ** 2 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 39 GLN 4 73 ASN ** 4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 73 ASN 8 36 GLN 8 39 GLN 8 73 ASN 8 98 ASN 8 126 ASN a 39 GLN a 98 ASN e 9 GLN ** e 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 36 GLN ** e 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 ASN e 127 ASN ** g 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 91 ASN g 127 ASN i 25 ASN i 91 ASN i 98 ASN k 29 ASN k 36 GLN k 39 GLN ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 98 ASN k 126 ASN ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 29 ASN o 127 ASN q 126 ASN q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 39 GLN s 57 GLN ** s 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 127 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 126 ASN w 39 GLN ** w 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 39 GLN ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 98 ASN AC 127 ASN ** AE 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 98 ASN ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 ASN ** AK 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 98 ASN ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 98 ASN AQ 126 ASN AS 33 ASN AS 45 GLN ** AS 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 98 ASN ** AU 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 98 ASN ** AU 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 45 GLN ** AW 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 98 ASN AW 126 ASN ** AY 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 36 GLN ** A0 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 98 ASN ** A2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 126 ASN A2 127 ASN ** A4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 98 ASN ** A8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 39 GLN A8 91 ASN A8 101 ASN A8 126 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 63945 Z= 0.219 Angle : 0.597 5.844 88004 Z= 0.327 Chirality : 0.041 0.136 10437 Planarity : 0.005 0.067 10878 Dihedral : 11.721 65.227 10094 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.29 % Allowed : 2.99 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.28 (0.09), residues: 7399 helix: -0.76 (0.07), residues: 4067 sheet: None (None), residues: 0 loop : -2.49 (0.09), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPAI 152 PHE 0.025 0.002 PHE 2 67 TYR 0.017 0.002 TYR W 70 ARG 0.008 0.001 ARG c 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1944 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1925 time to evaluate : 5.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 CYS cc_start: 0.8008 (p) cc_final: 0.7710 (p) REVERT: A 50 GLU cc_start: 0.7909 (tp30) cc_final: 0.7583 (tp30) REVERT: A 62 PHE cc_start: 0.7173 (t80) cc_final: 0.6744 (t80) REVERT: C 29 ASN cc_start: 0.7730 (t0) cc_final: 0.7521 (t0) REVERT: C 46 ARG cc_start: 0.8233 (mtt90) cc_final: 0.7891 (mmt-90) REVERT: C 112 ARG cc_start: 0.7282 (mmm-85) cc_final: 0.6886 (tpt-90) REVERT: C 127 ASN cc_start: 0.7874 (m-40) cc_final: 0.7493 (m-40) REVERT: E 53 LYS cc_start: 0.7883 (ptmt) cc_final: 0.7395 (pttp) REVERT: E 64 ASP cc_start: 0.7366 (t70) cc_final: 0.7133 (p0) REVERT: E 68 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7374 (mtmt) REVERT: E 112 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7487 (tpt-90) REVERT: E 139 TYR cc_start: 0.8107 (m-10) cc_final: 0.7519 (m-10) REVERT: G 70 TYR cc_start: 0.7743 (t80) cc_final: 0.7421 (t80) REVERT: I 22 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7707 (tm-30) REVERT: I 133 ILE cc_start: 0.7772 (pt) cc_final: 0.7384 (mm) REVERT: K 22 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7885 (tm-30) REVERT: M 29 ASN cc_start: 0.7689 (m-40) cc_final: 0.7009 (t0) REVERT: M 90 ARG cc_start: 0.6548 (ttm-80) cc_final: 0.5251 (mtp-110) REVERT: M 131 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7128 (tp30) REVERT: O 59 THR cc_start: 0.8362 (m) cc_final: 0.8144 (t) REVERT: O 60 VAL cc_start: 0.8108 (t) cc_final: 0.7862 (t) REVERT: O 89 THR cc_start: 0.7651 (m) cc_final: 0.6886 (p) REVERT: Q 62 PHE cc_start: 0.7886 (t80) cc_final: 0.7314 (t80) REVERT: Q 68 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7422 (mmmm) REVERT: S 38 GLN cc_start: 0.7217 (tp40) cc_final: 0.6898 (tp-100) REVERT: S 57 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6657 (mp-120) REVERT: S 59 THR cc_start: 0.8608 (m) cc_final: 0.8328 (t) REVERT: U 25 ASN cc_start: 0.8748 (m-40) cc_final: 0.8309 (m-40) REVERT: U 62 PHE cc_start: 0.7695 (t80) cc_final: 0.7219 (t80) REVERT: U 68 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7499 (mmmm) REVERT: U 89 THR cc_start: 0.7582 (m) cc_final: 0.6944 (p) REVERT: W 57 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6551 (mp10) REVERT: W 62 PHE cc_start: 0.7528 (t80) cc_final: 0.7017 (t80) REVERT: W 68 LYS cc_start: 0.8182 (mmmm) cc_final: 0.7961 (mmmm) REVERT: W 89 THR cc_start: 0.7883 (m) cc_final: 0.7467 (m) REVERT: Y 38 GLN cc_start: 0.7162 (tp40) cc_final: 0.6913 (tp40) REVERT: Y 59 THR cc_start: 0.8561 (m) cc_final: 0.8350 (t) REVERT: Y 93 ILE cc_start: 0.7988 (mt) cc_final: 0.7670 (tp) REVERT: Y 112 ARG cc_start: 0.8191 (tpp-160) cc_final: 0.7825 (tpt170) REVERT: 0 62 PHE cc_start: 0.7520 (t80) cc_final: 0.6956 (t80) REVERT: 0 89 THR cc_start: 0.7450 (m) cc_final: 0.7019 (p) REVERT: 0 93 ILE cc_start: 0.8016 (mt) cc_final: 0.7243 (tp) REVERT: 0 127 ASN cc_start: 0.8522 (m-40) cc_final: 0.8085 (m-40) REVERT: 2 22 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7423 (mm-30) REVERT: 2 38 GLN cc_start: 0.6824 (tp40) cc_final: 0.6422 (tp-100) REVERT: 2 89 THR cc_start: 0.7987 (m) cc_final: 0.7381 (p) REVERT: 2 93 ILE cc_start: 0.7980 (mt) cc_final: 0.7619 (tp) REVERT: 2 127 ASN cc_start: 0.8420 (m-40) cc_final: 0.7974 (m-40) REVERT: 4 62 PHE cc_start: 0.7042 (t80) cc_final: 0.6825 (t80) REVERT: 4 93 ILE cc_start: 0.8205 (mt) cc_final: 0.7800 (tp) REVERT: 4 127 ASN cc_start: 0.8434 (m110) cc_final: 0.8145 (m110) REVERT: 6 25 ASN cc_start: 0.8356 (m-40) cc_final: 0.8078 (m-40) REVERT: 6 27 CYS cc_start: 0.8483 (p) cc_final: 0.8151 (p) REVERT: 6 89 THR cc_start: 0.7641 (m) cc_final: 0.7225 (p) REVERT: 8 38 GLN cc_start: 0.7196 (tp40) cc_final: 0.6958 (tp40) REVERT: 8 94 ILE cc_start: 0.8246 (mm) cc_final: 0.7682 (mm) REVERT: 8 127 ASN cc_start: 0.8150 (m-40) cc_final: 0.7790 (m110) REVERT: a 25 ASN cc_start: 0.8825 (m-40) cc_final: 0.8395 (m-40) REVERT: a 59 THR cc_start: 0.8484 (m) cc_final: 0.8284 (t) REVERT: a 76 LEU cc_start: 0.8650 (mp) cc_final: 0.7855 (mm) REVERT: c 25 ASN cc_start: 0.8750 (m-40) cc_final: 0.8330 (m110) REVERT: c 27 CYS cc_start: 0.8609 (p) cc_final: 0.8245 (p) REVERT: c 38 GLN cc_start: 0.7059 (tp40) cc_final: 0.6816 (tp40) REVERT: c 60 VAL cc_start: 0.7917 (t) cc_final: 0.7544 (t) REVERT: c 62 PHE cc_start: 0.6788 (t80) cc_final: 0.6454 (t80) REVERT: c 93 ILE cc_start: 0.8151 (mt) cc_final: 0.7548 (tp) REVERT: c 141 ARG cc_start: 0.6757 (ttt90) cc_final: 0.6418 (ttt180) REVERT: e 25 ASN cc_start: 0.8764 (m-40) cc_final: 0.8513 (m110) REVERT: e 34 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7476 (mm-40) REVERT: e 50 GLU cc_start: 0.7319 (tp30) cc_final: 0.6806 (tp30) REVERT: g 62 PHE cc_start: 0.6914 (t80) cc_final: 0.6581 (t80) REVERT: i 62 PHE cc_start: 0.6648 (t80) cc_final: 0.6239 (t80) REVERT: i 131 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7962 (tm-30) REVERT: k 50 GLU cc_start: 0.7685 (tp30) cc_final: 0.7251 (tp30) REVERT: k 62 PHE cc_start: 0.7128 (t80) cc_final: 0.6816 (t80) REVERT: k 129 ILE cc_start: 0.8093 (tp) cc_final: 0.7881 (tp) REVERT: m 29 ASN cc_start: 0.8284 (m110) cc_final: 0.7758 (m110) REVERT: m 34 GLN cc_start: 0.7437 (tp40) cc_final: 0.7231 (tp40) REVERT: o 34 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7529 (mm-40) REVERT: o 111 THR cc_start: 0.8803 (p) cc_final: 0.8579 (p) REVERT: q 29 ASN cc_start: 0.7638 (m-40) cc_final: 0.7267 (m110) REVERT: q 34 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7223 (mm-40) REVERT: q 50 GLU cc_start: 0.7707 (tp30) cc_final: 0.7461 (tp30) REVERT: q 76 LEU cc_start: 0.8688 (mp) cc_final: 0.8441 (mm) REVERT: q 129 ILE cc_start: 0.7973 (tp) cc_final: 0.7763 (tp) REVERT: s 50 GLU cc_start: 0.7917 (tp30) cc_final: 0.7544 (tp30) REVERT: s 62 PHE cc_start: 0.7270 (t80) cc_final: 0.6782 (t80) REVERT: u 34 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7100 (mm-40) REVERT: u 62 PHE cc_start: 0.7203 (t80) cc_final: 0.6770 (t80) REVERT: u 113 ARG cc_start: 0.7351 (mtp85) cc_final: 0.6890 (mtp85) REVERT: w 19 ASP cc_start: 0.8256 (t0) cc_final: 0.7229 (m-30) REVERT: w 22 GLU cc_start: 0.8151 (pp20) cc_final: 0.7730 (pp20) REVERT: w 29 ASN cc_start: 0.8247 (m110) cc_final: 0.7509 (m110) REVERT: w 127 ASN cc_start: 0.8350 (m-40) cc_final: 0.8136 (m110) REVERT: y 19 ASP cc_start: 0.8031 (t0) cc_final: 0.7751 (t0) REVERT: y 22 GLU cc_start: 0.8096 (pp20) cc_final: 0.7840 (pp20) REVERT: y 62 PHE cc_start: 0.7244 (t80) cc_final: 0.6966 (t80) REVERT: y 141 ARG cc_start: 0.6527 (ttt180) cc_final: 0.6075 (ttt90) REVERT: AA 19 ASP cc_start: 0.8003 (t0) cc_final: 0.7682 (t0) REVERT: AA 22 GLU cc_start: 0.8036 (pp20) cc_final: 0.7770 (pp20) REVERT: AA 29 ASN cc_start: 0.8297 (m-40) cc_final: 0.7951 (m110) REVERT: AA 76 LEU cc_start: 0.8385 (mp) cc_final: 0.7849 (mp) REVERT: AA 129 ILE cc_start: 0.7901 (tp) cc_final: 0.7687 (tp) REVERT: AC 19 ASP cc_start: 0.7947 (t0) cc_final: 0.7552 (m-30) REVERT: AC 46 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7474 (mmm-85) REVERT: AC 57 GLN cc_start: 0.7582 (tp-100) cc_final: 0.7177 (mp10) REVERT: AC 90 ARG cc_start: 0.6587 (ttm-80) cc_final: 0.6123 (mtt180) REVERT: AC 92 ARG cc_start: 0.5850 (ttt180) cc_final: 0.4112 (ttm170) REVERT: AC 139 TYR cc_start: 0.8183 (m-80) cc_final: 0.7914 (m-80) REVERT: AE 39 GLN cc_start: 0.8168 (tt0) cc_final: 0.7587 (mp10) REVERT: AE 92 ARG cc_start: 0.5459 (ttt180) cc_final: 0.3881 (ttm170) REVERT: AG 22 GLU cc_start: 0.7753 (tp30) cc_final: 0.7522 (tp30) REVERT: AG 39 GLN cc_start: 0.8141 (tt0) cc_final: 0.7451 (mp10) REVERT: AG 46 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7547 (ppt170) REVERT: AG 92 ARG cc_start: 0.5737 (ttt180) cc_final: 0.3727 (ttm170) REVERT: AI 39 GLN cc_start: 0.8426 (tt0) cc_final: 0.7632 (mp10) REVERT: AI 46 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7856 (mmm-85) REVERT: AI 92 ARG cc_start: 0.5451 (ttt180) cc_final: 0.3965 (ttm170) REVERT: AK 19 ASP cc_start: 0.7932 (t0) cc_final: 0.7696 (t0) REVERT: AK 39 GLN cc_start: 0.8276 (tt0) cc_final: 0.7432 (mp10) REVERT: AK 46 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7629 (mmm-85) REVERT: AK 62 PHE cc_start: 0.7561 (t80) cc_final: 0.7352 (t80) REVERT: AK 92 ARG cc_start: 0.5050 (ttt180) cc_final: 0.3425 (ttm170) REVERT: AM 19 ASP cc_start: 0.7773 (t0) cc_final: 0.7470 (t0) REVERT: AM 22 GLU cc_start: 0.8266 (pp20) cc_final: 0.8038 (pp20) REVERT: AM 39 GLN cc_start: 0.8334 (tt0) cc_final: 0.7678 (mp10) REVERT: AM 46 ARG cc_start: 0.7968 (mmt90) cc_final: 0.7702 (mmm-85) REVERT: AM 53 LYS cc_start: 0.7478 (mmpt) cc_final: 0.7225 (mtpp) REVERT: AM 57 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7282 (mm-40) REVERT: AM 92 ARG cc_start: 0.5166 (ttt180) cc_final: 0.3305 (ttm170) REVERT: AO 33 ASN cc_start: 0.7871 (m-40) cc_final: 0.7638 (m-40) REVERT: AO 46 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7672 (mtp180) REVERT: AO 92 ARG cc_start: 0.4913 (ttt180) cc_final: 0.3469 (ttm-80) REVERT: AO 95 GLU cc_start: 0.4326 (tt0) cc_final: 0.4117 (tt0) REVERT: AO 139 TYR cc_start: 0.7865 (m-80) cc_final: 0.7602 (m-80) REVERT: AO 140 ASN cc_start: 0.7697 (p0) cc_final: 0.7322 (p0) REVERT: AQ 22 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7020 (tp30) REVERT: AQ 46 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7715 (mtp180) REVERT: AQ 76 LEU cc_start: 0.8145 (mp) cc_final: 0.7740 (mp) REVERT: AQ 92 ARG cc_start: 0.5061 (ttt180) cc_final: 0.3544 (ttm170) REVERT: AQ 109 ASP cc_start: 0.7473 (t70) cc_final: 0.7259 (t70) REVERT: AQ 129 ILE cc_start: 0.8327 (tp) cc_final: 0.8059 (tp) REVERT: AQ 139 TYR cc_start: 0.7941 (m-80) cc_final: 0.7728 (m-80) REVERT: AS 29 ASN cc_start: 0.8194 (m110) cc_final: 0.7682 (m110) REVERT: AS 46 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7626 (mtp180) REVERT: AS 50 GLU cc_start: 0.8061 (tp30) cc_final: 0.7848 (tp30) REVERT: AS 88 ASP cc_start: 0.6900 (t0) cc_final: 0.6639 (t0) REVERT: AS 90 ARG cc_start: 0.6889 (ttm-80) cc_final: 0.6420 (ttt180) REVERT: AS 92 ARG cc_start: 0.4456 (ttt180) cc_final: 0.3663 (ttm170) REVERT: AS 140 ASN cc_start: 0.7936 (p0) cc_final: 0.7229 (p0) REVERT: AU 22 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7091 (tp30) REVERT: AU 33 ASN cc_start: 0.7985 (m-40) cc_final: 0.7415 (m-40) REVERT: AU 34 GLN cc_start: 0.7117 (mt0) cc_final: 0.6880 (mt0) REVERT: AU 39 GLN cc_start: 0.8228 (tt0) cc_final: 0.7580 (mp10) REVERT: AU 46 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7399 (tmm160) REVERT: AU 88 ASP cc_start: 0.7132 (t0) cc_final: 0.6606 (t0) REVERT: AU 90 ARG cc_start: 0.6839 (ttm-80) cc_final: 0.5793 (mmm160) REVERT: AU 91 ASN cc_start: 0.6988 (t0) cc_final: 0.6367 (t0) REVERT: AU 92 ARG cc_start: 0.5472 (ttt180) cc_final: 0.4212 (ttm170) REVERT: AU 140 ASN cc_start: 0.7898 (p0) cc_final: 0.7490 (p0) REVERT: AW 19 ASP cc_start: 0.7861 (t0) cc_final: 0.7406 (t0) REVERT: AW 33 ASN cc_start: 0.7163 (m-40) cc_final: 0.6627 (m-40) REVERT: AW 39 GLN cc_start: 0.8038 (tt0) cc_final: 0.7750 (mp10) REVERT: AW 46 ARG cc_start: 0.8403 (mtt180) cc_final: 0.7512 (tmt170) REVERT: AW 50 GLU cc_start: 0.8186 (tp30) cc_final: 0.7875 (tp30) REVERT: AW 55 SER cc_start: 0.8691 (m) cc_final: 0.8379 (p) REVERT: AW 57 GLN cc_start: 0.6410 (mm-40) cc_final: 0.6089 (mm-40) REVERT: AW 92 ARG cc_start: 0.5623 (ttt180) cc_final: 0.4317 (ttm170) REVERT: AW 127 ASN cc_start: 0.8390 (m110) cc_final: 0.7939 (m110) REVERT: AW 140 ASN cc_start: 0.7883 (p0) cc_final: 0.7441 (p0) REVERT: AY 29 ASN cc_start: 0.8381 (m110) cc_final: 0.8073 (m-40) REVERT: AY 39 GLN cc_start: 0.8183 (tt0) cc_final: 0.7799 (mp10) REVERT: AY 46 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7367 (tmt170) REVERT: AY 88 ASP cc_start: 0.6700 (t0) cc_final: 0.5038 (p0) REVERT: AY 92 ARG cc_start: 0.4978 (ttt180) cc_final: 0.3552 (ttm170) REVERT: AY 96 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7763 (m) REVERT: AY 140 ASN cc_start: 0.7724 (p0) cc_final: 0.7372 (p0) REVERT: A0 13 LEU cc_start: 0.8688 (mp) cc_final: 0.8462 (mp) REVERT: A0 19 ASP cc_start: 0.8049 (t0) cc_final: 0.7382 (t0) REVERT: A0 36 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: A0 39 GLN cc_start: 0.8030 (tt0) cc_final: 0.7353 (mp10) REVERT: A0 46 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7107 (tmm160) REVERT: A0 127 ASN cc_start: 0.8481 (m110) cc_final: 0.7908 (m110) REVERT: A0 139 TYR cc_start: 0.7664 (m-80) cc_final: 0.7264 (m-80) REVERT: A2 33 ASN cc_start: 0.7519 (t0) cc_final: 0.7224 (m-40) REVERT: A2 39 GLN cc_start: 0.7668 (tt0) cc_final: 0.7101 (mp10) REVERT: A2 53 LYS cc_start: 0.7398 (mmtt) cc_final: 0.7093 (mtmm) REVERT: A2 92 ARG cc_start: 0.4613 (ttt180) cc_final: 0.4078 (ttm170) REVERT: A2 112 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.8026 (mmm160) REVERT: A2 132 LEU cc_start: 0.8325 (tp) cc_final: 0.8075 (tp) REVERT: A2 140 ASN cc_start: 0.7908 (p0) cc_final: 0.7263 (p0) REVERT: A4 29 ASN cc_start: 0.8385 (m-40) cc_final: 0.8109 (m-40) REVERT: A4 39 GLN cc_start: 0.7708 (tt0) cc_final: 0.7101 (mp10) REVERT: A4 46 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7158 (ppt170) REVERT: A4 92 ARG cc_start: 0.4399 (ttt180) cc_final: 0.3744 (ttm170) REVERT: A4 96 VAL cc_start: 0.7368 (p) cc_final: 0.7137 (m) REVERT: A4 131 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7546 (tp30) REVERT: A6 29 ASN cc_start: 0.7897 (m110) cc_final: 0.7421 (m110) REVERT: A6 38 GLN cc_start: 0.6718 (tp40) cc_final: 0.5546 (mp10) REVERT: A6 46 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7384 (ppt170) REVERT: A6 92 ARG cc_start: 0.5303 (ttt180) cc_final: 0.4611 (ttm170) REVERT: A6 97 GLU cc_start: 0.5445 (pm20) cc_final: 0.5218 (pm20) REVERT: A6 112 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7738 (mmp-170) REVERT: A8 38 GLN cc_start: 0.6786 (tp40) cc_final: 0.5546 (pm20) REVERT: A8 46 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.6952 (tmm160) REVERT: A8 90 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7351 (mtp-110) REVERT: A8 92 ARG cc_start: 0.6448 (ttt180) cc_final: 0.4880 (ttm170) outliers start: 19 outliers final: 3 residues processed: 1932 average time/residue: 0.6003 time to fit residues: 1935.6397 Evaluate side-chains 1492 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1485 time to evaluate : 6.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 20.0000 chunk 502 optimal weight: 9.9990 chunk 347 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 319 optimal weight: 8.9990 chunk 449 optimal weight: 7.9990 chunk 671 optimal weight: 30.0000 chunk 710 optimal weight: 5.9990 chunk 350 optimal weight: 10.0000 chunk 636 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN A 127 ASN C 36 GLN C 39 GLN C 45 GLN E 127 ASN K 39 GLN ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 ASN M 39 GLN O 39 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 73 ASN S 126 ASN U 73 ASN W 45 GLN W 91 ASN Y 73 ASN 6 9 GLN 6 73 ASN 8 73 ASN a 36 GLN a 73 ASN a 127 ASN c 98 ASN e 9 GLN ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 GLN g 73 ASN g 127 ASN ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 ASN k 34 GLN k 36 GLN ** k 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 73 ASN o 39 GLN q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 57 GLN s 98 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 GLN ** u 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 127 ASN w 57 GLN w 91 ASN w 98 ASN ** w 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 127 ASN ** AA 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 98 ASN AA 126 ASN AC 126 ASN AE 91 ASN AE 98 ASN ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 91 ASN AG 126 ASN AG 127 ASN ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 91 ASN AI 101 ASN AI 126 ASN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 91 ASN ** AK 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 91 ASN ** AM 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 91 ASN ** AO 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 57 GLN ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 126 ASN AU 57 GLN ** AU 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 33 ASN ** AW 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 98 ASN ** A0 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 91 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 63945 Z= 0.329 Angle : 0.673 6.252 88004 Z= 0.369 Chirality : 0.044 0.215 10437 Planarity : 0.006 0.052 10878 Dihedral : 12.152 70.393 10094 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.03 (0.09), residues: 7399 helix: -0.41 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -2.51 (0.09), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 152 PHE 0.022 0.003 PHE U 67 TYR 0.021 0.002 TYR W 70 ARG 0.011 0.001 ARG s 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1741 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1728 time to evaluate : 5.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7822 (tp30) cc_final: 0.7566 (tp30) REVERT: C 34 GLN cc_start: 0.7711 (mt0) cc_final: 0.7306 (tp-100) REVERT: C 39 GLN cc_start: 0.8215 (tt0) cc_final: 0.7984 (tt0) REVERT: C 57 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7421 (mm-40) REVERT: C 77 ASP cc_start: 0.7885 (t70) cc_final: 0.7605 (t70) REVERT: C 127 ASN cc_start: 0.7895 (m-40) cc_final: 0.7612 (m-40) REVERT: E 19 ASP cc_start: 0.7733 (t0) cc_final: 0.7480 (t0) REVERT: E 53 LYS cc_start: 0.7973 (ptmt) cc_final: 0.7578 (pttp) REVERT: E 112 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7638 (tpt-90) REVERT: E 127 ASN cc_start: 0.7746 (m110) cc_final: 0.7399 (m110) REVERT: E 139 TYR cc_start: 0.8073 (m-10) cc_final: 0.7698 (m-10) REVERT: G 68 LYS cc_start: 0.8218 (ptpp) cc_final: 0.7841 (ptpt) REVERT: G 139 TYR cc_start: 0.8308 (m-10) cc_final: 0.8013 (m-10) REVERT: I 22 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7691 (tm-30) REVERT: I 57 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6744 (mm-40) REVERT: I 131 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7370 (tp30) REVERT: K 22 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7698 (tm-30) REVERT: K 70 TYR cc_start: 0.7945 (t80) cc_final: 0.7157 (t80) REVERT: M 19 ASP cc_start: 0.7676 (t0) cc_final: 0.7461 (t0) REVERT: M 29 ASN cc_start: 0.7880 (m-40) cc_final: 0.7346 (t0) REVERT: M 59 THR cc_start: 0.8270 (m) cc_final: 0.7914 (t) REVERT: M 89 THR cc_start: 0.7288 (m) cc_final: 0.6982 (p) REVERT: M 90 ARG cc_start: 0.6552 (ttm-80) cc_final: 0.6205 (ttm110) REVERT: M 131 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7153 (tp30) REVERT: O 89 THR cc_start: 0.7714 (m) cc_final: 0.7307 (p) REVERT: O 131 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6865 (tp30) REVERT: Q 68 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7600 (mmmm) REVERT: U 31 LEU cc_start: 0.8247 (mt) cc_final: 0.8024 (mm) REVERT: U 89 THR cc_start: 0.7603 (m) cc_final: 0.7247 (p) REVERT: W 22 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7703 (mm-30) REVERT: W 127 ASN cc_start: 0.8405 (m110) cc_final: 0.8135 (m110) REVERT: Y 112 ARG cc_start: 0.8266 (tpp-160) cc_final: 0.7762 (tpt170) REVERT: 0 25 ASN cc_start: 0.8657 (m-40) cc_final: 0.8304 (m110) REVERT: 0 39 GLN cc_start: 0.7931 (tt0) cc_final: 0.7558 (tt0) REVERT: 0 62 PHE cc_start: 0.7790 (t80) cc_final: 0.7455 (t80) REVERT: 0 89 THR cc_start: 0.7533 (m) cc_final: 0.7280 (p) REVERT: 0 93 ILE cc_start: 0.8283 (mt) cc_final: 0.7661 (tp) REVERT: 0 127 ASN cc_start: 0.8564 (m-40) cc_final: 0.8299 (m110) REVERT: 2 38 GLN cc_start: 0.6800 (tp40) cc_final: 0.6383 (tp-100) REVERT: 2 89 THR cc_start: 0.7942 (m) cc_final: 0.7416 (p) REVERT: 2 93 ILE cc_start: 0.8209 (mt) cc_final: 0.7795 (tp) REVERT: 2 127 ASN cc_start: 0.8350 (m-40) cc_final: 0.7969 (m-40) REVERT: 4 39 GLN cc_start: 0.8044 (tt0) cc_final: 0.7794 (tt0) REVERT: 4 62 PHE cc_start: 0.7385 (t80) cc_final: 0.6869 (t80) REVERT: 4 89 THR cc_start: 0.7884 (m) cc_final: 0.7446 (p) REVERT: 4 93 ILE cc_start: 0.8345 (mt) cc_final: 0.8032 (tp) REVERT: 4 112 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7581 (tpt170) REVERT: 4 127 ASN cc_start: 0.8483 (m110) cc_final: 0.8229 (m110) REVERT: 6 27 CYS cc_start: 0.8724 (p) cc_final: 0.8479 (p) REVERT: 6 62 PHE cc_start: 0.7445 (t80) cc_final: 0.6804 (t80) REVERT: 6 93 ILE cc_start: 0.8283 (mt) cc_final: 0.7828 (mt) REVERT: 6 112 ARG cc_start: 0.8501 (tpp-160) cc_final: 0.7949 (tpt170) REVERT: 8 38 GLN cc_start: 0.7104 (tp40) cc_final: 0.6603 (tp40) REVERT: 8 89 THR cc_start: 0.7649 (m) cc_final: 0.7420 (m) REVERT: 8 127 ASN cc_start: 0.7984 (m-40) cc_final: 0.7782 (m110) REVERT: a 62 PHE cc_start: 0.7193 (t80) cc_final: 0.6742 (t80) REVERT: a 127 ASN cc_start: 0.8037 (m-40) cc_final: 0.7826 (m110) REVERT: c 27 CYS cc_start: 0.8756 (p) cc_final: 0.8531 (p) REVERT: c 93 ILE cc_start: 0.8034 (mt) cc_final: 0.7822 (tp) REVERT: e 34 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7185 (mm110) REVERT: e 50 GLU cc_start: 0.7447 (tp30) cc_final: 0.6793 (tp30) REVERT: e 129 ILE cc_start: 0.8082 (tp) cc_final: 0.7806 (tp) REVERT: i 24 ILE cc_start: 0.8800 (mm) cc_final: 0.8595 (mm) REVERT: i 34 GLN cc_start: 0.7824 (mm110) cc_final: 0.6947 (mm-40) REVERT: k 29 ASN cc_start: 0.8364 (m110) cc_final: 0.8126 (m110) REVERT: k 50 GLU cc_start: 0.7700 (tp30) cc_final: 0.7346 (tp30) REVERT: k 84 LEU cc_start: 0.8711 (mt) cc_final: 0.8491 (mm) REVERT: m 29 ASN cc_start: 0.8242 (m110) cc_final: 0.7912 (m110) REVERT: m 34 GLN cc_start: 0.7814 (tp40) cc_final: 0.7456 (tp40) REVERT: m 62 PHE cc_start: 0.7261 (t80) cc_final: 0.6839 (t80) REVERT: o 34 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7206 (mm-40) REVERT: o 76 LEU cc_start: 0.8627 (mp) cc_final: 0.8040 (mm) REVERT: o 108 LEU cc_start: 0.8233 (mp) cc_final: 0.8012 (mt) REVERT: o 129 ILE cc_start: 0.7992 (tp) cc_final: 0.7745 (tp) REVERT: q 29 ASN cc_start: 0.7952 (m-40) cc_final: 0.7445 (m110) REVERT: q 34 GLN cc_start: 0.7665 (mm-40) cc_final: 0.7352 (mm-40) REVERT: q 68 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7584 (mmtt) REVERT: q 129 ILE cc_start: 0.8124 (tp) cc_final: 0.7912 (tp) REVERT: s 19 ASP cc_start: 0.8232 (t0) cc_final: 0.7947 (t0) REVERT: s 50 GLU cc_start: 0.7912 (tp30) cc_final: 0.7395 (tp30) REVERT: s 53 LYS cc_start: 0.8057 (mttt) cc_final: 0.7640 (mttm) REVERT: s 113 ARG cc_start: 0.7207 (mtp85) cc_final: 0.6965 (mtp85) REVERT: s 152 TRP cc_start: 0.6250 (t-100) cc_final: 0.5695 (t-100) REVERT: u 19 ASP cc_start: 0.8346 (t0) cc_final: 0.8074 (t0) REVERT: w 19 ASP cc_start: 0.8214 (t0) cc_final: 0.7336 (m-30) REVERT: w 22 GLU cc_start: 0.8182 (pp20) cc_final: 0.7741 (pp20) REVERT: w 62 PHE cc_start: 0.7642 (t80) cc_final: 0.7328 (t80) REVERT: w 127 ASN cc_start: 0.8314 (m-40) cc_final: 0.8112 (m110) REVERT: y 19 ASP cc_start: 0.8061 (t0) cc_final: 0.7819 (t0) REVERT: y 29 ASN cc_start: 0.7776 (p0) cc_final: 0.7554 (p0) REVERT: y 62 PHE cc_start: 0.7523 (t80) cc_final: 0.7023 (t80) REVERT: AA 19 ASP cc_start: 0.7998 (t0) cc_final: 0.7722 (t0) REVERT: AA 29 ASN cc_start: 0.8364 (m-40) cc_final: 0.8069 (m-40) REVERT: AA 127 ASN cc_start: 0.8528 (m110) cc_final: 0.8189 (m110) REVERT: AC 19 ASP cc_start: 0.8113 (t0) cc_final: 0.7706 (m-30) REVERT: AC 22 GLU cc_start: 0.7751 (tp30) cc_final: 0.7426 (tp30) REVERT: AC 46 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7709 (mmm-85) REVERT: AC 57 GLN cc_start: 0.7251 (tp-100) cc_final: 0.7047 (mp10) REVERT: AC 90 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.6398 (mtp-110) REVERT: AC 92 ARG cc_start: 0.5891 (ttt180) cc_final: 0.4074 (ttm170) REVERT: AC 127 ASN cc_start: 0.8535 (m110) cc_final: 0.8255 (m110) REVERT: AC 139 TYR cc_start: 0.8127 (m-80) cc_final: 0.7831 (m-80) REVERT: AE 39 GLN cc_start: 0.8189 (tt0) cc_final: 0.7543 (mp10) REVERT: AE 109 ASP cc_start: 0.7408 (t70) cc_final: 0.7070 (t70) REVERT: AE 113 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7530 (mtp85) REVERT: AE 151 VAL cc_start: 0.8176 (p) cc_final: 0.7882 (m) REVERT: AG 19 ASP cc_start: 0.8157 (t0) cc_final: 0.7756 (m-30) REVERT: AG 22 GLU cc_start: 0.7848 (tp30) cc_final: 0.7524 (tp30) REVERT: AG 39 GLN cc_start: 0.8296 (tt0) cc_final: 0.7606 (mp10) REVERT: AG 46 ARG cc_start: 0.8230 (mtt180) cc_final: 0.7787 (ppt170) REVERT: AG 62 PHE cc_start: 0.7666 (t80) cc_final: 0.7405 (t80) REVERT: AG 76 LEU cc_start: 0.8329 (mp) cc_final: 0.7694 (mp) REVERT: AG 92 ARG cc_start: 0.6329 (ttt180) cc_final: 0.4219 (ttm170) REVERT: AG 139 TYR cc_start: 0.8006 (m-80) cc_final: 0.7711 (m-80) REVERT: AI 33 ASN cc_start: 0.7956 (m-40) cc_final: 0.7672 (m-40) REVERT: AI 39 GLN cc_start: 0.8502 (tt0) cc_final: 0.7382 (mp10) REVERT: AI 92 ARG cc_start: 0.6052 (ttt180) cc_final: 0.4432 (ttm170) REVERT: AK 19 ASP cc_start: 0.8144 (t0) cc_final: 0.7819 (t0) REVERT: AK 39 GLN cc_start: 0.8339 (tt0) cc_final: 0.7434 (mp10) REVERT: AK 46 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7840 (mmm-85) REVERT: AK 92 ARG cc_start: 0.5370 (ttt180) cc_final: 0.3914 (ttm170) REVERT: AK 95 GLU cc_start: 0.4248 (tt0) cc_final: 0.3864 (tt0) REVERT: AM 19 ASP cc_start: 0.8072 (t0) cc_final: 0.7809 (t0) REVERT: AM 39 GLN cc_start: 0.8411 (tt0) cc_final: 0.7823 (mp10) REVERT: AM 76 LEU cc_start: 0.8595 (mp) cc_final: 0.7913 (mp) REVERT: AM 92 ARG cc_start: 0.4980 (ttt180) cc_final: 0.3551 (ttm170) REVERT: AM 95 GLU cc_start: 0.4319 (tt0) cc_final: 0.4090 (tt0) REVERT: AM 139 TYR cc_start: 0.7943 (m-80) cc_final: 0.7534 (m-80) REVERT: AM 140 ASN cc_start: 0.7392 (p0) cc_final: 0.7123 (p0) REVERT: AO 22 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7355 (tp30) REVERT: AO 38 GLN cc_start: 0.6798 (tp40) cc_final: 0.6515 (tp40) REVERT: AO 46 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7777 (ppt170) REVERT: AO 88 ASP cc_start: 0.6657 (t0) cc_final: 0.5601 (p0) REVERT: AO 92 ARG cc_start: 0.5932 (ttt180) cc_final: 0.4024 (ttm-80) REVERT: AO 95 GLU cc_start: 0.4274 (tt0) cc_final: 0.3929 (tt0) REVERT: AO 140 ASN cc_start: 0.7779 (p0) cc_final: 0.7540 (p0) REVERT: AQ 22 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7313 (tp30) REVERT: AQ 34 GLN cc_start: 0.7783 (tt0) cc_final: 0.7531 (tt0) REVERT: AQ 46 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7709 (ppt170) REVERT: AQ 50 GLU cc_start: 0.7895 (tp30) cc_final: 0.7654 (tp30) REVERT: AQ 92 ARG cc_start: 0.5612 (ttt180) cc_final: 0.4127 (ttm170) REVERT: AQ 140 ASN cc_start: 0.7877 (p0) cc_final: 0.7583 (p0) REVERT: AS 29 ASN cc_start: 0.8090 (m110) cc_final: 0.7623 (m110) REVERT: AS 33 ASN cc_start: 0.7277 (m110) cc_final: 0.6722 (m-40) REVERT: AS 46 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7715 (ppt170) REVERT: AS 88 ASP cc_start: 0.7288 (t0) cc_final: 0.6704 (t0) REVERT: AS 90 ARG cc_start: 0.7163 (ttm-80) cc_final: 0.6808 (ttt180) REVERT: AS 91 ASN cc_start: 0.7148 (t0) cc_final: 0.6810 (t0) REVERT: AS 92 ARG cc_start: 0.5494 (ttt180) cc_final: 0.4011 (ttm170) REVERT: AS 95 GLU cc_start: 0.4119 (tt0) cc_final: 0.3805 (tt0) REVERT: AS 140 ASN cc_start: 0.8048 (p0) cc_final: 0.7096 (p0) REVERT: AU 19 ASP cc_start: 0.8183 (t0) cc_final: 0.7636 (t0) REVERT: AU 39 GLN cc_start: 0.8402 (tt0) cc_final: 0.7709 (mp10) REVERT: AU 46 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7686 (tmt170) REVERT: AU 88 ASP cc_start: 0.6927 (t0) cc_final: 0.6632 (t0) REVERT: AU 91 ASN cc_start: 0.6973 (t0) cc_final: 0.6458 (t0) REVERT: AU 92 ARG cc_start: 0.5563 (ttt180) cc_final: 0.4345 (ttm170) REVERT: AU 127 ASN cc_start: 0.8544 (t0) cc_final: 0.8257 (m110) REVERT: AU 140 ASN cc_start: 0.7923 (p0) cc_final: 0.7713 (p0) REVERT: AW 33 ASN cc_start: 0.7360 (m110) cc_final: 0.6715 (m-40) REVERT: AW 39 GLN cc_start: 0.8097 (tt0) cc_final: 0.7719 (mp10) REVERT: AW 46 ARG cc_start: 0.8403 (mtt180) cc_final: 0.7615 (tmt170) REVERT: AW 50 GLU cc_start: 0.8084 (tp30) cc_final: 0.7737 (tp30) REVERT: AW 57 GLN cc_start: 0.6394 (mm-40) cc_final: 0.6016 (mm-40) REVERT: AW 68 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7219 (mttm) REVERT: AW 92 ARG cc_start: 0.5522 (ttt180) cc_final: 0.4491 (ttm170) REVERT: AW 93 ILE cc_start: 0.8195 (mp) cc_final: 0.7964 (mt) REVERT: AW 140 ASN cc_start: 0.7939 (p0) cc_final: 0.7563 (p0) REVERT: AY 29 ASN cc_start: 0.8472 (m110) cc_final: 0.8080 (m-40) REVERT: AY 39 GLN cc_start: 0.8167 (tt0) cc_final: 0.7783 (mp10) REVERT: AY 46 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7474 (tmt170) REVERT: AY 140 ASN cc_start: 0.7709 (p0) cc_final: 0.7397 (p0) REVERT: A0 19 ASP cc_start: 0.8156 (t0) cc_final: 0.7602 (t0) REVERT: A0 22 GLU cc_start: 0.8282 (pp20) cc_final: 0.8003 (pp20) REVERT: A0 23 LEU cc_start: 0.8362 (tp) cc_final: 0.8078 (tp) REVERT: A0 38 GLN cc_start: 0.5964 (tp40) cc_final: 0.5338 (pm20) REVERT: A0 46 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7124 (tmm160) REVERT: A0 92 ARG cc_start: 0.4534 (ttt180) cc_final: 0.4270 (ttm-80) REVERT: A0 127 ASN cc_start: 0.8582 (m110) cc_final: 0.8156 (m110) REVERT: A2 39 GLN cc_start: 0.7577 (tt0) cc_final: 0.6916 (mp10) REVERT: A2 53 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7205 (mtmm) REVERT: A2 92 ARG cc_start: 0.4669 (ttt180) cc_final: 0.3900 (ttm-80) REVERT: A2 127 ASN cc_start: 0.8673 (m110) cc_final: 0.8344 (m110) REVERT: A2 140 ASN cc_start: 0.7985 (p0) cc_final: 0.7374 (p0) REVERT: A4 29 ASN cc_start: 0.8274 (m-40) cc_final: 0.7930 (m-40) REVERT: A4 39 GLN cc_start: 0.7607 (tt0) cc_final: 0.7151 (mp10) REVERT: A4 46 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7192 (ppt170) REVERT: A4 92 ARG cc_start: 0.4536 (ttt180) cc_final: 0.3789 (ttm170) REVERT: A4 112 ARG cc_start: 0.7890 (tpt170) cc_final: 0.7670 (tpt170) REVERT: A4 131 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7410 (tp30) REVERT: A6 21 ILE cc_start: 0.8291 (tt) cc_final: 0.8076 (tt) REVERT: A6 29 ASN cc_start: 0.7926 (m110) cc_final: 0.7505 (m110) REVERT: A6 38 GLN cc_start: 0.6843 (tp40) cc_final: 0.5430 (pm20) REVERT: A6 46 ARG cc_start: 0.7843 (mtt-85) cc_final: 0.7445 (ppt170) REVERT: A6 112 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.7768 (mmp-170) REVERT: A8 29 ASN cc_start: 0.7516 (m-40) cc_final: 0.7196 (t0) REVERT: A8 38 GLN cc_start: 0.6958 (tp40) cc_final: 0.5624 (pm20) outliers start: 13 outliers final: 1 residues processed: 1733 average time/residue: 0.5951 time to fit residues: 1723.3450 Evaluate side-chains 1393 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1392 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 7.9990 chunk 403 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 528 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 606 optimal weight: 6.9990 chunk 491 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 362 optimal weight: 0.9990 chunk 637 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN K 73 ASN M 39 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 57 GLN O 39 GLN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 GLN S 73 ASN W 39 GLN W 45 GLN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 ASN 0 39 GLN ** 0 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 39 GLN 2 98 ASN 6 9 GLN a 34 GLN a 39 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 91 ASN g 127 ASN ** i 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 91 ASN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 73 ASN ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN o 91 ASN ** q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 126 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 98 ASN s 99 GLN s 126 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 98 ASN ** w 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 126 ASN y 127 ASN AA 126 ASN ** AC 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 126 ASN ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 57 GLN ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 126 ASN ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 91 ASN ** AI 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 91 ASN ** AM 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 99 GLN ** AQ 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 45 GLN ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 99 GLN AQ 126 ASN ** AS 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 57 GLN ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 91 ASN AS 99 GLN AS 126 ASN ** AU 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 126 ASN ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 36 GLN ** A0 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 91 ASN ** A4 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 126 ASN A8 91 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 63945 Z= 0.295 Angle : 0.638 5.937 88004 Z= 0.350 Chirality : 0.043 0.227 10437 Planarity : 0.006 0.096 10878 Dihedral : 12.031 79.027 10094 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.27 % Allowed : 2.65 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.09), residues: 7399 helix: -0.23 (0.08), residues: 3871 sheet: None (None), residues: 0 loop : -2.58 (0.09), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP k 17 PHE 0.022 0.002 PHE S 67 TYR 0.016 0.002 TYR W 70 ARG 0.015 0.001 ARG k 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1730 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1712 time to evaluate : 5.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7817 (tp30) cc_final: 0.7494 (tp30) REVERT: C 6 THR cc_start: 0.7437 (t) cc_final: 0.7219 (p) REVERT: C 57 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7303 (mm-40) REVERT: C 77 ASP cc_start: 0.8008 (t70) cc_final: 0.7790 (t70) REVERT: C 127 ASN cc_start: 0.7945 (m-40) cc_final: 0.7691 (m-40) REVERT: E 34 GLN cc_start: 0.6874 (mt0) cc_final: 0.6615 (mt0) REVERT: E 53 LYS cc_start: 0.8014 (ptmt) cc_final: 0.7478 (pttp) REVERT: E 112 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7645 (tpt-90) REVERT: E 127 ASN cc_start: 0.7812 (m110) cc_final: 0.7456 (m-40) REVERT: E 139 TYR cc_start: 0.8065 (m-10) cc_final: 0.7850 (m-10) REVERT: E 140 ASN cc_start: 0.7390 (p0) cc_final: 0.7165 (p0) REVERT: G 68 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7685 (ptpt) REVERT: G 139 TYR cc_start: 0.8270 (m-10) cc_final: 0.7965 (m-10) REVERT: I 22 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7776 (tm-30) REVERT: I 55 SER cc_start: 0.8679 (m) cc_final: 0.8310 (t) REVERT: I 57 GLN cc_start: 0.7103 (mm-40) cc_final: 0.6714 (mm-40) REVERT: I 83 LEU cc_start: 0.8333 (tp) cc_final: 0.7939 (tp) REVERT: K 22 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7846 (tm-30) REVERT: M 29 ASN cc_start: 0.7807 (m-40) cc_final: 0.7186 (t0) REVERT: M 59 THR cc_start: 0.8314 (m) cc_final: 0.7919 (t) REVERT: M 89 THR cc_start: 0.7366 (m) cc_final: 0.7027 (p) REVERT: M 90 ARG cc_start: 0.6472 (ttm-80) cc_final: 0.6219 (ttm110) REVERT: M 131 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7175 (tp30) REVERT: O 53 LYS cc_start: 0.8170 (pttp) cc_final: 0.7961 (pttp) REVERT: O 89 THR cc_start: 0.7758 (m) cc_final: 0.7459 (p) REVERT: O 131 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6834 (tp30) REVERT: O 140 ASN cc_start: 0.7500 (p0) cc_final: 0.6907 (p0) REVERT: Q 68 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7614 (mmmm) REVERT: Q 140 ASN cc_start: 0.7370 (p0) cc_final: 0.7131 (p0) REVERT: S 57 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6776 (mp-120) REVERT: U 89 THR cc_start: 0.7635 (m) cc_final: 0.7362 (p) REVERT: W 62 PHE cc_start: 0.8053 (t80) cc_final: 0.7726 (t80) REVERT: W 127 ASN cc_start: 0.8378 (m110) cc_final: 0.8098 (m-40) REVERT: Y 38 GLN cc_start: 0.6781 (tp40) cc_final: 0.6517 (tp40) REVERT: Y 112 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.7804 (tpt170) REVERT: Y 141 ARG cc_start: 0.7152 (ttt-90) cc_final: 0.6036 (ttm-80) REVERT: 0 25 ASN cc_start: 0.8645 (m-40) cc_final: 0.8326 (m110) REVERT: 0 39 GLN cc_start: 0.7905 (tt0) cc_final: 0.7493 (tt0) REVERT: 0 62 PHE cc_start: 0.7871 (t80) cc_final: 0.7559 (t80) REVERT: 0 93 ILE cc_start: 0.8130 (mt) cc_final: 0.7857 (tp) REVERT: 0 127 ASN cc_start: 0.8499 (m-40) cc_final: 0.8219 (m-40) REVERT: 2 38 GLN cc_start: 0.6828 (tp40) cc_final: 0.6348 (tp-100) REVERT: 2 89 THR cc_start: 0.7927 (m) cc_final: 0.7372 (p) REVERT: 2 93 ILE cc_start: 0.8366 (mt) cc_final: 0.7922 (tp) REVERT: 2 112 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7820 (tpt170) REVERT: 4 62 PHE cc_start: 0.7480 (t80) cc_final: 0.7205 (t80) REVERT: 4 89 THR cc_start: 0.7693 (m) cc_final: 0.6985 (p) REVERT: 4 93 ILE cc_start: 0.8281 (mt) cc_final: 0.8018 (tp) REVERT: 4 112 ARG cc_start: 0.8266 (tpp-160) cc_final: 0.7607 (tpt170) REVERT: 4 127 ASN cc_start: 0.8398 (m110) cc_final: 0.8118 (m110) REVERT: 4 131 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7160 (mm-30) REVERT: 6 27 CYS cc_start: 0.8693 (p) cc_final: 0.8470 (p) REVERT: 6 62 PHE cc_start: 0.7121 (t80) cc_final: 0.6672 (t80) REVERT: 6 112 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.8010 (tpt170) REVERT: 8 127 ASN cc_start: 0.8052 (m-40) cc_final: 0.7816 (m110) REVERT: a 62 PHE cc_start: 0.7230 (t80) cc_final: 0.6620 (t80) REVERT: c 27 CYS cc_start: 0.8781 (p) cc_final: 0.8492 (p) REVERT: e 50 GLU cc_start: 0.7337 (tp30) cc_final: 0.6761 (tp30) REVERT: g 62 PHE cc_start: 0.7276 (t80) cc_final: 0.6948 (t80) REVERT: i 34 GLN cc_start: 0.7799 (mm110) cc_final: 0.6902 (mm-40) REVERT: k 29 ASN cc_start: 0.8356 (m110) cc_final: 0.8042 (m110) REVERT: k 50 GLU cc_start: 0.7621 (tp30) cc_final: 0.7281 (tp30) REVERT: k 69 VAL cc_start: 0.8797 (t) cc_final: 0.8580 (p) REVERT: k 84 LEU cc_start: 0.8672 (mt) cc_final: 0.8413 (mm) REVERT: m 29 ASN cc_start: 0.8203 (m110) cc_final: 0.7857 (m110) REVERT: m 34 GLN cc_start: 0.7861 (tp40) cc_final: 0.7526 (tp40) REVERT: m 62 PHE cc_start: 0.7482 (t80) cc_final: 0.6940 (t80) REVERT: o 34 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7221 (mm-40) REVERT: o 129 ILE cc_start: 0.8088 (tp) cc_final: 0.7820 (tp) REVERT: q 34 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7347 (mm-40) REVERT: q 68 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7763 (mmtp) REVERT: q 141 ARG cc_start: 0.7643 (ttt90) cc_final: 0.7016 (ttt180) REVERT: s 50 GLU cc_start: 0.7897 (tp30) cc_final: 0.7353 (tp30) REVERT: s 53 LYS cc_start: 0.8099 (mttt) cc_final: 0.7662 (mttm) REVERT: s 113 ARG cc_start: 0.7375 (mtp85) cc_final: 0.7054 (mtp85) REVERT: s 152 TRP cc_start: 0.6326 (t-100) cc_final: 0.5428 (t-100) REVERT: u 19 ASP cc_start: 0.8266 (t0) cc_final: 0.8013 (t0) REVERT: u 29 ASN cc_start: 0.7930 (m110) cc_final: 0.7590 (m110) REVERT: u 34 GLN cc_start: 0.7076 (mm-40) cc_final: 0.6866 (mm-40) REVERT: w 19 ASP cc_start: 0.8247 (t0) cc_final: 0.7304 (m-30) REVERT: w 22 GLU cc_start: 0.8191 (pp20) cc_final: 0.7744 (pp20) REVERT: w 127 ASN cc_start: 0.8417 (m-40) cc_final: 0.8144 (m110) REVERT: w 140 ASN cc_start: 0.7442 (p0) cc_final: 0.7038 (p0) REVERT: y 62 PHE cc_start: 0.7318 (t80) cc_final: 0.6709 (t80) REVERT: y 76 LEU cc_start: 0.8416 (mt) cc_final: 0.8150 (mt) REVERT: y 95 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7944 (mm-30) REVERT: AA 19 ASP cc_start: 0.8093 (t0) cc_final: 0.7843 (t0) REVERT: AA 29 ASN cc_start: 0.8398 (m-40) cc_final: 0.8118 (m-40) REVERT: AA 126 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.7058 (m-40) REVERT: AA 127 ASN cc_start: 0.8521 (m110) cc_final: 0.8183 (m110) REVERT: AA 130 VAL cc_start: 0.8685 (t) cc_final: 0.8443 (p) REVERT: AA 151 VAL cc_start: 0.7950 (p) cc_final: 0.7663 (m) REVERT: AC 19 ASP cc_start: 0.8142 (t0) cc_final: 0.7747 (m-30) REVERT: AC 46 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7715 (mmm-85) REVERT: AC 92 ARG cc_start: 0.6191 (ttt180) cc_final: 0.4200 (ttm170) REVERT: AC 127 ASN cc_start: 0.8524 (m110) cc_final: 0.7965 (m110) REVERT: AC 139 TYR cc_start: 0.8038 (m-80) cc_final: 0.7645 (m-80) REVERT: AE 39 GLN cc_start: 0.8137 (tt0) cc_final: 0.7496 (mp10) REVERT: AE 92 ARG cc_start: 0.6229 (ttt180) cc_final: 0.4576 (ttm-80) REVERT: AE 109 ASP cc_start: 0.7434 (t70) cc_final: 0.7047 (t70) REVERT: AE 139 TYR cc_start: 0.8385 (m-80) cc_final: 0.7879 (m-80) REVERT: AG 19 ASP cc_start: 0.8174 (t0) cc_final: 0.7787 (m-30) REVERT: AG 22 GLU cc_start: 0.7838 (tp30) cc_final: 0.7494 (tp30) REVERT: AG 39 GLN cc_start: 0.8322 (tt0) cc_final: 0.7624 (mp10) REVERT: AG 46 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7800 (ppt170) REVERT: AG 76 LEU cc_start: 0.8337 (mp) cc_final: 0.7999 (tp) REVERT: AG 92 ARG cc_start: 0.6192 (ttt180) cc_final: 0.4252 (ttm170) REVERT: AG 139 TYR cc_start: 0.8030 (m-80) cc_final: 0.7540 (m-80) REVERT: AI 39 GLN cc_start: 0.8513 (tt0) cc_final: 0.7380 (mp10) REVERT: AI 92 ARG cc_start: 0.6018 (ttt180) cc_final: 0.4464 (ttm170) REVERT: AI 140 ASN cc_start: 0.7838 (p0) cc_final: 0.7357 (p0) REVERT: AK 6 THR cc_start: 0.7640 (t) cc_final: 0.7364 (m) REVERT: AK 19 ASP cc_start: 0.8181 (t0) cc_final: 0.7868 (t0) REVERT: AK 39 GLN cc_start: 0.8139 (tt0) cc_final: 0.7322 (mp10) REVERT: AK 46 ARG cc_start: 0.8292 (mtt180) cc_final: 0.7849 (mmm-85) REVERT: AK 92 ARG cc_start: 0.5298 (ttt180) cc_final: 0.3846 (ttm170) REVERT: AK 95 GLU cc_start: 0.3846 (tt0) cc_final: 0.3558 (tt0) REVERT: AK 140 ASN cc_start: 0.7871 (p0) cc_final: 0.7515 (p0) REVERT: AM 19 ASP cc_start: 0.8098 (t0) cc_final: 0.7881 (t0) REVERT: AM 39 GLN cc_start: 0.8361 (tt0) cc_final: 0.7792 (mp10) REVERT: AM 92 ARG cc_start: 0.4903 (ttt180) cc_final: 0.3382 (ttm170) REVERT: AM 95 GLU cc_start: 0.4248 (tt0) cc_final: 0.4007 (tt0) REVERT: AM 139 TYR cc_start: 0.8043 (m-80) cc_final: 0.7598 (m-80) REVERT: AM 140 ASN cc_start: 0.7039 (p0) cc_final: 0.6557 (p0) REVERT: AO 22 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7334 (tp30) REVERT: AO 46 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7810 (ppt170) REVERT: AO 88 ASP cc_start: 0.6585 (t0) cc_final: 0.6259 (p0) REVERT: AO 92 ARG cc_start: 0.5203 (ttt180) cc_final: 0.3604 (ttm170) REVERT: AO 95 GLU cc_start: 0.4357 (tt0) cc_final: 0.4045 (tt0) REVERT: AQ 22 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7342 (tp30) REVERT: AQ 34 GLN cc_start: 0.7557 (tt0) cc_final: 0.7342 (tp40) REVERT: AQ 46 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7759 (mmm160) REVERT: AQ 92 ARG cc_start: 0.5487 (ttt180) cc_final: 0.3944 (ttm170) REVERT: AQ 109 ASP cc_start: 0.7568 (t70) cc_final: 0.7289 (t70) REVERT: AQ 140 ASN cc_start: 0.7380 (p0) cc_final: 0.6687 (p0) REVERT: AS 29 ASN cc_start: 0.8071 (m110) cc_final: 0.7569 (m110) REVERT: AS 33 ASN cc_start: 0.7298 (m110) cc_final: 0.6886 (m-40) REVERT: AS 34 GLN cc_start: 0.7391 (tt0) cc_final: 0.7012 (tp40) REVERT: AS 38 GLN cc_start: 0.6660 (tp40) cc_final: 0.6436 (tp40) REVERT: AS 88 ASP cc_start: 0.7313 (t0) cc_final: 0.6742 (t0) REVERT: AS 92 ARG cc_start: 0.5483 (ttt180) cc_final: 0.4023 (ttm170) REVERT: AS 95 GLU cc_start: 0.4340 (tt0) cc_final: 0.4025 (tt0) REVERT: AS 139 TYR cc_start: 0.7832 (m-80) cc_final: 0.7497 (m-80) REVERT: AS 140 ASN cc_start: 0.7181 (p0) cc_final: 0.6903 (p0) REVERT: AU 39 GLN cc_start: 0.8358 (tt0) cc_final: 0.7702 (mp10) REVERT: AU 46 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7639 (tmt170) REVERT: AU 57 GLN cc_start: 0.7282 (mm110) cc_final: 0.6947 (mm-40) REVERT: AU 91 ASN cc_start: 0.6806 (t0) cc_final: 0.6487 (t0) REVERT: AU 92 ARG cc_start: 0.5589 (ttt180) cc_final: 0.4258 (ttm170) REVERT: AU 127 ASN cc_start: 0.8499 (t0) cc_final: 0.8157 (m110) REVERT: AU 140 ASN cc_start: 0.7460 (p0) cc_final: 0.7111 (p0) REVERT: AW 33 ASN cc_start: 0.7417 (m110) cc_final: 0.6736 (m-40) REVERT: AW 39 GLN cc_start: 0.8218 (tt0) cc_final: 0.7796 (mp10) REVERT: AW 46 ARG cc_start: 0.8395 (mtt180) cc_final: 0.7647 (tmt170) REVERT: AW 50 GLU cc_start: 0.8042 (tp30) cc_final: 0.7676 (tp30) REVERT: AW 57 GLN cc_start: 0.6387 (mm-40) cc_final: 0.5997 (mm-40) REVERT: AW 90 ARG cc_start: 0.5068 (mtt-85) cc_final: 0.4820 (mtt180) REVERT: AW 92 ARG cc_start: 0.5466 (ttt180) cc_final: 0.4605 (ttm170) REVERT: AW 93 ILE cc_start: 0.8159 (mp) cc_final: 0.7928 (mt) REVERT: AW 127 ASN cc_start: 0.8461 (m110) cc_final: 0.7974 (m110) REVERT: AW 140 ASN cc_start: 0.7986 (p0) cc_final: 0.7609 (p0) REVERT: AY 29 ASN cc_start: 0.8456 (m110) cc_final: 0.8059 (m-40) REVERT: AY 34 GLN cc_start: 0.7691 (tt0) cc_final: 0.7340 (pt0) REVERT: AY 39 GLN cc_start: 0.8079 (tt0) cc_final: 0.7714 (mp10) REVERT: AY 46 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7513 (tmt170) REVERT: AY 88 ASP cc_start: 0.6065 (t0) cc_final: 0.5811 (p0) REVERT: AY 139 TYR cc_start: 0.7739 (m-80) cc_final: 0.7252 (m-80) REVERT: AY 140 ASN cc_start: 0.7810 (p0) cc_final: 0.7440 (p0) REVERT: A0 19 ASP cc_start: 0.8155 (t0) cc_final: 0.7547 (t0) REVERT: A0 22 GLU cc_start: 0.8293 (pp20) cc_final: 0.8000 (pp20) REVERT: A0 23 LEU cc_start: 0.8153 (tp) cc_final: 0.7828 (tt) REVERT: A0 39 GLN cc_start: 0.7398 (tt0) cc_final: 0.6823 (mp10) REVERT: A0 46 ARG cc_start: 0.7755 (mmt90) cc_final: 0.7102 (tmm160) REVERT: A0 92 ARG cc_start: 0.5307 (ttt180) cc_final: 0.4344 (ttm110) REVERT: A2 39 GLN cc_start: 0.7513 (tt0) cc_final: 0.6939 (mp10) REVERT: A2 53 LYS cc_start: 0.7706 (mmtt) cc_final: 0.7291 (mtmm) REVERT: A2 92 ARG cc_start: 0.4980 (ttt180) cc_final: 0.4273 (ttm-80) REVERT: A2 127 ASN cc_start: 0.8685 (m110) cc_final: 0.8281 (m110) REVERT: A2 140 ASN cc_start: 0.7909 (p0) cc_final: 0.7282 (p0) REVERT: A4 29 ASN cc_start: 0.8248 (m-40) cc_final: 0.7832 (m-40) REVERT: A4 39 GLN cc_start: 0.7628 (tt0) cc_final: 0.7146 (mp10) REVERT: A4 46 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7188 (ppt170) REVERT: A4 50 GLU cc_start: 0.7844 (tp30) cc_final: 0.7641 (tp30) REVERT: A4 92 ARG cc_start: 0.4500 (ttt180) cc_final: 0.4153 (ttm170) REVERT: A4 112 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7587 (tpt170) REVERT: A6 23 LEU cc_start: 0.8532 (tp) cc_final: 0.8279 (tp) REVERT: A6 29 ASN cc_start: 0.7934 (m110) cc_final: 0.7558 (m110) REVERT: A6 38 GLN cc_start: 0.7005 (tp40) cc_final: 0.5353 (pm20) REVERT: A6 46 ARG cc_start: 0.7791 (mtt-85) cc_final: 0.7399 (ppt170) REVERT: A6 93 ILE cc_start: 0.7874 (tp) cc_final: 0.7155 (tp) REVERT: A6 112 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7659 (mmp-170) REVERT: A8 21 ILE cc_start: 0.8299 (tt) cc_final: 0.7917 (tt) REVERT: A8 29 ASN cc_start: 0.7582 (m-40) cc_final: 0.7216 (t0) REVERT: A8 33 ASN cc_start: 0.8384 (m-40) cc_final: 0.8068 (m-40) REVERT: A8 38 GLN cc_start: 0.6994 (tp40) cc_final: 0.5679 (pm20) REVERT: A8 46 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7149 (tmm160) outliers start: 18 outliers final: 0 residues processed: 1717 average time/residue: 0.6049 time to fit residues: 1729.8165 Evaluate side-chains 1412 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1410 time to evaluate : 5.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 10.0000 chunk 639 optimal weight: 9.9990 chunk 140 optimal weight: 0.0020 chunk 417 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 711 optimal weight: 1.9990 chunk 590 optimal weight: 0.0040 chunk 329 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 235 optimal weight: 30.0000 chunk 373 optimal weight: 20.0000 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 36 GLN A 99 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 39 GLN I 39 GLN K 39 GLN K 57 GLN ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 ASN S 127 ASN U 39 GLN W 45 GLN ** W 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 ASN 0 33 ASN 4 98 ASN 6 47 GLN a 25 ASN a 36 GLN a 127 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 99 GLN ** g 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 91 ASN g 101 ASN g 126 ASN i 9 GLN i 73 ASN k 36 GLN ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 126 ASN ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 126 ASN s 127 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 GLN u 91 ASN ** u 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 126 ASN u 127 ASN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 GLN w 101 ASN y 47 GLN y 98 ASN y 127 ASN AA 101 ASN ** AC 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 126 ASN ** AE 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 99 GLN ** AG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 126 ASN ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 126 ASN AK 57 GLN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 101 ASN ** AK 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 91 ASN ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 91 ASN AQ 126 ASN ** AS 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 57 GLN ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 91 ASN AS 126 ASN ** AU 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 99 GLN AU 126 ASN ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 99 GLN AW 126 ASN ** A0 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 101 ASN A2 34 GLN A4 91 ASN A4 126 ASN ** A6 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 91 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 63945 Z= 0.194 Angle : 0.572 6.205 88004 Z= 0.311 Chirality : 0.040 0.159 10437 Planarity : 0.005 0.054 10878 Dihedral : 11.703 78.188 10094 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.33 % Allowed : 1.78 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.09), residues: 7399 helix: 0.05 (0.08), residues: 3871 sheet: None (None), residues: 0 loop : -2.27 (0.09), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP k 17 PHE 0.024 0.002 PHEAI 62 TYR 0.012 0.001 TYR W 70 ARG 0.006 0.001 ARG k 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1780 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1758 time to evaluate : 5.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8204 (mp) cc_final: 0.7856 (tt) REVERT: A 50 GLU cc_start: 0.7795 (tp30) cc_final: 0.7439 (tp30) REVERT: C 6 THR cc_start: 0.7518 (t) cc_final: 0.7278 (p) REVERT: C 57 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7250 (mm-40) REVERT: C 77 ASP cc_start: 0.7971 (t70) cc_final: 0.7768 (t70) REVERT: C 127 ASN cc_start: 0.7946 (m-40) cc_final: 0.7606 (m-40) REVERT: E 34 GLN cc_start: 0.6715 (mt0) cc_final: 0.6488 (mt0) REVERT: E 53 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7497 (pttp) REVERT: E 91 ASN cc_start: 0.7269 (t0) cc_final: 0.6912 (p0) REVERT: E 112 ARG cc_start: 0.8017 (tpp-160) cc_final: 0.7755 (tpt-90) REVERT: E 139 TYR cc_start: 0.8106 (m-10) cc_final: 0.7763 (m-10) REVERT: E 140 ASN cc_start: 0.7615 (p0) cc_final: 0.7391 (p0) REVERT: G 68 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7603 (ptpt) REVERT: G 91 ASN cc_start: 0.6604 (t0) cc_final: 0.6392 (p0) REVERT: G 139 TYR cc_start: 0.8416 (m-10) cc_final: 0.8131 (m-10) REVERT: I 57 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6731 (mm-40) REVERT: I 76 LEU cc_start: 0.8112 (mt) cc_final: 0.7609 (mt) REVERT: I 77 ASP cc_start: 0.7975 (t70) cc_final: 0.7771 (t70) REVERT: I 83 LEU cc_start: 0.8348 (tp) cc_final: 0.8109 (tp) REVERT: I 91 ASN cc_start: 0.6996 (t0) cc_final: 0.6632 (p0) REVERT: K 22 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7790 (tm-30) REVERT: K 25 ASN cc_start: 0.8787 (m-40) cc_final: 0.8284 (m-40) REVERT: K 77 ASP cc_start: 0.8013 (t70) cc_final: 0.7807 (t0) REVERT: M 29 ASN cc_start: 0.7790 (m-40) cc_final: 0.7277 (t0) REVERT: M 59 THR cc_start: 0.8131 (m) cc_final: 0.7806 (t) REVERT: M 89 THR cc_start: 0.7333 (m) cc_final: 0.7070 (p) REVERT: M 90 ARG cc_start: 0.6298 (ttm-80) cc_final: 0.6085 (ttm110) REVERT: O 89 THR cc_start: 0.7760 (m) cc_final: 0.7437 (p) REVERT: O 140 ASN cc_start: 0.7532 (p0) cc_final: 0.6846 (p0) REVERT: Q 68 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7601 (mmmm) REVERT: Q 140 ASN cc_start: 0.6982 (p0) cc_final: 0.6775 (p0) REVERT: Q 141 ARG cc_start: 0.7237 (ttt90) cc_final: 0.6696 (ttt90) REVERT: S 38 GLN cc_start: 0.7059 (tp40) cc_final: 0.6577 (tp-100) REVERT: U 25 ASN cc_start: 0.8944 (m-40) cc_final: 0.8616 (m-40) REVERT: U 77 ASP cc_start: 0.7921 (t70) cc_final: 0.7632 (t70) REVERT: U 88 ASP cc_start: 0.7251 (t0) cc_final: 0.6964 (t0) REVERT: U 89 THR cc_start: 0.7695 (m) cc_final: 0.7259 (p) REVERT: W 62 PHE cc_start: 0.7957 (t80) cc_final: 0.7625 (t80) REVERT: W 127 ASN cc_start: 0.8345 (m110) cc_final: 0.8048 (m-40) REVERT: Y 62 PHE cc_start: 0.7270 (t80) cc_final: 0.6828 (t80) REVERT: Y 112 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.7834 (tpt170) REVERT: Y 141 ARG cc_start: 0.6821 (ttt-90) cc_final: 0.6111 (ttm-80) REVERT: 0 25 ASN cc_start: 0.8694 (m-40) cc_final: 0.8368 (m110) REVERT: 0 39 GLN cc_start: 0.7886 (tt0) cc_final: 0.7428 (tt0) REVERT: 0 127 ASN cc_start: 0.8444 (m-40) cc_final: 0.8148 (m-40) REVERT: 2 38 GLN cc_start: 0.6746 (tp40) cc_final: 0.6309 (tp-100) REVERT: 2 87 PHE cc_start: 0.7080 (m-80) cc_final: 0.6773 (m-80) REVERT: 2 89 THR cc_start: 0.7869 (m) cc_final: 0.7005 (p) REVERT: 4 62 PHE cc_start: 0.7461 (t80) cc_final: 0.7215 (t80) REVERT: 4 89 THR cc_start: 0.7603 (m) cc_final: 0.7220 (p) REVERT: 4 93 ILE cc_start: 0.8302 (mt) cc_final: 0.8018 (tp) REVERT: 4 112 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7598 (tpt170) REVERT: 4 127 ASN cc_start: 0.8453 (m110) cc_final: 0.8135 (m110) REVERT: 6 112 ARG cc_start: 0.8581 (tpp-160) cc_final: 0.8003 (tpt170) REVERT: 6 143 SER cc_start: 0.8150 (p) cc_final: 0.7778 (t) REVERT: 8 127 ASN cc_start: 0.8051 (m-40) cc_final: 0.7789 (m110) REVERT: a 21 ILE cc_start: 0.8484 (mp) cc_final: 0.8132 (tt) REVERT: a 62 PHE cc_start: 0.7006 (t80) cc_final: 0.6624 (t80) REVERT: c 27 CYS cc_start: 0.8693 (p) cc_final: 0.8430 (p) REVERT: c 62 PHE cc_start: 0.6839 (t80) cc_final: 0.6416 (t80) REVERT: e 34 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7361 (mm-40) REVERT: e 50 GLU cc_start: 0.7365 (tp30) cc_final: 0.6733 (tp30) REVERT: e 94 ILE cc_start: 0.8529 (mp) cc_final: 0.8276 (mm) REVERT: e 129 ILE cc_start: 0.7894 (tp) cc_final: 0.7683 (tp) REVERT: g 29 ASN cc_start: 0.8199 (m110) cc_final: 0.7975 (m110) REVERT: g 62 PHE cc_start: 0.7259 (t80) cc_final: 0.6824 (t80) REVERT: g 67 PHE cc_start: 0.6834 (m-80) cc_final: 0.6370 (m-80) REVERT: i 34 GLN cc_start: 0.7705 (mm110) cc_final: 0.6835 (mm-40) REVERT: k 29 ASN cc_start: 0.8201 (m110) cc_final: 0.7944 (m110) REVERT: k 50 GLU cc_start: 0.7569 (tp30) cc_final: 0.7178 (tp30) REVERT: k 69 VAL cc_start: 0.8753 (t) cc_final: 0.8522 (p) REVERT: k 84 LEU cc_start: 0.8694 (mt) cc_final: 0.8474 (mm) REVERT: m 29 ASN cc_start: 0.8157 (m110) cc_final: 0.7908 (m110) REVERT: m 34 GLN cc_start: 0.7917 (tp40) cc_final: 0.7654 (tp40) REVERT: m 62 PHE cc_start: 0.7545 (t80) cc_final: 0.6935 (t80) REVERT: m 129 ILE cc_start: 0.7890 (tp) cc_final: 0.7660 (tp) REVERT: o 34 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7285 (mm-40) REVERT: o 129 ILE cc_start: 0.7981 (tp) cc_final: 0.7758 (tp) REVERT: q 24 ILE cc_start: 0.8662 (mm) cc_final: 0.8410 (mm) REVERT: q 34 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7364 (mm-40) REVERT: q 68 LYS cc_start: 0.8299 (mmmm) cc_final: 0.8097 (mmtt) REVERT: q 129 ILE cc_start: 0.8160 (tp) cc_final: 0.7829 (tp) REVERT: s 50 GLU cc_start: 0.7825 (tp30) cc_final: 0.7427 (tp30) REVERT: s 53 LYS cc_start: 0.8155 (mttt) cc_final: 0.7794 (mttm) REVERT: s 93 ILE cc_start: 0.7974 (mt) cc_final: 0.7764 (tp) REVERT: s 129 ILE cc_start: 0.7923 (tp) cc_final: 0.7710 (tp) REVERT: s 152 TRP cc_start: 0.6255 (t-100) cc_final: 0.5277 (t-100) REVERT: u 29 ASN cc_start: 0.7926 (m110) cc_final: 0.7606 (m110) REVERT: u 126 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6855 (m-40) REVERT: u 140 ASN cc_start: 0.7115 (p0) cc_final: 0.6502 (p0) REVERT: w 19 ASP cc_start: 0.8232 (t0) cc_final: 0.7486 (m-30) REVERT: w 22 GLU cc_start: 0.8227 (pp20) cc_final: 0.7798 (pp20) REVERT: w 23 LEU cc_start: 0.8549 (tt) cc_final: 0.7971 (tt) REVERT: w 62 PHE cc_start: 0.7464 (t80) cc_final: 0.7244 (t80) REVERT: w 95 GLU cc_start: 0.7814 (mm-30) cc_final: 0.6946 (tp30) REVERT: w 140 ASN cc_start: 0.7369 (p0) cc_final: 0.7049 (p0) REVERT: y 62 PHE cc_start: 0.7425 (t80) cc_final: 0.6816 (t80) REVERT: y 76 LEU cc_start: 0.8409 (mt) cc_final: 0.8148 (mt) REVERT: y 126 ASN cc_start: 0.6588 (t0) cc_final: 0.6356 (t0) REVERT: AA 19 ASP cc_start: 0.8131 (t0) cc_final: 0.7838 (t0) REVERT: AA 29 ASN cc_start: 0.8388 (m-40) cc_final: 0.8097 (m-40) REVERT: AA 127 ASN cc_start: 0.8340 (m110) cc_final: 0.8039 (m110) REVERT: AC 22 GLU cc_start: 0.7471 (tp30) cc_final: 0.7009 (tp30) REVERT: AC 46 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7626 (mmm-85) REVERT: AC 92 ARG cc_start: 0.5701 (ttt180) cc_final: 0.3988 (ttm170) REVERT: AC 139 TYR cc_start: 0.8024 (m-80) cc_final: 0.7745 (m-80) REVERT: AC 140 ASN cc_start: 0.6761 (p0) cc_final: 0.6412 (p0) REVERT: AE 39 GLN cc_start: 0.7996 (tt0) cc_final: 0.7473 (mp10) REVERT: AE 62 PHE cc_start: 0.7506 (t80) cc_final: 0.7290 (t80) REVERT: AE 92 ARG cc_start: 0.5328 (ttt180) cc_final: 0.4045 (ttm170) REVERT: AE 109 ASP cc_start: 0.7451 (t70) cc_final: 0.7024 (t70) REVERT: AE 131 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7908 (tm-30) REVERT: AG 19 ASP cc_start: 0.8080 (t0) cc_final: 0.7577 (m-30) REVERT: AG 22 GLU cc_start: 0.7732 (tp30) cc_final: 0.7421 (tp30) REVERT: AG 39 GLN cc_start: 0.8201 (tt0) cc_final: 0.7462 (mp10) REVERT: AG 46 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7729 (ppt170) REVERT: AG 76 LEU cc_start: 0.8383 (mp) cc_final: 0.8092 (mp) REVERT: AG 92 ARG cc_start: 0.6083 (ttt180) cc_final: 0.4044 (ttm170) REVERT: AG 139 TYR cc_start: 0.7962 (m-80) cc_final: 0.7547 (m-80) REVERT: AI 33 ASN cc_start: 0.8020 (m-40) cc_final: 0.7696 (m-40) REVERT: AI 39 GLN cc_start: 0.8425 (tt0) cc_final: 0.7319 (mp10) REVERT: AI 92 ARG cc_start: 0.6022 (ttt180) cc_final: 0.4478 (ttm170) REVERT: AI 95 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7276 (tp30) REVERT: AI 140 ASN cc_start: 0.7424 (p0) cc_final: 0.6890 (p0) REVERT: AK 6 THR cc_start: 0.7599 (t) cc_final: 0.7298 (m) REVERT: AK 19 ASP cc_start: 0.8167 (t0) cc_final: 0.7789 (t0) REVERT: AK 39 GLN cc_start: 0.8256 (tt0) cc_final: 0.7447 (mp10) REVERT: AK 46 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7759 (mmm-85) REVERT: AK 83 LEU cc_start: 0.8788 (tp) cc_final: 0.8562 (tp) REVERT: AK 92 ARG cc_start: 0.5295 (ttt180) cc_final: 0.3561 (ttm170) REVERT: AK 140 ASN cc_start: 0.7681 (p0) cc_final: 0.7324 (p0) REVERT: AM 19 ASP cc_start: 0.8056 (t0) cc_final: 0.7727 (t0) REVERT: AM 39 GLN cc_start: 0.8325 (tt0) cc_final: 0.7756 (mp10) REVERT: AM 92 ARG cc_start: 0.4694 (ttt180) cc_final: 0.3163 (ttm170) REVERT: AM 95 GLU cc_start: 0.4199 (tt0) cc_final: 0.3974 (tt0) REVERT: AM 139 TYR cc_start: 0.8057 (m-80) cc_final: 0.7596 (m-80) REVERT: AM 140 ASN cc_start: 0.7181 (p0) cc_final: 0.6572 (p0) REVERT: AO 22 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7239 (tp30) REVERT: AO 46 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7740 (tmt170) REVERT: AO 57 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7716 (tp-100) REVERT: AO 92 ARG cc_start: 0.4793 (ttt180) cc_final: 0.3291 (ttm-80) REVERT: AO 95 GLU cc_start: 0.4144 (tt0) cc_final: 0.3894 (tt0) REVERT: AQ 22 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7345 (tp30) REVERT: AQ 33 ASN cc_start: 0.7854 (m-40) cc_final: 0.7102 (m-40) REVERT: AQ 46 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7741 (mmm160) REVERT: AQ 92 ARG cc_start: 0.5339 (ttt180) cc_final: 0.3932 (ttm170) REVERT: AQ 140 ASN cc_start: 0.7468 (p0) cc_final: 0.6771 (p0) REVERT: AS 29 ASN cc_start: 0.8090 (m110) cc_final: 0.7582 (m110) REVERT: AS 33 ASN cc_start: 0.7508 (m110) cc_final: 0.7038 (m-40) REVERT: AS 92 ARG cc_start: 0.5330 (ttt180) cc_final: 0.3829 (ttm170) REVERT: AS 95 GLU cc_start: 0.4016 (tt0) cc_final: 0.3725 (tt0) REVERT: AS 139 TYR cc_start: 0.7787 (m-80) cc_final: 0.7536 (m-80) REVERT: AS 140 ASN cc_start: 0.6550 (p0) cc_final: 0.6245 (p0) REVERT: AU 33 ASN cc_start: 0.8144 (m-40) cc_final: 0.7698 (m-40) REVERT: AU 34 GLN cc_start: 0.7815 (mt0) cc_final: 0.7351 (mt0) REVERT: AU 39 GLN cc_start: 0.8226 (tt0) cc_final: 0.7598 (mp10) REVERT: AU 46 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7669 (tmt170) REVERT: AU 50 GLU cc_start: 0.7688 (tp30) cc_final: 0.7432 (tp30) REVERT: AU 57 GLN cc_start: 0.7291 (mm110) cc_final: 0.6928 (mm-40) REVERT: AU 91 ASN cc_start: 0.6764 (t0) cc_final: 0.6480 (t0) REVERT: AU 92 ARG cc_start: 0.5612 (ttt180) cc_final: 0.4428 (ttm170) REVERT: AU 127 ASN cc_start: 0.8446 (t0) cc_final: 0.8111 (m110) REVERT: AU 140 ASN cc_start: 0.7837 (p0) cc_final: 0.7362 (p0) REVERT: AW 33 ASN cc_start: 0.7725 (m110) cc_final: 0.6886 (m-40) REVERT: AW 39 GLN cc_start: 0.8197 (tt0) cc_final: 0.7888 (mp10) REVERT: AW 46 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7576 (tmt170) REVERT: AW 50 GLU cc_start: 0.7935 (tp30) cc_final: 0.7557 (tp30) REVERT: AW 57 GLN cc_start: 0.6411 (mm-40) cc_final: 0.5993 (mm-40) REVERT: AW 92 ARG cc_start: 0.5409 (ttt180) cc_final: 0.4564 (ttm170) REVERT: AW 127 ASN cc_start: 0.8371 (m110) cc_final: 0.7875 (m110) REVERT: AW 131 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7577 (mp0) REVERT: AW 140 ASN cc_start: 0.7921 (p0) cc_final: 0.7690 (p0) REVERT: AY 29 ASN cc_start: 0.8365 (m110) cc_final: 0.7990 (m-40) REVERT: AY 34 GLN cc_start: 0.7537 (tt0) cc_final: 0.7102 (tp-100) REVERT: AY 39 GLN cc_start: 0.8025 (tt0) cc_final: 0.7672 (mp10) REVERT: AY 46 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7472 (tmt170) REVERT: AY 88 ASP cc_start: 0.6392 (t0) cc_final: 0.5720 (p0) REVERT: AY 92 ARG cc_start: 0.4789 (ttt180) cc_final: 0.3867 (ttm170) REVERT: AY 93 ILE cc_start: 0.7905 (tp) cc_final: 0.7665 (tp) REVERT: AY 139 TYR cc_start: 0.7676 (m-80) cc_final: 0.7196 (m-80) REVERT: AY 140 ASN cc_start: 0.7766 (p0) cc_final: 0.7319 (p0) REVERT: A0 19 ASP cc_start: 0.8165 (t0) cc_final: 0.7677 (t0) REVERT: A0 22 GLU cc_start: 0.8274 (pp20) cc_final: 0.7934 (pp20) REVERT: A0 39 GLN cc_start: 0.7257 (tt0) cc_final: 0.6807 (mp10) REVERT: A0 46 ARG cc_start: 0.7734 (mmt90) cc_final: 0.7067 (tmm160) REVERT: A0 92 ARG cc_start: 0.5041 (ttt180) cc_final: 0.4512 (ttm170) REVERT: A0 112 ARG cc_start: 0.8199 (tpt170) cc_final: 0.7976 (tpt170) REVERT: A0 127 ASN cc_start: 0.8497 (m110) cc_final: 0.7998 (m110) REVERT: A2 39 GLN cc_start: 0.7396 (tt0) cc_final: 0.6947 (mp10) REVERT: A2 53 LYS cc_start: 0.7723 (mmtt) cc_final: 0.7338 (mtmm) REVERT: A2 92 ARG cc_start: 0.4652 (ttt180) cc_final: 0.4167 (ttm170) REVERT: A2 127 ASN cc_start: 0.8658 (m110) cc_final: 0.8204 (m-40) REVERT: A2 140 ASN cc_start: 0.7879 (p0) cc_final: 0.7316 (p0) REVERT: A4 29 ASN cc_start: 0.8277 (m-40) cc_final: 0.7843 (m-40) REVERT: A4 39 GLN cc_start: 0.7477 (tt0) cc_final: 0.7074 (mp10) REVERT: A4 46 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.7187 (ppt170) REVERT: A4 92 ARG cc_start: 0.3798 (ttt180) cc_final: 0.3434 (ttm170) REVERT: A6 29 ASN cc_start: 0.7954 (m110) cc_final: 0.7488 (m110) REVERT: A6 38 GLN cc_start: 0.6910 (tp40) cc_final: 0.5407 (pm20) REVERT: A6 46 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7428 (ppt170) REVERT: A6 93 ILE cc_start: 0.7828 (tp) cc_final: 0.7309 (tp) REVERT: A6 112 ARG cc_start: 0.8181 (tpp-160) cc_final: 0.7725 (mmp-170) REVERT: A8 19 ASP cc_start: 0.7667 (t70) cc_final: 0.7423 (t0) REVERT: A8 29 ASN cc_start: 0.7526 (m-40) cc_final: 0.7155 (t0) REVERT: A8 33 ASN cc_start: 0.8409 (m-40) cc_final: 0.8101 (m-40) REVERT: A8 38 GLN cc_start: 0.6943 (tp40) cc_final: 0.5611 (pm20) outliers start: 22 outliers final: 4 residues processed: 1764 average time/residue: 0.5928 time to fit residues: 1749.1478 Evaluate side-chains 1450 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1445 time to evaluate : 5.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 405 optimal weight: 30.0000 chunk 519 optimal weight: 5.9990 chunk 402 optimal weight: 10.0000 chunk 598 optimal weight: 5.9990 chunk 397 optimal weight: 6.9990 chunk 708 optimal weight: 0.3980 chunk 443 optimal weight: 0.5980 chunk 431 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN E 33 ASN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 ASN K 39 GLN ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN ** M 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 GLN W 9 GLN W 45 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 101 ASN 6 98 ASN 6 101 ASN ** 8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN a 126 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 91 ASN g 101 ASN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 36 GLN ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 39 GLN ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 101 ASN u 126 ASN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 98 ASN w 101 ASN ** w 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 127 ASN AA 101 ASN ** AC 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 57 GLN ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 57 GLN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 101 ASN AK 126 ASN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 91 ASN ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 126 ASN ** AS 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 57 GLN ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AU 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 126 ASN ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 126 ASN ** A0 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 36 GLN ** A0 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 101 ASN A4 99 GLN ** A6 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 91 ASN A8 101 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 63945 Z= 0.213 Angle : 0.577 6.354 88004 Z= 0.313 Chirality : 0.041 0.177 10437 Planarity : 0.005 0.055 10878 Dihedral : 11.561 78.311 10094 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.24 % Allowed : 1.75 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.09), residues: 7399 helix: 0.06 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -2.34 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP k 17 PHE 0.025 0.002 PHEAI 62 TYR 0.012 0.001 TYR W 70 ARG 0.010 0.001 ARGAS 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1715 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1699 time to evaluate : 6.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7798 (tp30) cc_final: 0.7439 (tp30) REVERT: C 6 THR cc_start: 0.7500 (t) cc_final: 0.7263 (p) REVERT: C 127 ASN cc_start: 0.7873 (m-40) cc_final: 0.7548 (m-40) REVERT: E 53 LYS cc_start: 0.7979 (ptmt) cc_final: 0.7466 (pttp) REVERT: E 91 ASN cc_start: 0.7297 (t0) cc_final: 0.6966 (p0) REVERT: E 112 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7793 (tpt-90) REVERT: G 68 LYS cc_start: 0.8134 (ptpp) cc_final: 0.7718 (ptpt) REVERT: G 139 TYR cc_start: 0.8409 (m-10) cc_final: 0.8126 (m-10) REVERT: I 57 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6756 (mm-40) REVERT: I 77 ASP cc_start: 0.7980 (t70) cc_final: 0.7754 (t70) REVERT: I 83 LEU cc_start: 0.8292 (tp) cc_final: 0.8052 (tp) REVERT: I 91 ASN cc_start: 0.6919 (t0) cc_final: 0.6704 (p0) REVERT: K 22 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7835 (tm-30) REVERT: K 25 ASN cc_start: 0.8882 (m-40) cc_final: 0.8332 (m-40) REVERT: M 29 ASN cc_start: 0.7802 (m-40) cc_final: 0.7239 (t0) REVERT: M 59 THR cc_start: 0.8324 (m) cc_final: 0.7950 (t) REVERT: M 89 THR cc_start: 0.7303 (m) cc_final: 0.7003 (p) REVERT: M 90 ARG cc_start: 0.6315 (ttm-80) cc_final: 0.6024 (ttm110) REVERT: O 89 THR cc_start: 0.7730 (m) cc_final: 0.7418 (p) REVERT: O 140 ASN cc_start: 0.7386 (p0) cc_final: 0.6671 (p0) REVERT: Q 50 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7197 (mm-30) REVERT: Q 68 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7649 (mmmm) REVERT: S 38 GLN cc_start: 0.7028 (tp40) cc_final: 0.6600 (tp-100) REVERT: S 127 ASN cc_start: 0.7807 (m110) cc_final: 0.7565 (m110) REVERT: U 25 ASN cc_start: 0.9004 (m-40) cc_final: 0.8559 (m-40) REVERT: U 34 GLN cc_start: 0.7052 (mm-40) cc_final: 0.6478 (mm-40) REVERT: U 77 ASP cc_start: 0.8077 (t70) cc_final: 0.7800 (t0) REVERT: U 89 THR cc_start: 0.7556 (m) cc_final: 0.7260 (p) REVERT: U 112 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.7705 (tpt170) REVERT: W 19 ASP cc_start: 0.8010 (t0) cc_final: 0.7759 (t0) REVERT: W 22 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7420 (mm-30) REVERT: W 127 ASN cc_start: 0.8310 (m110) cc_final: 0.7991 (m-40) REVERT: Y 112 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.7764 (tpt170) REVERT: 0 93 ILE cc_start: 0.8289 (mt) cc_final: 0.8043 (tp) REVERT: 0 127 ASN cc_start: 0.8389 (m-40) cc_final: 0.8088 (m-40) REVERT: 2 38 GLN cc_start: 0.6703 (tp40) cc_final: 0.6402 (tp-100) REVERT: 2 89 THR cc_start: 0.7558 (m) cc_final: 0.7071 (p) REVERT: 4 62 PHE cc_start: 0.7418 (t80) cc_final: 0.7161 (t80) REVERT: 4 89 THR cc_start: 0.7603 (m) cc_final: 0.7218 (p) REVERT: 4 93 ILE cc_start: 0.8346 (mt) cc_final: 0.8029 (tp) REVERT: 4 112 ARG cc_start: 0.8313 (tpp-160) cc_final: 0.7573 (tpt170) REVERT: 4 127 ASN cc_start: 0.8425 (m110) cc_final: 0.8127 (m110) REVERT: 6 27 CYS cc_start: 0.8748 (p) cc_final: 0.8461 (p) REVERT: 6 143 SER cc_start: 0.8260 (p) cc_final: 0.7878 (t) REVERT: 8 127 ASN cc_start: 0.8033 (m-40) cc_final: 0.7740 (m110) REVERT: a 25 ASN cc_start: 0.9002 (m-40) cc_final: 0.8766 (m-40) REVERT: a 62 PHE cc_start: 0.7135 (t80) cc_final: 0.6554 (t80) REVERT: c 27 CYS cc_start: 0.8739 (p) cc_final: 0.8488 (p) REVERT: e 34 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7216 (mm-40) REVERT: e 50 GLU cc_start: 0.7333 (tp30) cc_final: 0.6725 (tp30) REVERT: e 127 ASN cc_start: 0.7790 (m110) cc_final: 0.7590 (m110) REVERT: e 129 ILE cc_start: 0.7969 (tp) cc_final: 0.7742 (tp) REVERT: g 62 PHE cc_start: 0.7065 (t80) cc_final: 0.6614 (t80) REVERT: i 34 GLN cc_start: 0.7796 (mm110) cc_final: 0.6911 (mm-40) REVERT: k 34 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6507 (mm-40) REVERT: k 46 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7455 (mmm-85) REVERT: k 50 GLU cc_start: 0.7583 (tp30) cc_final: 0.7250 (tp30) REVERT: k 84 LEU cc_start: 0.8665 (mt) cc_final: 0.8439 (mm) REVERT: m 29 ASN cc_start: 0.8186 (m110) cc_final: 0.7818 (m110) REVERT: m 34 GLN cc_start: 0.7903 (tp40) cc_final: 0.7580 (tp40) REVERT: m 127 ASN cc_start: 0.8153 (m110) cc_final: 0.7878 (m110) REVERT: m 129 ILE cc_start: 0.7934 (tp) cc_final: 0.7734 (tp) REVERT: m 130 VAL cc_start: 0.8197 (t) cc_final: 0.7731 (p) REVERT: o 34 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7190 (mm-40) REVERT: q 90 ARG cc_start: 0.7148 (ttm-80) cc_final: 0.6349 (ttm-80) REVERT: q 129 ILE cc_start: 0.8197 (tp) cc_final: 0.7910 (tp) REVERT: s 36 GLN cc_start: 0.7809 (mt0) cc_final: 0.7478 (mt0) REVERT: s 53 LYS cc_start: 0.8195 (mttt) cc_final: 0.7802 (mttm) REVERT: s 95 GLU cc_start: 0.7212 (mm-30) cc_final: 0.7007 (tp30) REVERT: s 113 ARG cc_start: 0.7365 (mtp85) cc_final: 0.7037 (mtp85) REVERT: u 29 ASN cc_start: 0.7926 (m110) cc_final: 0.7596 (m110) REVERT: u 129 ILE cc_start: 0.8104 (tp) cc_final: 0.7897 (tp) REVERT: w 19 ASP cc_start: 0.8294 (t0) cc_final: 0.7472 (m-30) REVERT: w 22 GLU cc_start: 0.8270 (pp20) cc_final: 0.7839 (pp20) REVERT: w 23 LEU cc_start: 0.8632 (tt) cc_final: 0.8028 (tt) REVERT: w 29 ASN cc_start: 0.7992 (m110) cc_final: 0.7619 (m110) REVERT: w 62 PHE cc_start: 0.7557 (t80) cc_final: 0.7321 (t80) REVERT: w 95 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7089 (tp30) REVERT: w 127 ASN cc_start: 0.8661 (m110) cc_final: 0.8442 (m110) REVERT: w 140 ASN cc_start: 0.7427 (p0) cc_final: 0.6745 (p0) REVERT: y 76 LEU cc_start: 0.8377 (mt) cc_final: 0.8159 (mt) REVERT: y 126 ASN cc_start: 0.6729 (t0) cc_final: 0.6508 (t0) REVERT: AA 19 ASP cc_start: 0.8128 (t0) cc_final: 0.7854 (t0) REVERT: AA 29 ASN cc_start: 0.8351 (m-40) cc_final: 0.8132 (m-40) REVERT: AA 46 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7322 (mmt90) REVERT: AA 127 ASN cc_start: 0.8340 (m110) cc_final: 0.7994 (m-40) REVERT: AC 19 ASP cc_start: 0.8174 (t0) cc_final: 0.7801 (m-30) REVERT: AC 22 GLU cc_start: 0.7462 (tp30) cc_final: 0.7131 (tp30) REVERT: AC 45 GLN cc_start: 0.7164 (tt0) cc_final: 0.6947 (tt0) REVERT: AC 46 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7650 (mmm-85) REVERT: AC 92 ARG cc_start: 0.5805 (ttt180) cc_final: 0.3976 (ttm170) REVERT: AE 14 SER cc_start: 0.8412 (m) cc_final: 0.8097 (p) REVERT: AE 22 GLU cc_start: 0.7438 (tp30) cc_final: 0.7139 (tp30) REVERT: AE 39 GLN cc_start: 0.8042 (tt0) cc_final: 0.7473 (mp10) REVERT: AE 92 ARG cc_start: 0.5480 (ttt180) cc_final: 0.4167 (ttm170) REVERT: AE 109 ASP cc_start: 0.7426 (t70) cc_final: 0.7038 (t70) REVERT: AE 131 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7955 (tm-30) REVERT: AG 19 ASP cc_start: 0.8165 (t0) cc_final: 0.7668 (m-30) REVERT: AG 22 GLU cc_start: 0.7726 (tp30) cc_final: 0.7389 (tp30) REVERT: AG 29 ASN cc_start: 0.7970 (m-40) cc_final: 0.7680 (m110) REVERT: AG 39 GLN cc_start: 0.8187 (tt0) cc_final: 0.7434 (mp10) REVERT: AG 46 ARG cc_start: 0.8190 (mtt180) cc_final: 0.7735 (ppt170) REVERT: AG 76 LEU cc_start: 0.8284 (mp) cc_final: 0.7957 (tp) REVERT: AG 92 ARG cc_start: 0.5578 (ttt180) cc_final: 0.3506 (ttm170) REVERT: AG 139 TYR cc_start: 0.7814 (m-80) cc_final: 0.7443 (m-80) REVERT: AI 33 ASN cc_start: 0.8045 (m-40) cc_final: 0.7752 (m-40) REVERT: AI 39 GLN cc_start: 0.8427 (tt0) cc_final: 0.7321 (mp10) REVERT: AI 92 ARG cc_start: 0.5883 (ttt180) cc_final: 0.4306 (ttm170) REVERT: AI 140 ASN cc_start: 0.7549 (p0) cc_final: 0.6993 (p0) REVERT: AK 6 THR cc_start: 0.7534 (t) cc_final: 0.7234 (m) REVERT: AK 19 ASP cc_start: 0.8205 (t0) cc_final: 0.7834 (t0) REVERT: AK 39 GLN cc_start: 0.8258 (tt0) cc_final: 0.7460 (mp10) REVERT: AK 46 ARG cc_start: 0.8244 (mtt180) cc_final: 0.7763 (mmm-85) REVERT: AK 83 LEU cc_start: 0.8784 (tp) cc_final: 0.8541 (tp) REVERT: AK 92 ARG cc_start: 0.5428 (ttt180) cc_final: 0.3723 (ttm170) REVERT: AK 95 GLU cc_start: 0.3742 (tt0) cc_final: 0.3473 (tt0) REVERT: AK 140 ASN cc_start: 0.7751 (p0) cc_final: 0.7381 (p0) REVERT: AM 19 ASP cc_start: 0.8100 (t0) cc_final: 0.7764 (t0) REVERT: AM 39 GLN cc_start: 0.8316 (tt0) cc_final: 0.7793 (mp10) REVERT: AM 46 ARG cc_start: 0.7989 (mmt90) cc_final: 0.7745 (mmm-85) REVERT: AM 92 ARG cc_start: 0.4584 (ttt180) cc_final: 0.3277 (ttm170) REVERT: AM 95 GLU cc_start: 0.4089 (tt0) cc_final: 0.3860 (tt0) REVERT: AM 139 TYR cc_start: 0.8040 (m-80) cc_final: 0.7539 (m-80) REVERT: AM 140 ASN cc_start: 0.6857 (p0) cc_final: 0.6556 (p0) REVERT: AO 46 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7760 (tmt170) REVERT: AO 92 ARG cc_start: 0.4443 (ttt180) cc_final: 0.3128 (ttm170) REVERT: AO 95 GLU cc_start: 0.4139 (tt0) cc_final: 0.3835 (tt0) REVERT: AQ 22 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7351 (tp30) REVERT: AQ 34 GLN cc_start: 0.7449 (tp40) cc_final: 0.6977 (tp40) REVERT: AQ 46 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7753 (mmm160) REVERT: AQ 92 ARG cc_start: 0.4562 (ttt180) cc_final: 0.3231 (ttm170) REVERT: AQ 140 ASN cc_start: 0.7066 (p0) cc_final: 0.6578 (p0) REVERT: AS 29 ASN cc_start: 0.8132 (m110) cc_final: 0.7642 (m110) REVERT: AS 33 ASN cc_start: 0.7568 (m110) cc_final: 0.7082 (m-40) REVERT: AS 38 GLN cc_start: 0.6753 (tp40) cc_final: 0.6501 (tp40) REVERT: AS 92 ARG cc_start: 0.5315 (ttt180) cc_final: 0.4024 (ttm170) REVERT: AS 95 GLU cc_start: 0.4283 (tt0) cc_final: 0.3993 (tt0) REVERT: AS 129 ILE cc_start: 0.8643 (tp) cc_final: 0.8434 (tp) REVERT: AS 139 TYR cc_start: 0.7807 (m-80) cc_final: 0.7446 (m-80) REVERT: AS 140 ASN cc_start: 0.6930 (p0) cc_final: 0.6655 (p0) REVERT: AU 24 ILE cc_start: 0.8408 (mm) cc_final: 0.8204 (mm) REVERT: AU 39 GLN cc_start: 0.8110 (tt0) cc_final: 0.7516 (mp10) REVERT: AU 46 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7627 (tmt170) REVERT: AU 57 GLN cc_start: 0.7286 (mm110) cc_final: 0.6892 (mm-40) REVERT: AU 92 ARG cc_start: 0.5364 (ttt180) cc_final: 0.4152 (ttm170) REVERT: AU 127 ASN cc_start: 0.8406 (t0) cc_final: 0.8060 (m110) REVERT: AU 140 ASN cc_start: 0.7101 (p0) cc_final: 0.6808 (p0) REVERT: AW 33 ASN cc_start: 0.7639 (m110) cc_final: 0.6755 (m-40) REVERT: AW 34 GLN cc_start: 0.5263 (pt0) cc_final: 0.5054 (pt0) REVERT: AW 39 GLN cc_start: 0.8172 (tt0) cc_final: 0.7850 (mp10) REVERT: AW 46 ARG cc_start: 0.8389 (mtt180) cc_final: 0.7593 (tmt170) REVERT: AW 50 GLU cc_start: 0.7941 (tp30) cc_final: 0.7497 (tp30) REVERT: AW 57 GLN cc_start: 0.6904 (mm-40) cc_final: 0.6652 (mm-40) REVERT: AW 127 ASN cc_start: 0.8333 (m110) cc_final: 0.7780 (m110) REVERT: AW 131 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7622 (mp0) REVERT: AW 140 ASN cc_start: 0.7932 (p0) cc_final: 0.7689 (p0) REVERT: AY 29 ASN cc_start: 0.8325 (m110) cc_final: 0.7959 (m-40) REVERT: AY 33 ASN cc_start: 0.7636 (t0) cc_final: 0.7001 (m-40) REVERT: AY 34 GLN cc_start: 0.7223 (tt0) cc_final: 0.6561 (tp40) REVERT: AY 39 GLN cc_start: 0.8032 (tt0) cc_final: 0.7678 (mp10) REVERT: AY 46 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7462 (tmt170) REVERT: AY 88 ASP cc_start: 0.6219 (t0) cc_final: 0.5759 (p0) REVERT: AY 92 ARG cc_start: 0.4854 (ttt180) cc_final: 0.3773 (ttm170) REVERT: AY 139 TYR cc_start: 0.7748 (m-80) cc_final: 0.7237 (m-80) REVERT: AY 140 ASN cc_start: 0.7837 (p0) cc_final: 0.7344 (p0) REVERT: A0 19 ASP cc_start: 0.8207 (t0) cc_final: 0.7698 (t0) REVERT: A0 22 GLU cc_start: 0.8284 (pp20) cc_final: 0.7935 (pp20) REVERT: A0 39 GLN cc_start: 0.7333 (tt0) cc_final: 0.6866 (mp10) REVERT: A0 46 ARG cc_start: 0.7787 (mmt90) cc_final: 0.7110 (tmm160) REVERT: A0 92 ARG cc_start: 0.4801 (ttt180) cc_final: 0.4241 (ttm170) REVERT: A0 127 ASN cc_start: 0.8486 (m110) cc_final: 0.7871 (m110) REVERT: A2 33 ASN cc_start: 0.7878 (m-40) cc_final: 0.7592 (m-40) REVERT: A2 39 GLN cc_start: 0.7420 (tt0) cc_final: 0.6968 (mp10) REVERT: A2 53 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7339 (mtmm) REVERT: A2 92 ARG cc_start: 0.4636 (ttt180) cc_final: 0.4044 (ttm170) REVERT: A2 127 ASN cc_start: 0.8639 (m110) cc_final: 0.8225 (m-40) REVERT: A2 140 ASN cc_start: 0.7932 (p0) cc_final: 0.7347 (p0) REVERT: A4 29 ASN cc_start: 0.8272 (m-40) cc_final: 0.7892 (m-40) REVERT: A4 39 GLN cc_start: 0.7469 (tt0) cc_final: 0.7073 (mp10) REVERT: A4 46 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7185 (ppt170) REVERT: A4 112 ARG cc_start: 0.8037 (tpt170) cc_final: 0.7578 (tpt170) REVERT: A6 22 GLU cc_start: 0.8440 (pp20) cc_final: 0.8070 (pp20) REVERT: A6 23 LEU cc_start: 0.8304 (tp) cc_final: 0.7926 (tp) REVERT: A6 29 ASN cc_start: 0.7872 (m110) cc_final: 0.7482 (m110) REVERT: A6 38 GLN cc_start: 0.6945 (tp40) cc_final: 0.5391 (pm20) REVERT: A6 45 GLN cc_start: 0.7531 (tt0) cc_final: 0.6879 (tt0) REVERT: A6 46 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7427 (ppt170) REVERT: A6 93 ILE cc_start: 0.7569 (tp) cc_final: 0.7355 (tp) REVERT: A6 97 GLU cc_start: 0.5383 (mp0) cc_final: 0.5031 (mp0) REVERT: A8 19 ASP cc_start: 0.7595 (t70) cc_final: 0.7390 (t0) REVERT: A8 29 ASN cc_start: 0.7557 (m-40) cc_final: 0.7185 (t0) REVERT: A8 38 GLN cc_start: 0.6972 (tp40) cc_final: 0.5600 (pm20) outliers start: 16 outliers final: 9 residues processed: 1703 average time/residue: 0.5964 time to fit residues: 1699.3175 Evaluate side-chains 1437 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1428 time to evaluate : 5.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 7.9990 chunk 282 optimal weight: 6.9990 chunk 423 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 450 optimal weight: 30.0000 chunk 482 optimal weight: 10.0000 chunk 350 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 556 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 126 ASN C 91 ASN E 98 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 GLN ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 GLN W 45 GLN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 101 ASN ** 6 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 101 ASN 8 25 ASN 8 101 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 9 GLN ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 101 ASN i 91 ASN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 36 GLN ** m 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 101 ASN u 127 ASN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 GLN ** w 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 101 ASN ** w 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 98 ASN y 127 ASN AA 101 ASN ** AC 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 57 GLN ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 126 ASN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 101 ASN AK 126 ASN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 91 ASN ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 91 ASN AQ 126 ASN AS 57 GLN ** AS 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 101 ASN ** AS 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 91 ASN AU 126 ASN ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 101 ASN ** A2 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 126 ASN ** A6 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A6 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 45 GLN A8 33 ASN A8 91 ASN A8 98 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 63945 Z= 0.173 Angle : 0.553 6.873 88004 Z= 0.298 Chirality : 0.040 0.156 10437 Planarity : 0.005 0.054 10878 Dihedral : 11.300 77.395 10094 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.30 % Allowed : 1.15 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 7399 helix: 0.25 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -2.28 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 152 PHE 0.026 0.002 PHE K 67 TYR 0.010 0.001 TYR W 70 ARG 0.009 0.001 ARGAE 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1758 time to evaluate : 5.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ILE cc_start: 0.8159 (mp) cc_final: 0.7861 (tt) REVERT: A 27 CYS cc_start: 0.8232 (p) cc_final: 0.8023 (p) REVERT: A 50 GLU cc_start: 0.7781 (tp30) cc_final: 0.7378 (tp30) REVERT: C 6 THR cc_start: 0.7478 (t) cc_final: 0.7214 (p) REVERT: C 77 ASP cc_start: 0.7910 (t70) cc_final: 0.7554 (t70) REVERT: C 127 ASN cc_start: 0.7925 (m-40) cc_final: 0.7578 (m-40) REVERT: E 53 LYS cc_start: 0.7962 (ptmt) cc_final: 0.7498 (pttp) REVERT: E 91 ASN cc_start: 0.7305 (t0) cc_final: 0.6958 (p0) REVERT: E 112 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7771 (tpt-90) REVERT: E 139 TYR cc_start: 0.8442 (m-10) cc_final: 0.8203 (m-10) REVERT: G 68 LYS cc_start: 0.8051 (ptpp) cc_final: 0.7646 (ptpt) REVERT: G 139 TYR cc_start: 0.8278 (m-10) cc_final: 0.8072 (m-10) REVERT: I 57 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6789 (mm-40) REVERT: I 77 ASP cc_start: 0.7930 (t70) cc_final: 0.7653 (t70) REVERT: I 83 LEU cc_start: 0.8328 (tp) cc_final: 0.7997 (tp) REVERT: I 112 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7860 (tpt-90) REVERT: K 22 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7900 (tm-30) REVERT: M 59 THR cc_start: 0.8242 (m) cc_final: 0.7890 (t) REVERT: M 89 THR cc_start: 0.7325 (m) cc_final: 0.6807 (p) REVERT: O 89 THR cc_start: 0.7637 (m) cc_final: 0.7329 (p) REVERT: Q 83 LEU cc_start: 0.8202 (tp) cc_final: 0.7984 (tp) REVERT: S 38 GLN cc_start: 0.7003 (tp40) cc_final: 0.6714 (tp40) REVERT: S 89 THR cc_start: 0.7184 (m) cc_final: 0.6889 (m) REVERT: S 127 ASN cc_start: 0.7763 (m110) cc_final: 0.7514 (m110) REVERT: U 34 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6551 (mm-40) REVERT: U 38 GLN cc_start: 0.6581 (tp40) cc_final: 0.6030 (tp-100) REVERT: U 77 ASP cc_start: 0.8026 (t70) cc_final: 0.7790 (t0) REVERT: U 89 THR cc_start: 0.7653 (m) cc_final: 0.7085 (p) REVERT: U 112 ARG cc_start: 0.8377 (tpp-160) cc_final: 0.7719 (tpt170) REVERT: U 133 ILE cc_start: 0.8310 (pt) cc_final: 0.7819 (mm) REVERT: W 19 ASP cc_start: 0.8014 (t0) cc_final: 0.7746 (t0) REVERT: W 127 ASN cc_start: 0.8168 (m110) cc_final: 0.7843 (m-40) REVERT: Y 112 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.7795 (tpt170) REVERT: 0 50 GLU cc_start: 0.7036 (tp30) cc_final: 0.6739 (tp30) REVERT: 0 93 ILE cc_start: 0.8254 (mt) cc_final: 0.7976 (tp) REVERT: 0 127 ASN cc_start: 0.8373 (m-40) cc_final: 0.7711 (m-40) REVERT: 0 130 VAL cc_start: 0.6752 (t) cc_final: 0.6281 (m) REVERT: 0 131 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6777 (mm-30) REVERT: 2 38 GLN cc_start: 0.6798 (tp40) cc_final: 0.6350 (tp-100) REVERT: 2 89 THR cc_start: 0.7606 (m) cc_final: 0.7035 (p) REVERT: 2 131 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6812 (mm-30) REVERT: 4 62 PHE cc_start: 0.7286 (t80) cc_final: 0.7049 (t80) REVERT: 4 89 THR cc_start: 0.7601 (m) cc_final: 0.7247 (p) REVERT: 4 112 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.7557 (tpt170) REVERT: 4 127 ASN cc_start: 0.8391 (m110) cc_final: 0.8080 (m110) REVERT: 6 27 CYS cc_start: 0.8681 (p) cc_final: 0.8465 (p) REVERT: 6 112 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.7918 (tpt170) REVERT: 6 143 SER cc_start: 0.8320 (p) cc_final: 0.7924 (t) REVERT: 8 21 ILE cc_start: 0.8379 (mp) cc_final: 0.7940 (tt) REVERT: a 21 ILE cc_start: 0.8468 (mp) cc_final: 0.8021 (tt) REVERT: a 25 ASN cc_start: 0.9090 (m-40) cc_final: 0.8739 (m-40) REVERT: a 62 PHE cc_start: 0.7079 (t80) cc_final: 0.6574 (t80) REVERT: a 83 LEU cc_start: 0.8640 (tp) cc_final: 0.8423 (tp) REVERT: c 27 CYS cc_start: 0.8732 (p) cc_final: 0.8523 (p) REVERT: e 25 ASN cc_start: 0.8807 (m-40) cc_final: 0.8600 (m110) REVERT: e 34 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7169 (mm-40) REVERT: e 50 GLU cc_start: 0.7341 (tp30) cc_final: 0.6695 (tp30) REVERT: e 129 ILE cc_start: 0.7976 (tp) cc_final: 0.7728 (tp) REVERT: g 31 LEU cc_start: 0.7851 (mp) cc_final: 0.7570 (mt) REVERT: g 62 PHE cc_start: 0.6988 (t80) cc_final: 0.6627 (t80) REVERT: i 34 GLN cc_start: 0.7817 (mm110) cc_final: 0.6934 (mm-40) REVERT: i 97 GLU cc_start: 0.7769 (tp30) cc_final: 0.7540 (tp30) REVERT: k 22 GLU cc_start: 0.7963 (tp30) cc_final: 0.7702 (mm-30) REVERT: k 46 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7439 (mmm-85) REVERT: k 50 GLU cc_start: 0.7613 (tp30) cc_final: 0.7293 (tp30) REVERT: k 112 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8488 (tpp80) REVERT: m 29 ASN cc_start: 0.8080 (m110) cc_final: 0.7692 (m110) REVERT: m 129 ILE cc_start: 0.7895 (tp) cc_final: 0.7676 (tp) REVERT: o 29 ASN cc_start: 0.7974 (m110) cc_final: 0.7710 (m110) REVERT: o 34 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7250 (mm-40) REVERT: q 34 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7461 (mm-40) REVERT: q 90 ARG cc_start: 0.6944 (ttm-80) cc_final: 0.6543 (ttm-80) REVERT: q 104 THR cc_start: 0.7740 (t) cc_final: 0.7520 (m) REVERT: q 129 ILE cc_start: 0.8053 (tp) cc_final: 0.7774 (tp) REVERT: s 22 GLU cc_start: 0.7539 (tp30) cc_final: 0.7098 (tp30) REVERT: s 50 GLU cc_start: 0.7709 (tp30) cc_final: 0.7099 (tp30) REVERT: s 127 ASN cc_start: 0.8653 (m110) cc_final: 0.8392 (m-40) REVERT: u 14 SER cc_start: 0.8459 (m) cc_final: 0.8226 (m) REVERT: u 29 ASN cc_start: 0.7928 (m110) cc_final: 0.7600 (m110) REVERT: u 129 ILE cc_start: 0.8068 (tp) cc_final: 0.7860 (tp) REVERT: w 19 ASP cc_start: 0.8176 (t0) cc_final: 0.7430 (m-30) REVERT: w 29 ASN cc_start: 0.8085 (m110) cc_final: 0.7753 (m110) REVERT: w 62 PHE cc_start: 0.7583 (t80) cc_final: 0.7240 (t80) REVERT: w 93 ILE cc_start: 0.8254 (mm) cc_final: 0.8001 (pt) REVERT: w 95 GLU cc_start: 0.7750 (mm-30) cc_final: 0.6912 (tp30) REVERT: w 127 ASN cc_start: 0.8731 (m110) cc_final: 0.8476 (m110) REVERT: w 140 ASN cc_start: 0.7337 (p0) cc_final: 0.6573 (p0) REVERT: w 141 ARG cc_start: 0.6907 (ptm160) cc_final: 0.6395 (ptm160) REVERT: y 62 PHE cc_start: 0.7489 (t80) cc_final: 0.6635 (t80) REVERT: y 76 LEU cc_start: 0.8387 (mt) cc_final: 0.8167 (mt) REVERT: AA 19 ASP cc_start: 0.8127 (t0) cc_final: 0.7752 (t0) REVERT: AA 22 GLU cc_start: 0.7961 (pp20) cc_final: 0.7682 (pp20) REVERT: AA 46 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7288 (mmt90) REVERT: AA 127 ASN cc_start: 0.8333 (m110) cc_final: 0.8051 (m-40) REVERT: AC 46 ARG cc_start: 0.8231 (mtt180) cc_final: 0.7596 (mmm-85) REVERT: AC 53 LYS cc_start: 0.8387 (mtmm) cc_final: 0.8153 (mtpp) REVERT: AC 92 ARG cc_start: 0.5813 (ttt180) cc_final: 0.3987 (ttm170) REVERT: AC 127 ASN cc_start: 0.8370 (m110) cc_final: 0.8072 (m-40) REVERT: AC 140 ASN cc_start: 0.6562 (p0) cc_final: 0.6172 (p0) REVERT: AE 14 SER cc_start: 0.8322 (m) cc_final: 0.8003 (p) REVERT: AE 22 GLU cc_start: 0.7401 (tp30) cc_final: 0.7129 (tp30) REVERT: AE 25 ASN cc_start: 0.8624 (m-40) cc_final: 0.8205 (m110) REVERT: AE 29 ASN cc_start: 0.8250 (m-40) cc_final: 0.8042 (m-40) REVERT: AE 39 GLN cc_start: 0.7986 (tt0) cc_final: 0.7433 (mp10) REVERT: AE 76 LEU cc_start: 0.7994 (mp) cc_final: 0.7740 (mp) REVERT: AE 92 ARG cc_start: 0.5501 (ttt180) cc_final: 0.3999 (ttm170) REVERT: AE 99 GLN cc_start: 0.6451 (pt0) cc_final: 0.6226 (pt0) REVERT: AE 109 ASP cc_start: 0.7420 (t70) cc_final: 0.7076 (t70) REVERT: AE 129 ILE cc_start: 0.8216 (tp) cc_final: 0.7997 (tp) REVERT: AE 131 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7875 (tm-30) REVERT: AG 19 ASP cc_start: 0.8113 (t0) cc_final: 0.7518 (m-30) REVERT: AG 22 GLU cc_start: 0.7781 (tp30) cc_final: 0.7411 (tp30) REVERT: AG 29 ASN cc_start: 0.8018 (m-40) cc_final: 0.7619 (m110) REVERT: AG 39 GLN cc_start: 0.8072 (tt0) cc_final: 0.7351 (mp10) REVERT: AG 46 ARG cc_start: 0.8186 (mtt180) cc_final: 0.7701 (ppt170) REVERT: AG 76 LEU cc_start: 0.8296 (mp) cc_final: 0.8054 (mp) REVERT: AG 92 ARG cc_start: 0.5335 (ttt180) cc_final: 0.3298 (ttm170) REVERT: AG 139 TYR cc_start: 0.7814 (m-80) cc_final: 0.7573 (m-80) REVERT: AI 33 ASN cc_start: 0.8010 (m-40) cc_final: 0.7693 (m-40) REVERT: AI 39 GLN cc_start: 0.8366 (tt0) cc_final: 0.7444 (mp10) REVERT: AI 46 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7600 (mtp180) REVERT: AI 92 ARG cc_start: 0.5481 (ttt180) cc_final: 0.4082 (ttm170) REVERT: AI 140 ASN cc_start: 0.7553 (p0) cc_final: 0.6937 (p0) REVERT: AK 6 THR cc_start: 0.7590 (t) cc_final: 0.7306 (m) REVERT: AK 19 ASP cc_start: 0.8151 (t0) cc_final: 0.7774 (t0) REVERT: AK 39 GLN cc_start: 0.8199 (tt0) cc_final: 0.7526 (mp10) REVERT: AK 46 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7759 (mmm-85) REVERT: AK 83 LEU cc_start: 0.8764 (tp) cc_final: 0.8549 (tp) REVERT: AK 92 ARG cc_start: 0.5384 (ttt180) cc_final: 0.3688 (ttm170) REVERT: AK 95 GLU cc_start: 0.3756 (tt0) cc_final: 0.3450 (tt0) REVERT: AM 19 ASP cc_start: 0.8088 (t0) cc_final: 0.7886 (t0) REVERT: AM 33 ASN cc_start: 0.7889 (m-40) cc_final: 0.7513 (m-40) REVERT: AM 39 GLN cc_start: 0.8274 (tt0) cc_final: 0.7836 (mp10) REVERT: AM 46 ARG cc_start: 0.7956 (mmt90) cc_final: 0.7660 (mmm-85) REVERT: AM 76 LEU cc_start: 0.8224 (mp) cc_final: 0.7970 (mp) REVERT: AM 92 ARG cc_start: 0.3601 (ttt180) cc_final: 0.2631 (ttm170) REVERT: AM 113 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.7002 (ttp80) REVERT: AM 139 TYR cc_start: 0.7932 (m-80) cc_final: 0.7455 (m-80) REVERT: AM 140 ASN cc_start: 0.7036 (p0) cc_final: 0.6672 (p0) REVERT: AO 46 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7762 (tmt170) REVERT: AQ 22 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7396 (tp30) REVERT: AQ 34 GLN cc_start: 0.7413 (tp40) cc_final: 0.6862 (mm-40) REVERT: AQ 46 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7748 (mmm160) REVERT: AQ 83 LEU cc_start: 0.8432 (tp) cc_final: 0.8219 (tp) REVERT: AQ 92 ARG cc_start: 0.4277 (ttt180) cc_final: 0.3075 (ttm170) REVERT: AQ 140 ASN cc_start: 0.7209 (p0) cc_final: 0.6657 (p0) REVERT: AS 29 ASN cc_start: 0.8038 (m110) cc_final: 0.7584 (m110) REVERT: AS 33 ASN cc_start: 0.7817 (m110) cc_final: 0.7236 (m-40) REVERT: AS 91 ASN cc_start: 0.6811 (t0) cc_final: 0.6313 (p0) REVERT: AS 139 TYR cc_start: 0.7821 (m-80) cc_final: 0.7286 (m-80) REVERT: AS 140 ASN cc_start: 0.6965 (p0) cc_final: 0.6478 (p0) REVERT: AU 19 ASP cc_start: 0.8096 (t0) cc_final: 0.7608 (t0) REVERT: AU 22 GLU cc_start: 0.8079 (pp20) cc_final: 0.7800 (pp20) REVERT: AU 24 ILE cc_start: 0.8287 (mm) cc_final: 0.8041 (mm) REVERT: AU 33 ASN cc_start: 0.8186 (m-40) cc_final: 0.7422 (m-40) REVERT: AU 39 GLN cc_start: 0.8108 (tt0) cc_final: 0.7565 (mp10) REVERT: AU 46 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7646 (tmt170) REVERT: AU 50 GLU cc_start: 0.7524 (tp30) cc_final: 0.7181 (tp30) REVERT: AU 57 GLN cc_start: 0.7235 (mm110) cc_final: 0.6817 (mm-40) REVERT: AU 92 ARG cc_start: 0.4861 (ttt180) cc_final: 0.3968 (ttm170) REVERT: AU 127 ASN cc_start: 0.8310 (t0) cc_final: 0.8034 (m110) REVERT: AU 129 ILE cc_start: 0.8603 (tp) cc_final: 0.8194 (tp) REVERT: AU 140 ASN cc_start: 0.7180 (p0) cc_final: 0.6866 (p0) REVERT: AW 6 THR cc_start: 0.7462 (m) cc_final: 0.7137 (m) REVERT: AW 31 LEU cc_start: 0.8950 (mt) cc_final: 0.8691 (mt) REVERT: AW 33 ASN cc_start: 0.7649 (m110) cc_final: 0.6688 (m-40) REVERT: AW 39 GLN cc_start: 0.8136 (tt0) cc_final: 0.7816 (mp10) REVERT: AW 46 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7592 (tmt170) REVERT: AW 50 GLU cc_start: 0.7921 (tp30) cc_final: 0.7499 (tp30) REVERT: AW 57 GLN cc_start: 0.6781 (mm-40) cc_final: 0.6332 (mm-40) REVERT: AW 131 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7520 (mp0) REVERT: AW 140 ASN cc_start: 0.7956 (p0) cc_final: 0.7718 (p0) REVERT: AY 29 ASN cc_start: 0.8203 (m110) cc_final: 0.7862 (m-40) REVERT: AY 39 GLN cc_start: 0.8194 (tt0) cc_final: 0.7829 (mp10) REVERT: AY 46 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7437 (tmt170) REVERT: AY 88 ASP cc_start: 0.6384 (t0) cc_final: 0.5665 (p0) REVERT: AY 92 ARG cc_start: 0.4909 (ttt180) cc_final: 0.3794 (ttm170) REVERT: AY 139 TYR cc_start: 0.7805 (m-80) cc_final: 0.7250 (m-80) REVERT: AY 140 ASN cc_start: 0.7806 (p0) cc_final: 0.7261 (p0) REVERT: A0 19 ASP cc_start: 0.8245 (t0) cc_final: 0.7892 (t0) REVERT: A0 39 GLN cc_start: 0.7472 (tt0) cc_final: 0.6896 (mp10) REVERT: A0 46 ARG cc_start: 0.7748 (mmt90) cc_final: 0.7093 (tmm160) REVERT: A0 92 ARG cc_start: 0.3925 (ttt180) cc_final: 0.3486 (tpp-160) REVERT: A0 112 ARG cc_start: 0.7959 (tpt170) cc_final: 0.7648 (tpt170) REVERT: A0 127 ASN cc_start: 0.8458 (m110) cc_final: 0.7949 (m110) REVERT: A2 33 ASN cc_start: 0.7990 (m-40) cc_final: 0.7697 (m-40) REVERT: A2 39 GLN cc_start: 0.7462 (tt0) cc_final: 0.7009 (mp10) REVERT: A2 53 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7356 (mtmm) REVERT: A2 92 ARG cc_start: 0.4332 (ttt180) cc_final: 0.3644 (ttm170) REVERT: A2 127 ASN cc_start: 0.8615 (m110) cc_final: 0.8225 (m-40) REVERT: A2 140 ASN cc_start: 0.7856 (p0) cc_final: 0.7293 (p0) REVERT: A4 29 ASN cc_start: 0.8351 (m-40) cc_final: 0.7997 (m-40) REVERT: A4 39 GLN cc_start: 0.7411 (tt0) cc_final: 0.7114 (mp10) REVERT: A4 46 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7145 (ppt170) REVERT: A4 139 TYR cc_start: 0.8058 (m-80) cc_final: 0.7847 (m-80) REVERT: A6 19 ASP cc_start: 0.7971 (t0) cc_final: 0.7765 (t0) REVERT: A6 22 GLU cc_start: 0.8477 (pp20) cc_final: 0.8073 (pp20) REVERT: A6 23 LEU cc_start: 0.8330 (tp) cc_final: 0.7909 (tp) REVERT: A6 29 ASN cc_start: 0.7884 (m110) cc_final: 0.7447 (m110) REVERT: A6 38 GLN cc_start: 0.6937 (tp40) cc_final: 0.5596 (mp10) REVERT: A6 46 ARG cc_start: 0.7809 (mtt-85) cc_final: 0.7362 (ppt170) REVERT: A8 19 ASP cc_start: 0.7636 (t70) cc_final: 0.7412 (t0) REVERT: A8 29 ASN cc_start: 0.7482 (m-40) cc_final: 0.7157 (t0) REVERT: A8 38 GLN cc_start: 0.6934 (tp40) cc_final: 0.5686 (pm20) REVERT: A8 46 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7088 (tmm160) outliers start: 20 outliers final: 10 residues processed: 1766 average time/residue: 0.6150 time to fit residues: 1819.3659 Evaluate side-chains 1438 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1428 time to evaluate : 5.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 7.9990 chunk 678 optimal weight: 9.9990 chunk 619 optimal weight: 2.9990 chunk 660 optimal weight: 30.0000 chunk 397 optimal weight: 9.9990 chunk 287 optimal weight: 5.9990 chunk 518 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 596 optimal weight: 10.0000 chunk 624 optimal weight: 20.0000 chunk 657 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN C 36 GLN C 91 ASN E 29 ASN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 ASN O 29 ASN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 38 GLN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 101 ASN 6 101 ASN ** 8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 101 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 9 GLN ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 ASN g 91 ASN g 101 ASN i 9 GLN i 91 ASN k 36 GLN m 91 ASN m 99 GLN ** o 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 99 GLN ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 98 ASN q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 101 ASN u 127 ASN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 91 ASN w 101 ASN ** w 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 101 ASN AC 126 ASN ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 101 ASN ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 126 ASN AI 127 ASN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 99 GLN ** AK 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 126 ASN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 91 ASN AS 57 GLN ** AS 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 101 ASN AS 126 ASN AU 91 ASN AU 126 ASN ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A0 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 36 GLN A0 101 ASN A2 126 ASN ** A4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 36 GLN ** A6 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 33 ASN ** A8 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 91 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.8000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 63945 Z= 0.260 Angle : 0.612 6.556 88004 Z= 0.332 Chirality : 0.042 0.208 10437 Planarity : 0.005 0.056 10878 Dihedral : 11.499 76.258 10094 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.32 % Allowed : 0.86 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.09), residues: 7399 helix: 0.13 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -2.32 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP o 152 PHE 0.044 0.002 PHEAS 67 TYR 0.015 0.001 TYR 0 139 ARG 0.009 0.001 ARG s 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1648 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1627 time to evaluate : 5.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7786 (tp30) cc_final: 0.7413 (tp30) REVERT: C 6 THR cc_start: 0.7552 (t) cc_final: 0.7306 (p) REVERT: C 77 ASP cc_start: 0.7955 (t70) cc_final: 0.7659 (t70) REVERT: C 127 ASN cc_start: 0.7789 (m-40) cc_final: 0.7506 (m-40) REVERT: E 53 LYS cc_start: 0.7952 (ptmt) cc_final: 0.7468 (pttp) REVERT: E 112 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7796 (tpt-90) REVERT: E 139 TYR cc_start: 0.8428 (m-10) cc_final: 0.8136 (m-10) REVERT: G 68 LYS cc_start: 0.8203 (ptpp) cc_final: 0.7752 (ptpt) REVERT: G 131 GLU cc_start: 0.7578 (tp30) cc_final: 0.6842 (tp30) REVERT: G 139 TYR cc_start: 0.8295 (m-10) cc_final: 0.8021 (m-10) REVERT: I 55 SER cc_start: 0.8592 (m) cc_final: 0.8247 (t) REVERT: I 83 LEU cc_start: 0.8314 (tp) cc_final: 0.7979 (tp) REVERT: I 112 ARG cc_start: 0.8215 (tpp-160) cc_final: 0.7830 (tpt-90) REVERT: K 22 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7743 (tm-30) REVERT: M 50 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6857 (mm-30) REVERT: M 59 THR cc_start: 0.8237 (m) cc_final: 0.7890 (t) REVERT: M 89 THR cc_start: 0.7237 (m) cc_final: 0.6897 (p) REVERT: O 46 ARG cc_start: 0.8118 (mmt90) cc_final: 0.7356 (mmt-90) REVERT: O 89 THR cc_start: 0.7665 (m) cc_final: 0.7396 (p) REVERT: Q 50 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7150 (mm-30) REVERT: S 50 GLU cc_start: 0.7947 (tp30) cc_final: 0.7265 (mm-30) REVERT: S 127 ASN cc_start: 0.7754 (m110) cc_final: 0.7504 (m110) REVERT: S 145 GLU cc_start: 0.6853 (pm20) cc_final: 0.6431 (pm20) REVERT: U 25 ASN cc_start: 0.9038 (m-40) cc_final: 0.8643 (m-40) REVERT: U 34 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6454 (mm-40) REVERT: U 50 GLU cc_start: 0.7530 (tp30) cc_final: 0.7276 (mm-30) REVERT: U 77 ASP cc_start: 0.7989 (t70) cc_final: 0.7771 (t0) REVERT: U 89 THR cc_start: 0.7454 (m) cc_final: 0.7225 (p) REVERT: U 112 ARG cc_start: 0.8428 (tpp-160) cc_final: 0.7767 (tpt170) REVERT: W 19 ASP cc_start: 0.8040 (t0) cc_final: 0.7764 (t0) REVERT: W 22 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7451 (mm-30) REVERT: W 127 ASN cc_start: 0.8225 (m110) cc_final: 0.7934 (m-40) REVERT: Y 95 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7679 (mm-30) REVERT: Y 112 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.7775 (tpt170) REVERT: 0 50 GLU cc_start: 0.7035 (tp30) cc_final: 0.6729 (tp30) REVERT: 0 93 ILE cc_start: 0.8301 (mt) cc_final: 0.8043 (tp) REVERT: 0 127 ASN cc_start: 0.8385 (m-40) cc_final: 0.8057 (m-40) REVERT: 2 38 GLN cc_start: 0.6802 (tp40) cc_final: 0.6449 (tp-100) REVERT: 2 83 LEU cc_start: 0.8528 (tp) cc_final: 0.8314 (tp) REVERT: 2 89 THR cc_start: 0.7584 (m) cc_final: 0.7126 (p) REVERT: 2 131 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6808 (mm-30) REVERT: 4 27 CYS cc_start: 0.8524 (p) cc_final: 0.8209 (p) REVERT: 4 62 PHE cc_start: 0.7399 (t80) cc_final: 0.7104 (t80) REVERT: 4 89 THR cc_start: 0.7631 (m) cc_final: 0.7206 (p) REVERT: 4 93 ILE cc_start: 0.8340 (mt) cc_final: 0.8114 (tp) REVERT: 4 112 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.7598 (tpt170) REVERT: 4 127 ASN cc_start: 0.8441 (m110) cc_final: 0.8124 (m110) REVERT: 6 27 CYS cc_start: 0.8753 (p) cc_final: 0.8481 (p) REVERT: 6 112 ARG cc_start: 0.8601 (tpp-160) cc_final: 0.7919 (tpt170) REVERT: 6 130 VAL cc_start: 0.7924 (t) cc_final: 0.7698 (m) REVERT: 6 143 SER cc_start: 0.8420 (p) cc_final: 0.8033 (t) REVERT: c 27 CYS cc_start: 0.8821 (p) cc_final: 0.8501 (p) REVERT: e 34 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7161 (mm-40) REVERT: e 50 GLU cc_start: 0.7287 (tp30) cc_final: 0.6717 (tp30) REVERT: e 129 ILE cc_start: 0.7956 (tp) cc_final: 0.7728 (tp) REVERT: i 34 GLN cc_start: 0.7819 (mm110) cc_final: 0.6949 (mm-40) REVERT: i 97 GLU cc_start: 0.7663 (tp30) cc_final: 0.7413 (tp30) REVERT: k 46 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7461 (mmm-85) REVERT: k 50 GLU cc_start: 0.7649 (tp30) cc_final: 0.7294 (tp30) REVERT: k 69 VAL cc_start: 0.8695 (t) cc_final: 0.8436 (p) REVERT: m 29 ASN cc_start: 0.8240 (m110) cc_final: 0.7865 (m-40) REVERT: o 34 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7203 (mm-40) REVERT: o 129 ILE cc_start: 0.7987 (tp) cc_final: 0.7778 (tp) REVERT: q 34 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7416 (mm-40) REVERT: q 90 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6627 (ttm-80) REVERT: q 129 ILE cc_start: 0.8174 (tp) cc_final: 0.7863 (tp) REVERT: s 22 GLU cc_start: 0.7629 (tp30) cc_final: 0.7149 (tp30) REVERT: s 127 ASN cc_start: 0.8767 (m110) cc_final: 0.8476 (m-40) REVERT: u 29 ASN cc_start: 0.7807 (m110) cc_final: 0.7517 (m110) REVERT: u 83 LEU cc_start: 0.8574 (tp) cc_final: 0.8352 (tp) REVERT: w 19 ASP cc_start: 0.8098 (t0) cc_final: 0.7388 (m-30) REVERT: w 22 GLU cc_start: 0.8220 (pp20) cc_final: 0.7807 (pp20) REVERT: w 29 ASN cc_start: 0.8011 (m110) cc_final: 0.7651 (m110) REVERT: w 62 PHE cc_start: 0.7690 (t80) cc_final: 0.7399 (t80) REVERT: w 93 ILE cc_start: 0.8200 (mm) cc_final: 0.7967 (pt) REVERT: w 95 GLU cc_start: 0.7794 (mm-30) cc_final: 0.6873 (tp30) REVERT: w 127 ASN cc_start: 0.8856 (m110) cc_final: 0.8600 (m-40) REVERT: w 140 ASN cc_start: 0.7427 (p0) cc_final: 0.6766 (p0) REVERT: AA 19 ASP cc_start: 0.8172 (t0) cc_final: 0.7767 (t0) REVERT: AA 22 GLU cc_start: 0.8025 (pp20) cc_final: 0.7735 (pp20) REVERT: AA 29 ASN cc_start: 0.8430 (m-40) cc_final: 0.8043 (m-40) REVERT: AA 46 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7435 (mmt90) REVERT: AA 127 ASN cc_start: 0.8322 (m110) cc_final: 0.7942 (m-40) REVERT: AC 19 ASP cc_start: 0.8199 (t0) cc_final: 0.7787 (m-30) REVERT: AC 22 GLU cc_start: 0.7642 (tp30) cc_final: 0.7422 (tp30) REVERT: AC 46 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7600 (mmm-85) REVERT: AC 62 PHE cc_start: 0.7936 (t80) cc_final: 0.7687 (t80) REVERT: AC 92 ARG cc_start: 0.5803 (ttt180) cc_final: 0.3940 (ttm170) REVERT: AC 127 ASN cc_start: 0.8451 (m110) cc_final: 0.8208 (m-40) REVERT: AC 140 ASN cc_start: 0.6618 (p0) cc_final: 0.6105 (p0) REVERT: AE 14 SER cc_start: 0.8394 (m) cc_final: 0.8082 (p) REVERT: AE 22 GLU cc_start: 0.7514 (tp30) cc_final: 0.7268 (tp30) REVERT: AE 25 ASN cc_start: 0.8653 (m-40) cc_final: 0.8241 (m110) REVERT: AE 39 GLN cc_start: 0.8052 (tt0) cc_final: 0.7470 (mp10) REVERT: AE 76 LEU cc_start: 0.7981 (mp) cc_final: 0.7749 (mp) REVERT: AE 92 ARG cc_start: 0.5171 (ttt180) cc_final: 0.3956 (ttm170) REVERT: AE 109 ASP cc_start: 0.7451 (t70) cc_final: 0.7136 (t70) REVERT: AE 131 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7955 (tm-30) REVERT: AG 19 ASP cc_start: 0.8141 (t0) cc_final: 0.7692 (m-30) REVERT: AG 22 GLU cc_start: 0.7801 (tp30) cc_final: 0.7476 (tp30) REVERT: AG 29 ASN cc_start: 0.7987 (m-40) cc_final: 0.7647 (m110) REVERT: AG 39 GLN cc_start: 0.8150 (tt0) cc_final: 0.7420 (mp10) REVERT: AG 46 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7745 (ppt170) REVERT: AG 76 LEU cc_start: 0.8124 (mp) cc_final: 0.7898 (mp) REVERT: AG 83 LEU cc_start: 0.8932 (tp) cc_final: 0.8731 (tp) REVERT: AG 92 ARG cc_start: 0.5422 (ttt180) cc_final: 0.3212 (ttm170) REVERT: AG 139 TYR cc_start: 0.7918 (m-80) cc_final: 0.7626 (m-80) REVERT: AI 39 GLN cc_start: 0.8429 (tt0) cc_final: 0.7279 (mp10) REVERT: AI 92 ARG cc_start: 0.5385 (ttt180) cc_final: 0.4028 (ttm170) REVERT: AK 6 THR cc_start: 0.7700 (t) cc_final: 0.7414 (m) REVERT: AK 19 ASP cc_start: 0.8216 (t0) cc_final: 0.7896 (t0) REVERT: AK 39 GLN cc_start: 0.8261 (tt0) cc_final: 0.7490 (mp10) REVERT: AK 46 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7847 (mmm-85) REVERT: AK 83 LEU cc_start: 0.8775 (tp) cc_final: 0.8554 (tp) REVERT: AK 92 ARG cc_start: 0.5016 (ttt180) cc_final: 0.3676 (ttm170) REVERT: AM 19 ASP cc_start: 0.8148 (t0) cc_final: 0.7825 (t0) REVERT: AM 39 GLN cc_start: 0.8313 (tt0) cc_final: 0.7829 (mp10) REVERT: AM 46 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7697 (mmm-85) REVERT: AM 113 ARG cc_start: 0.7286 (mtp-110) cc_final: 0.7038 (ttp80) REVERT: AM 131 GLU cc_start: 0.8401 (pp20) cc_final: 0.8093 (pp20) REVERT: AM 139 TYR cc_start: 0.7926 (m-80) cc_final: 0.7437 (m-80) REVERT: AM 140 ASN cc_start: 0.7137 (p0) cc_final: 0.6773 (p0) REVERT: AO 46 ARG cc_start: 0.8204 (mtt180) cc_final: 0.7816 (ppt170) REVERT: AQ 22 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7341 (tp30) REVERT: AQ 34 GLN cc_start: 0.7404 (tp40) cc_final: 0.6839 (mm-40) REVERT: AQ 46 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7790 (mtp180) REVERT: AQ 140 ASN cc_start: 0.7372 (p0) cc_final: 0.6967 (p0) REVERT: AS 29 ASN cc_start: 0.8041 (m110) cc_final: 0.7602 (m110) REVERT: AS 33 ASN cc_start: 0.7811 (m110) cc_final: 0.7109 (m-40) REVERT: AS 34 GLN cc_start: 0.7409 (tp-100) cc_final: 0.6939 (tp-100) REVERT: AU 19 ASP cc_start: 0.8210 (t0) cc_final: 0.7951 (t0) REVERT: AU 33 ASN cc_start: 0.8089 (m-40) cc_final: 0.7387 (m-40) REVERT: AU 39 GLN cc_start: 0.8248 (tt0) cc_final: 0.7684 (mp10) REVERT: AU 46 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7632 (tmt170) REVERT: AU 50 GLU cc_start: 0.7529 (tp30) cc_final: 0.7189 (tp30) REVERT: AU 57 GLN cc_start: 0.7309 (mm110) cc_final: 0.6928 (mm-40) REVERT: AU 92 ARG cc_start: 0.4400 (ttt180) cc_final: 0.3597 (ttm170) REVERT: AU 127 ASN cc_start: 0.8374 (t0) cc_final: 0.8081 (m110) REVERT: AU 140 ASN cc_start: 0.7262 (p0) cc_final: 0.6983 (p0) REVERT: AW 33 ASN cc_start: 0.7637 (m110) cc_final: 0.6737 (m-40) REVERT: AW 39 GLN cc_start: 0.8201 (tt0) cc_final: 0.7805 (mp10) REVERT: AW 46 ARG cc_start: 0.8438 (mtt180) cc_final: 0.7621 (tmt170) REVERT: AW 50 GLU cc_start: 0.7892 (tp30) cc_final: 0.7541 (tp30) REVERT: AW 57 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6302 (mm110) REVERT: AW 127 ASN cc_start: 0.8369 (m110) cc_final: 0.7778 (m110) REVERT: AW 131 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7636 (mp0) REVERT: AW 140 ASN cc_start: 0.8016 (p0) cc_final: 0.7766 (p0) REVERT: AY 29 ASN cc_start: 0.8290 (m110) cc_final: 0.7946 (m-40) REVERT: AY 34 GLN cc_start: 0.7333 (tp40) cc_final: 0.7002 (tp-100) REVERT: AY 39 GLN cc_start: 0.8046 (tt0) cc_final: 0.7717 (mp10) REVERT: AY 46 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7489 (ppt170) REVERT: AY 88 ASP cc_start: 0.6189 (t0) cc_final: 0.5811 (p0) REVERT: AY 92 ARG cc_start: 0.4886 (ttt180) cc_final: 0.3831 (ttm170) REVERT: AY 139 TYR cc_start: 0.7855 (m-80) cc_final: 0.7335 (m-80) REVERT: AY 140 ASN cc_start: 0.7922 (p0) cc_final: 0.7418 (p0) REVERT: A0 19 ASP cc_start: 0.8187 (t0) cc_final: 0.7887 (t0) REVERT: A0 39 GLN cc_start: 0.7383 (tt0) cc_final: 0.6909 (mp10) REVERT: A0 46 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7087 (tmm160) REVERT: A0 92 ARG cc_start: 0.4281 (ttt180) cc_final: 0.3636 (tpp-160) REVERT: A0 127 ASN cc_start: 0.8459 (m110) cc_final: 0.7869 (m110) REVERT: A0 139 TYR cc_start: 0.7694 (m-80) cc_final: 0.7295 (m-80) REVERT: A2 33 ASN cc_start: 0.7985 (m-40) cc_final: 0.7599 (m-40) REVERT: A2 39 GLN cc_start: 0.7411 (tt0) cc_final: 0.6949 (mp10) REVERT: A2 53 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7404 (mtmm) REVERT: A2 92 ARG cc_start: 0.4332 (ttt180) cc_final: 0.3637 (ttm170) REVERT: A2 127 ASN cc_start: 0.8704 (m110) cc_final: 0.8188 (m-40) REVERT: A2 140 ASN cc_start: 0.7985 (p0) cc_final: 0.7360 (p0) REVERT: A4 29 ASN cc_start: 0.8251 (m-40) cc_final: 0.7912 (m-40) REVERT: A4 39 GLN cc_start: 0.7496 (tt0) cc_final: 0.7149 (mp10) REVERT: A4 46 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7215 (ppt170) REVERT: A4 112 ARG cc_start: 0.8078 (tpt170) cc_final: 0.7341 (tpt170) REVERT: A6 29 ASN cc_start: 0.7879 (m110) cc_final: 0.7474 (m110) REVERT: A6 38 GLN cc_start: 0.7061 (tp40) cc_final: 0.5376 (pm20) REVERT: A6 46 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7422 (ppt170) REVERT: A8 38 GLN cc_start: 0.7030 (tp40) cc_final: 0.5657 (pm20) REVERT: A8 50 GLU cc_start: 0.8040 (tp30) cc_final: 0.7624 (tp30) REVERT: A8 99 GLN cc_start: 0.7517 (pt0) cc_final: 0.7233 (pt0) outliers start: 21 outliers final: 12 residues processed: 1634 average time/residue: 0.5995 time to fit residues: 1647.1593 Evaluate side-chains 1403 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1391 time to evaluate : 5.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 8.9990 chunk 698 optimal weight: 10.0000 chunk 426 optimal weight: 8.9990 chunk 331 optimal weight: 5.9990 chunk 485 optimal weight: 30.0000 chunk 732 optimal weight: 6.9990 chunk 673 optimal weight: 20.0000 chunk 583 optimal weight: 0.3980 chunk 60 optimal weight: 20.0000 chunk 450 optimal weight: 30.0000 chunk 357 optimal weight: 5.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN C 91 ASN E 29 ASN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 98 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 57 GLN ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN M 29 ASN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN S 57 GLN 4 101 ASN 6 101 ASN ** 8 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 101 ASN a 36 GLN a 99 GLN c 73 ASN c 99 GLN ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 126 ASN ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 101 ASN g 91 ASN g 101 ASN i 99 GLN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 36 GLN k 91 ASN k 99 GLN m 91 ASN ** m 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 73 ASN o 91 ASN ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 39 GLN u 101 ASN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 GLN w 91 ASN w 101 ASN ** w 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 126 ASN AA 101 ASN ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 57 GLN ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 91 ASN AI 127 ASN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 126 ASN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 99 GLN ** AO 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 91 ASN ** AQ 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 45 GLN AS 57 GLN AS 101 ASN AU 126 ASN AU 127 ASN ** AW 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A0 34 GLN A0 101 ASN ** A4 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4 126 ASN ** A6 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 101 ASN A8 33 ASN ** A8 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 91 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.8089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 63945 Z= 0.274 Angle : 0.625 7.561 88004 Z= 0.339 Chirality : 0.042 0.227 10437 Planarity : 0.005 0.056 10878 Dihedral : 11.588 77.330 10094 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.30 % Allowed : 0.44 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.56 (0.09), residues: 7399 helix: 0.03 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -2.35 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 17 PHE 0.037 0.002 PHEAS 67 TYR 0.015 0.001 TYR W 70 ARG 0.007 0.001 ARGA4 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14798 Ramachandran restraints generated. 7399 Oldfield, 0 Emsley, 7399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1628 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1608 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7770 (tp30) cc_final: 0.7391 (tp30) REVERT: C 6 THR cc_start: 0.7540 (t) cc_final: 0.7233 (p) REVERT: C 77 ASP cc_start: 0.7957 (t70) cc_final: 0.7668 (t70) REVERT: C 127 ASN cc_start: 0.7811 (m-40) cc_final: 0.7509 (m-40) REVERT: E 53 LYS cc_start: 0.7969 (ptmt) cc_final: 0.7468 (pttp) REVERT: E 91 ASN cc_start: 0.7467 (t0) cc_final: 0.7067 (p0) REVERT: E 112 ARG cc_start: 0.8044 (tpp-160) cc_final: 0.7774 (tpt-90) REVERT: G 68 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7749 (ptpt) REVERT: G 139 TYR cc_start: 0.8290 (m-10) cc_final: 0.7995 (m-10) REVERT: I 77 ASP cc_start: 0.8002 (t70) cc_final: 0.7794 (t70) REVERT: I 83 LEU cc_start: 0.8339 (tp) cc_final: 0.8004 (tp) REVERT: K 22 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7794 (tm-30) REVERT: M 50 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6900 (mm-30) REVERT: M 59 THR cc_start: 0.8229 (m) cc_final: 0.7892 (t) REVERT: M 89 THR cc_start: 0.7307 (m) cc_final: 0.7027 (p) REVERT: O 39 GLN cc_start: 0.8287 (tt0) cc_final: 0.8083 (tt0) REVERT: O 89 THR cc_start: 0.7613 (m) cc_final: 0.7281 (p) REVERT: Q 50 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7229 (mm-30) REVERT: S 50 GLU cc_start: 0.7908 (tp30) cc_final: 0.7270 (mm-30) REVERT: S 127 ASN cc_start: 0.7781 (m110) cc_final: 0.7493 (m110) REVERT: U 34 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6319 (mm-40) REVERT: U 89 THR cc_start: 0.7441 (m) cc_final: 0.7155 (p) REVERT: U 112 ARG cc_start: 0.8424 (tpp-160) cc_final: 0.7779 (tpt170) REVERT: W 19 ASP cc_start: 0.8010 (t0) cc_final: 0.7759 (t0) REVERT: W 22 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7392 (mm-30) REVERT: W 127 ASN cc_start: 0.8241 (m110) cc_final: 0.7870 (m-40) REVERT: W 129 ILE cc_start: 0.7929 (tp) cc_final: 0.7695 (tp) REVERT: Y 112 ARG cc_start: 0.8399 (tpp-160) cc_final: 0.7789 (tpt170) REVERT: 0 50 GLU cc_start: 0.6993 (tp30) cc_final: 0.6670 (tp30) REVERT: 0 93 ILE cc_start: 0.8281 (mt) cc_final: 0.7992 (tp) REVERT: 0 127 ASN cc_start: 0.8445 (m-40) cc_final: 0.8136 (m-40) REVERT: 2 38 GLN cc_start: 0.6862 (tp40) cc_final: 0.6362 (tp-100) REVERT: 2 89 THR cc_start: 0.7579 (m) cc_final: 0.7097 (p) REVERT: 2 131 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6763 (mm-30) REVERT: 4 62 PHE cc_start: 0.7457 (t80) cc_final: 0.7150 (t80) REVERT: 4 89 THR cc_start: 0.7592 (m) cc_final: 0.7202 (p) REVERT: 4 93 ILE cc_start: 0.8357 (mt) cc_final: 0.8122 (tp) REVERT: 4 112 ARG cc_start: 0.8324 (tpp-160) cc_final: 0.7577 (tpt170) REVERT: 4 127 ASN cc_start: 0.8260 (m110) cc_final: 0.8010 (m110) REVERT: 6 27 CYS cc_start: 0.8774 (p) cc_final: 0.8546 (p) REVERT: 6 112 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.7982 (tpt170) REVERT: 6 143 SER cc_start: 0.8377 (p) cc_final: 0.8003 (t) REVERT: 8 34 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7168 (mm-40) REVERT: 8 143 SER cc_start: 0.8060 (p) cc_final: 0.7770 (p) REVERT: a 21 ILE cc_start: 0.8574 (mp) cc_final: 0.8171 (tt) REVERT: c 27 CYS cc_start: 0.8835 (p) cc_final: 0.8518 (p) REVERT: c 95 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7732 (mm-30) REVERT: e 34 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7219 (mm-40) REVERT: e 50 GLU cc_start: 0.7329 (tp30) cc_final: 0.6876 (tp30) REVERT: e 129 ILE cc_start: 0.7972 (tp) cc_final: 0.7730 (tp) REVERT: g 127 ASN cc_start: 0.7884 (m-40) cc_final: 0.7669 (m110) REVERT: i 34 GLN cc_start: 0.7775 (mm110) cc_final: 0.6927 (mm-40) REVERT: i 95 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7520 (mm-30) REVERT: k 34 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6709 (mm-40) REVERT: k 46 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7473 (mmm-85) REVERT: k 50 GLU cc_start: 0.7663 (tp30) cc_final: 0.7298 (tp30) REVERT: k 69 VAL cc_start: 0.8679 (t) cc_final: 0.8432 (p) REVERT: k 112 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.8499 (tpp80) REVERT: m 29 ASN cc_start: 0.8217 (m110) cc_final: 0.7887 (m110) REVERT: o 34 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7137 (mm-40) REVERT: o 91 ASN cc_start: 0.7738 (t0) cc_final: 0.7372 (t0) REVERT: o 129 ILE cc_start: 0.7997 (tp) cc_final: 0.7780 (tp) REVERT: q 34 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7419 (mm-40) REVERT: q 90 ARG cc_start: 0.7082 (ttm-80) cc_final: 0.6632 (ttm-80) REVERT: q 129 ILE cc_start: 0.8130 (tp) cc_final: 0.7839 (tp) REVERT: s 22 GLU cc_start: 0.7624 (tp30) cc_final: 0.7179 (tp30) REVERT: s 127 ASN cc_start: 0.8778 (m110) cc_final: 0.8394 (m-40) REVERT: u 29 ASN cc_start: 0.7848 (m110) cc_final: 0.7554 (m110) REVERT: u 83 LEU cc_start: 0.8597 (tp) cc_final: 0.8367 (tp) REVERT: w 19 ASP cc_start: 0.8126 (t0) cc_final: 0.7328 (m-30) REVERT: w 22 GLU cc_start: 0.8183 (pp20) cc_final: 0.7848 (pp20) REVERT: w 29 ASN cc_start: 0.8067 (m110) cc_final: 0.7735 (m110) REVERT: w 62 PHE cc_start: 0.7689 (t80) cc_final: 0.7393 (t80) REVERT: w 93 ILE cc_start: 0.8214 (mm) cc_final: 0.7942 (pt) REVERT: w 127 ASN cc_start: 0.8818 (m110) cc_final: 0.8574 (m-40) REVERT: w 140 ASN cc_start: 0.7512 (p0) cc_final: 0.6823 (p0) REVERT: y 19 ASP cc_start: 0.8028 (t0) cc_final: 0.7803 (t0) REVERT: y 62 PHE cc_start: 0.7680 (t80) cc_final: 0.7436 (t80) REVERT: AA 19 ASP cc_start: 0.8143 (t0) cc_final: 0.7777 (t0) REVERT: AA 22 GLU cc_start: 0.8048 (pp20) cc_final: 0.7755 (pp20) REVERT: AA 29 ASN cc_start: 0.8326 (m-40) cc_final: 0.8065 (m-40) REVERT: AA 127 ASN cc_start: 0.8315 (m110) cc_final: 0.7931 (m-40) REVERT: AC 19 ASP cc_start: 0.8252 (t0) cc_final: 0.7843 (m-30) REVERT: AC 46 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7576 (mmm-85) REVERT: AC 53 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8019 (mtpp) REVERT: AC 62 PHE cc_start: 0.7931 (t80) cc_final: 0.7675 (t80) REVERT: AC 92 ARG cc_start: 0.5830 (ttt180) cc_final: 0.4025 (ttm170) REVERT: AC 127 ASN cc_start: 0.8333 (m110) cc_final: 0.8126 (m-40) REVERT: AC 140 ASN cc_start: 0.6539 (p0) cc_final: 0.6058 (p0) REVERT: AE 14 SER cc_start: 0.8442 (m) cc_final: 0.8159 (p) REVERT: AE 22 GLU cc_start: 0.7503 (tp30) cc_final: 0.7190 (tp30) REVERT: AE 39 GLN cc_start: 0.8017 (tt0) cc_final: 0.7466 (mp10) REVERT: AE 92 ARG cc_start: 0.5122 (ttt180) cc_final: 0.3818 (ttm170) REVERT: AE 109 ASP cc_start: 0.7556 (t70) cc_final: 0.7182 (t70) REVERT: AE 129 ILE cc_start: 0.8335 (tp) cc_final: 0.8113 (tp) REVERT: AE 131 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7928 (tm-30) REVERT: AG 19 ASP cc_start: 0.8138 (t0) cc_final: 0.7710 (m-30) REVERT: AG 22 GLU cc_start: 0.7805 (tp30) cc_final: 0.7464 (tp30) REVERT: AG 29 ASN cc_start: 0.7952 (m-40) cc_final: 0.7631 (m110) REVERT: AG 39 GLN cc_start: 0.8159 (tt0) cc_final: 0.7417 (mp10) REVERT: AG 46 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7754 (ppt170) REVERT: AG 76 LEU cc_start: 0.8173 (mp) cc_final: 0.7959 (mp) REVERT: AG 92 ARG cc_start: 0.5212 (ttt180) cc_final: 0.3478 (ttm170) REVERT: AG 139 TYR cc_start: 0.7923 (m-80) cc_final: 0.7590 (m-80) REVERT: AI 39 GLN cc_start: 0.8460 (tt0) cc_final: 0.7383 (mp10) REVERT: AI 46 ARG cc_start: 0.8278 (mtt90) cc_final: 0.7718 (mtp180) REVERT: AI 109 ASP cc_start: 0.7797 (t70) cc_final: 0.7577 (t70) REVERT: AK 6 THR cc_start: 0.7680 (t) cc_final: 0.7434 (m) REVERT: AK 19 ASP cc_start: 0.8212 (t0) cc_final: 0.7854 (t0) REVERT: AK 39 GLN cc_start: 0.8252 (tt0) cc_final: 0.7473 (mp10) REVERT: AK 46 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7816 (mmm-85) REVERT: AK 92 ARG cc_start: 0.5138 (ttt180) cc_final: 0.3667 (ttm170) REVERT: AM 19 ASP cc_start: 0.8073 (t0) cc_final: 0.7734 (t0) REVERT: AM 39 GLN cc_start: 0.8388 (tt0) cc_final: 0.7872 (mp10) REVERT: AM 46 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7693 (mmm-85) REVERT: AM 95 GLU cc_start: 0.4267 (tt0) cc_final: 0.3912 (tt0) REVERT: AM 113 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.7113 (ttp80) REVERT: AM 131 GLU cc_start: 0.8459 (pp20) cc_final: 0.8100 (pp20) REVERT: AM 139 TYR cc_start: 0.7945 (m-80) cc_final: 0.7463 (m-80) REVERT: AM 140 ASN cc_start: 0.7207 (p0) cc_final: 0.6920 (p0) REVERT: AO 38 GLN cc_start: 0.7081 (tp40) cc_final: 0.6750 (tp40) REVERT: AO 46 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7812 (ppt170) REVERT: AO 57 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7547 (tp40) REVERT: AO 95 GLU cc_start: 0.4061 (tt0) cc_final: 0.3709 (tt0) REVERT: AQ 22 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7367 (tp30) REVERT: AQ 34 GLN cc_start: 0.7281 (tp40) cc_final: 0.6818 (mm-40) REVERT: AQ 46 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7785 (mmm160) REVERT: AQ 140 ASN cc_start: 0.7351 (p0) cc_final: 0.7013 (p0) REVERT: AS 29 ASN cc_start: 0.8027 (m110) cc_final: 0.7609 (m110) REVERT: AS 33 ASN cc_start: 0.7706 (m110) cc_final: 0.7348 (m-40) REVERT: AS 34 GLN cc_start: 0.7340 (tp-100) cc_final: 0.6992 (tp-100) REVERT: AU 33 ASN cc_start: 0.8124 (m-40) cc_final: 0.7307 (m-40) REVERT: AU 39 GLN cc_start: 0.8345 (tt0) cc_final: 0.7749 (mp10) REVERT: AU 46 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7621 (tmt170) REVERT: AU 50 GLU cc_start: 0.7509 (tp30) cc_final: 0.7177 (tp30) REVERT: AU 57 GLN cc_start: 0.7369 (mm110) cc_final: 0.7000 (mm-40) REVERT: AU 92 ARG cc_start: 0.3827 (ttt180) cc_final: 0.2987 (ttm170) REVERT: AU 127 ASN cc_start: 0.8336 (t160) cc_final: 0.8104 (m-40) REVERT: AU 140 ASN cc_start: 0.7231 (p0) cc_final: 0.7005 (p0) REVERT: AW 33 ASN cc_start: 0.7701 (m110) cc_final: 0.6815 (m-40) REVERT: AW 39 GLN cc_start: 0.8209 (tt0) cc_final: 0.7891 (mp10) REVERT: AW 46 ARG cc_start: 0.8427 (mtt180) cc_final: 0.7640 (tmt170) REVERT: AW 50 GLU cc_start: 0.7877 (tp30) cc_final: 0.7446 (tp30) REVERT: AW 57 GLN cc_start: 0.6732 (mm-40) cc_final: 0.6240 (mm-40) REVERT: AW 92 ARG cc_start: 0.4537 (ttt180) cc_final: 0.3954 (ttm170) REVERT: AW 127 ASN cc_start: 0.8396 (m110) cc_final: 0.7812 (m110) REVERT: AW 131 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7588 (mp0) REVERT: AW 140 ASN cc_start: 0.7993 (p0) cc_final: 0.7742 (p0) REVERT: AY 29 ASN cc_start: 0.8316 (m110) cc_final: 0.7988 (m-40) REVERT: AY 34 GLN cc_start: 0.7551 (tp40) cc_final: 0.6888 (tp40) REVERT: AY 39 GLN cc_start: 0.8036 (tt0) cc_final: 0.7704 (mp10) REVERT: AY 46 ARG cc_start: 0.8131 (mtt180) cc_final: 0.7536 (ppt170) REVERT: AY 88 ASP cc_start: 0.6310 (t0) cc_final: 0.5447 (p0) REVERT: AY 92 ARG cc_start: 0.4862 (ttt180) cc_final: 0.4048 (ttm170) REVERT: AY 140 ASN cc_start: 0.7927 (p0) cc_final: 0.7342 (p0) REVERT: A0 19 ASP cc_start: 0.8139 (t0) cc_final: 0.7730 (t0) REVERT: A0 22 GLU cc_start: 0.8155 (pp20) cc_final: 0.7883 (pp20) REVERT: A0 39 GLN cc_start: 0.7285 (tt0) cc_final: 0.6858 (mp10) REVERT: A0 46 ARG cc_start: 0.7755 (mmt90) cc_final: 0.7102 (tmm160) REVERT: A0 92 ARG cc_start: 0.4674 (ttt180) cc_final: 0.4018 (ttm170) REVERT: A0 112 ARG cc_start: 0.7841 (tpt170) cc_final: 0.7637 (tpt170) REVERT: A0 127 ASN cc_start: 0.8483 (m110) cc_final: 0.7927 (m110) REVERT: A0 139 TYR cc_start: 0.7783 (m-80) cc_final: 0.7533 (m-80) REVERT: A2 33 ASN cc_start: 0.8098 (m-40) cc_final: 0.7746 (m-40) REVERT: A2 39 GLN cc_start: 0.7466 (tt0) cc_final: 0.6972 (mp10) REVERT: A2 53 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7414 (mtmm) REVERT: A2 92 ARG cc_start: 0.4514 (ttt180) cc_final: 0.3729 (ttm170) REVERT: A2 127 ASN cc_start: 0.8734 (m110) cc_final: 0.8198 (m-40) REVERT: A2 140 ASN cc_start: 0.8007 (p0) cc_final: 0.7380 (p0) REVERT: A4 29 ASN cc_start: 0.8320 (m-40) cc_final: 0.7965 (m-40) REVERT: A4 39 GLN cc_start: 0.7512 (tt0) cc_final: 0.7150 (mp10) REVERT: A4 46 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.7216 (ppt170) REVERT: A4 112 ARG cc_start: 0.7981 (mmm160) cc_final: 0.7627 (tpt170) REVERT: A6 29 ASN cc_start: 0.7857 (m110) cc_final: 0.7464 (m110) REVERT: A6 38 GLN cc_start: 0.7074 (tp40) cc_final: 0.5346 (pm20) REVERT: A6 46 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7406 (ppt170) REVERT: A8 21 ILE cc_start: 0.8508 (tt) cc_final: 0.8264 (tt) REVERT: A8 38 GLN cc_start: 0.7056 (tp40) cc_final: 0.5688 (pm20) REVERT: A8 46 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7161 (tmm160) REVERT: A8 50 GLU cc_start: 0.8002 (tp30) cc_final: 0.7594 (tp30) outliers start: 20 outliers final: 13 residues processed: 1615 average time/residue: 0.6187 time to fit residues: 1680.3268 Evaluate side-chains 1397 residues out of total 6615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1384 time to evaluate : 6.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 7.9990 chunk 621 optimal weight: 0.0970 chunk 178 optimal weight: 7.9990 chunk 537 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 162 optimal weight: 30.0000 chunk 584 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 599 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN C 91 ASN E 29 ASN ** E 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** G 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 ASN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN M 29 ASN ** M 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 101 ASN ** 6 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 101 ASN ** 8 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 101 ASN a 25 ASN ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 126 ASN ** e 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 101 ASN g 91 ASN g 101 ASN ** k 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 36 GLN k 126 ASN m 91 ASN ** m 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 99 GLN q 127 ASN ** s 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 101 ASN ** w 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 91 ASN w 101 ASN ** w 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 101 ASN AC 99 GLN ** AE 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 91 ASN ** AK 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 126 ASN AM 57 GLN ** AM 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 126 ASN AS 57 GLN AS 101 ASN AU 91 ASN AU 99 GLN AU 126 ASN AW 91 ASN A0 36 GLN A0 101 ASN A4 36 GLN A6 36 GLN ** A6 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 101 ASN A8 33 ASN A8 45 GLN ** A8 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A8 91 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.077995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.068147 restraints weight = 187700.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.070336 restraints weight = 100510.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.071734 restraints weight = 63189.243| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 63945 Z= 0.240 Angle : 0.602 7.206 88004 Z= 0.326 Chirality : 0.041 0.209 10437 Planarity : 0.005 0.055 10878 Dihedral : 11.508 75.878 10094 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.32 % Allowed : 0.35 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.09), residues: 7399 helix: 0.08 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -2.35 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP k 17 PHE 0.033 0.002 PHEAS 67 TYR 0.013 0.001 TYR W 70 ARG 0.006 0.001 ARG m 134 =============================================================================== Job complete usr+sys time: 23524.20 seconds wall clock time: 408 minutes 50.28 seconds (24530.28 seconds total)