Starting phenix.real_space_refine on Sun Mar 10 14:43:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opc_17048/03_2024/8opc_17048.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opc_17048/03_2024/8opc_17048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opc_17048/03_2024/8opc_17048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opc_17048/03_2024/8opc_17048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opc_17048/03_2024/8opc_17048.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opc_17048/03_2024/8opc_17048.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.022 sd= 0.275 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 140 5.49 5 S 392 5.16 5 C 32760 2.51 5 N 9100 2.21 5 O 10696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Aa GLU 107": "OE1" <-> "OE2" Residue "Aa PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac GLU 107": "OE1" <-> "OE2" Residue "Ac PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae GLU 107": "OE1" <-> "OE2" Residue "Ae PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag GLU 107": "OE1" <-> "OE2" Residue "Ag PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai GLU 107": "OE1" <-> "OE2" Residue "Ai PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak GLU 107": "OE1" <-> "OE2" Residue "Ak PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Am GLU 107": "OE1" <-> "OE2" Residue "Am PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao GLU 107": "OE1" <-> "OE2" Residue "Ao PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aq GLU 107": "OE1" <-> "OE2" Residue "Aq PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "As GLU 107": "OE1" <-> "OE2" Residue "As PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Au GLU 107": "OE1" <-> "OE2" Residue "Au PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aw GLU 107": "OE1" <-> "OE2" Residue "Aw PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ay GLU 107": "OE1" <-> "OE2" Residue "Ay PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba GLU 107": "OE1" <-> "OE2" Residue "Ba PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc GLU 107": "OE1" <-> "OE2" Residue "Bc PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Be GLU 107": "OE1" <-> "OE2" Residue "Be PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bg GLU 107": "OE1" <-> "OE2" Residue "Bg PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi GLU 107": "OE1" <-> "OE2" Residue "Bi PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk GLU 107": "OE1" <-> "OE2" Residue "Bk PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bm GLU 107": "OE1" <-> "OE2" Residue "Bm PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bo GLU 107": "OE1" <-> "OE2" Residue "Bo PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq GLU 107": "OE1" <-> "OE2" Residue "Bq PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bs GLU 107": "OE1" <-> "OE2" Residue "Bs PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bu GLU 107": "OE1" <-> "OE2" Residue "Bu PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw GLU 107": "OE1" <-> "OE2" Residue "Bw PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "By GLU 107": "OE1" <-> "OE2" Residue "By PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ca GLU 107": "OE1" <-> "OE2" Residue "Ca PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cc GLU 107": "OE1" <-> "OE2" Residue "Cc PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53088 Number of models: 1 Model: "" Number of chains: 56 Chain: "Aa" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Ab" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ac" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Ad" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ae" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Af" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ag" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Ah" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ai" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Aj" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ak" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Al" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Am" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "An" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ao" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Ap" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Aq" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Ar" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "As" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "At" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Au" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Av" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Aw" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Ax" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ay" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Az" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ba" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bb" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bc" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bd" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Be" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bf" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bg" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bh" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bi" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bj" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bk" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bl" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bm" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bn" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bo" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bp" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bq" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Br" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bs" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bt" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bu" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bv" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Bw" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bx" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "By" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Bz" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Ca" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Cb" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "Cc" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1796 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "Cd" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 3} Time building chain proxies: 21.08, per 1000 atoms: 0.40 Number of scatterers: 53088 At special positions: 0 Unit cell: (145.35, 144.4, 234.65, 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 392 16.00 P 140 15.00 O 10696 8.00 N 9100 7.00 C 32760 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: 16.10 Conformation dependent library (CDL) restraints added in 6.8 seconds 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11984 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 56 sheets defined 46.0% alpha, 5.3% beta 0 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 12.14 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAa 72 " --> pdb=" O GLUAa 68 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 76 through 81 Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAa 151 " --> pdb=" O PROAa 147 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 175 Processing helix chain 'Aa' and resid 182 through 188 Processing helix chain 'Aa' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 226 Processing helix chain 'Ac' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAc 72 " --> pdb=" O GLUAc 68 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 76 through 81 Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAc 151 " --> pdb=" O PROAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 175 Processing helix chain 'Ac' and resid 182 through 188 Processing helix chain 'Ac' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 226 Processing helix chain 'Ae' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAe 72 " --> pdb=" O GLUAe 68 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 81 Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAe 151 " --> pdb=" O PROAe 147 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 175 Processing helix chain 'Ae' and resid 182 through 188 Processing helix chain 'Ae' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 226 Processing helix chain 'Ag' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAg 72 " --> pdb=" O GLUAg 68 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 76 through 81 Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAg 151 " --> pdb=" O PROAg 147 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 175 Processing helix chain 'Ag' and resid 182 through 188 Processing helix chain 'Ag' and resid 192 through 197 removed outlier: 4.508A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 226 Processing helix chain 'Ai' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAi 72 " --> pdb=" O GLUAi 68 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 76 through 81 Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAi 151 " --> pdb=" O PROAi 147 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 175 Processing helix chain 'Ai' and resid 182 through 188 Processing helix chain 'Ai' and resid 192 through 197 removed outlier: 4.508A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 226 Processing helix chain 'Ak' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAk 72 " --> pdb=" O GLUAk 68 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEAk 80 " --> pdb=" O GLNAk 76 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAk 151 " --> pdb=" O PROAk 147 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 175 Processing helix chain 'Ak' and resid 182 through 188 Processing helix chain 'Ak' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 226 Processing helix chain 'Am' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAm 72 " --> pdb=" O GLUAm 68 " (cutoff:3.500A) Processing helix chain 'Am' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEAm 80 " --> pdb=" O GLNAm 76 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAm 151 " --> pdb=" O PROAm 147 " (cutoff:3.500A) Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 175 Processing helix chain 'Am' and resid 182 through 188 Processing helix chain 'Am' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 226 Processing helix chain 'Ao' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAo 72 " --> pdb=" O GLUAo 68 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEAo 80 " --> pdb=" O GLNAo 76 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 removed outlier: 3.572A pdb=" N ASNAo 151 " --> pdb=" O PROAo 147 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 175 Processing helix chain 'Ao' and resid 182 through 188 Processing helix chain 'Ao' and resid 192 through 197 removed outlier: 4.508A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 226 Processing helix chain 'Aq' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAq 72 " --> pdb=" O GLUAq 68 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 76 through 81 Processing helix chain 'Aq' and resid 86 through 102 Processing helix chain 'Aq' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAq 151 " --> pdb=" O PROAq 147 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 175 Processing helix chain 'Aq' and resid 182 through 188 Processing helix chain 'Aq' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAq 197 " --> pdb=" O SERAq 194 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 210 through 226 Processing helix chain 'As' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAs 72 " --> pdb=" O GLUAs 68 " (cutoff:3.500A) Processing helix chain 'As' and resid 76 through 81 Processing helix chain 'As' and resid 86 through 102 Processing helix chain 'As' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAs 151 " --> pdb=" O PROAs 147 " (cutoff:3.500A) Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 175 Processing helix chain 'As' and resid 182 through 188 Processing helix chain 'As' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAs 197 " --> pdb=" O SERAs 194 " (cutoff:3.500A) Processing helix chain 'As' and resid 210 through 226 Processing helix chain 'Au' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAu 72 " --> pdb=" O GLUAu 68 " (cutoff:3.500A) Processing helix chain 'Au' and resid 76 through 81 Processing helix chain 'Au' and resid 86 through 102 Processing helix chain 'Au' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAu 151 " --> pdb=" O PROAu 147 " (cutoff:3.500A) Processing helix chain 'Au' and resid 155 through 161 Processing helix chain 'Au' and resid 163 through 175 Processing helix chain 'Au' and resid 182 through 188 Processing helix chain 'Au' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAu 197 " --> pdb=" O SERAu 194 " (cutoff:3.500A) Processing helix chain 'Au' and resid 210 through 226 Processing helix chain 'Aw' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUAw 72 " --> pdb=" O GLUAw 68 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 76 through 81 Processing helix chain 'Aw' and resid 86 through 102 Processing helix chain 'Aw' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 151 removed outlier: 3.574A pdb=" N ASNAw 151 " --> pdb=" O PROAw 147 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 155 through 161 Processing helix chain 'Aw' and resid 163 through 175 Processing helix chain 'Aw' and resid 182 through 188 Processing helix chain 'Aw' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGAw 197 " --> pdb=" O SERAw 194 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 210 through 226 Processing helix chain 'Ay' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUAy 72 " --> pdb=" O GLUAy 68 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 76 through 81 Processing helix chain 'Ay' and resid 86 through 102 Processing helix chain 'Ay' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALAy 111 " --> pdb=" O GLUAy 107 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNAy 151 " --> pdb=" O PROAy 147 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 155 through 161 Processing helix chain 'Ay' and resid 163 through 175 Processing helix chain 'Ay' and resid 182 through 188 Processing helix chain 'Ay' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGAy 197 " --> pdb=" O SERAy 194 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 210 through 226 Processing helix chain 'Ba' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBa 72 " --> pdb=" O GLUBa 68 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 76 through 81 Processing helix chain 'Ba' and resid 86 through 102 Processing helix chain 'Ba' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBa 111 " --> pdb=" O GLUBa 107 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBa 151 " --> pdb=" O PROBa 147 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 155 through 161 Processing helix chain 'Ba' and resid 163 through 175 Processing helix chain 'Ba' and resid 182 through 188 Processing helix chain 'Ba' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBa 197 " --> pdb=" O SERBa 194 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 210 through 226 Processing helix chain 'Bc' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBc 72 " --> pdb=" O GLUBc 68 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 76 through 81 Processing helix chain 'Bc' and resid 86 through 102 Processing helix chain 'Bc' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBc 111 " --> pdb=" O GLUBc 107 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBc 151 " --> pdb=" O PROBc 147 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 155 through 161 Processing helix chain 'Bc' and resid 163 through 175 Processing helix chain 'Bc' and resid 182 through 188 Processing helix chain 'Bc' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBc 197 " --> pdb=" O SERBc 194 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 210 through 226 Processing helix chain 'Be' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBe 72 " --> pdb=" O GLUBe 68 " (cutoff:3.500A) Processing helix chain 'Be' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEBe 80 " --> pdb=" O GLNBe 76 " (cutoff:3.500A) Processing helix chain 'Be' and resid 86 through 102 Processing helix chain 'Be' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBe 111 " --> pdb=" O GLUBe 107 " (cutoff:3.500A) Processing helix chain 'Be' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBe 151 " --> pdb=" O PROBe 147 " (cutoff:3.500A) Processing helix chain 'Be' and resid 155 through 161 Processing helix chain 'Be' and resid 163 through 175 Processing helix chain 'Be' and resid 182 through 188 Processing helix chain 'Be' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBe 197 " --> pdb=" O SERBe 194 " (cutoff:3.500A) Processing helix chain 'Be' and resid 210 through 226 Processing helix chain 'Bg' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBg 72 " --> pdb=" O GLUBg 68 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 76 through 81 Processing helix chain 'Bg' and resid 86 through 102 Processing helix chain 'Bg' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBg 111 " --> pdb=" O GLUBg 107 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBg 151 " --> pdb=" O PROBg 147 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 155 through 161 Processing helix chain 'Bg' and resid 163 through 175 Processing helix chain 'Bg' and resid 182 through 188 Processing helix chain 'Bg' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBg 197 " --> pdb=" O SERBg 194 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 210 through 226 Processing helix chain 'Bi' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBi 72 " --> pdb=" O GLUBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 76 through 81 Processing helix chain 'Bi' and resid 86 through 102 Processing helix chain 'Bi' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBi 111 " --> pdb=" O GLUBi 107 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBi 151 " --> pdb=" O PROBi 147 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 155 through 161 Processing helix chain 'Bi' and resid 163 through 175 Processing helix chain 'Bi' and resid 182 through 188 Processing helix chain 'Bi' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBi 197 " --> pdb=" O SERBi 194 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 210 through 226 Processing helix chain 'Bk' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBk 72 " --> pdb=" O GLUBk 68 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 76 through 81 Processing helix chain 'Bk' and resid 86 through 102 Processing helix chain 'Bk' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBk 111 " --> pdb=" O GLUBk 107 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBk 151 " --> pdb=" O PROBk 147 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 155 through 161 Processing helix chain 'Bk' and resid 163 through 175 Processing helix chain 'Bk' and resid 182 through 188 Processing helix chain 'Bk' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBk 197 " --> pdb=" O SERBk 194 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 210 through 226 Processing helix chain 'Bm' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBm 72 " --> pdb=" O GLUBm 68 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 76 through 81 Processing helix chain 'Bm' and resid 86 through 102 Processing helix chain 'Bm' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBm 111 " --> pdb=" O GLUBm 107 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBm 151 " --> pdb=" O PROBm 147 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 155 through 161 Processing helix chain 'Bm' and resid 163 through 175 Processing helix chain 'Bm' and resid 182 through 188 Processing helix chain 'Bm' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBm 197 " --> pdb=" O SERBm 194 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 210 through 226 Processing helix chain 'Bo' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBo 72 " --> pdb=" O GLUBo 68 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 76 through 81 Processing helix chain 'Bo' and resid 86 through 102 Processing helix chain 'Bo' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBo 111 " --> pdb=" O GLUBo 107 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBo 151 " --> pdb=" O PROBo 147 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 155 through 161 Processing helix chain 'Bo' and resid 163 through 175 Processing helix chain 'Bo' and resid 182 through 188 Processing helix chain 'Bo' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBo 197 " --> pdb=" O SERBo 194 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 210 through 226 Processing helix chain 'Bq' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBq 72 " --> pdb=" O GLUBq 68 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 76 through 81 removed outlier: 3.501A pdb=" N ILEBq 80 " --> pdb=" O GLNBq 76 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 86 through 102 Processing helix chain 'Bq' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBq 111 " --> pdb=" O GLUBq 107 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBq 151 " --> pdb=" O PROBq 147 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 155 through 161 Processing helix chain 'Bq' and resid 163 through 175 Processing helix chain 'Bq' and resid 182 through 188 Processing helix chain 'Bq' and resid 192 through 197 removed outlier: 4.510A pdb=" N ARGBq 197 " --> pdb=" O SERBq 194 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 210 through 226 Processing helix chain 'Bs' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBs 72 " --> pdb=" O GLUBs 68 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 76 through 81 Processing helix chain 'Bs' and resid 86 through 102 Processing helix chain 'Bs' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBs 111 " --> pdb=" O GLUBs 107 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBs 151 " --> pdb=" O PROBs 147 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 155 through 161 Processing helix chain 'Bs' and resid 163 through 175 Processing helix chain 'Bs' and resid 182 through 188 Processing helix chain 'Bs' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBs 197 " --> pdb=" O SERBs 194 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 210 through 226 Processing helix chain 'Bu' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUBu 72 " --> pdb=" O GLUBu 68 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 76 through 81 removed outlier: 3.500A pdb=" N ILEBu 80 " --> pdb=" O GLNBu 76 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 86 through 102 Processing helix chain 'Bu' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALBu 111 " --> pdb=" O GLUBu 107 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBu 151 " --> pdb=" O PROBu 147 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 155 through 161 Processing helix chain 'Bu' and resid 163 through 175 Processing helix chain 'Bu' and resid 182 through 188 Processing helix chain 'Bu' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBu 197 " --> pdb=" O SERBu 194 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 210 through 226 Processing helix chain 'Bw' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBw 72 " --> pdb=" O GLUBw 68 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 76 through 81 Processing helix chain 'Bw' and resid 86 through 102 Processing helix chain 'Bw' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBw 111 " --> pdb=" O GLUBw 107 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBw 151 " --> pdb=" O PROBw 147 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 155 through 161 Processing helix chain 'Bw' and resid 163 through 175 Processing helix chain 'Bw' and resid 182 through 188 Processing helix chain 'Bw' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBw 197 " --> pdb=" O SERBw 194 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 210 through 226 Processing helix chain 'By' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUBy 72 " --> pdb=" O GLUBy 68 " (cutoff:3.500A) Processing helix chain 'By' and resid 76 through 81 Processing helix chain 'By' and resid 86 through 102 Processing helix chain 'By' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALBy 111 " --> pdb=" O GLUBy 107 " (cutoff:3.500A) Processing helix chain 'By' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNBy 151 " --> pdb=" O PROBy 147 " (cutoff:3.500A) Processing helix chain 'By' and resid 155 through 161 Processing helix chain 'By' and resid 163 through 175 Processing helix chain 'By' and resid 182 through 188 Processing helix chain 'By' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGBy 197 " --> pdb=" O SERBy 194 " (cutoff:3.500A) Processing helix chain 'By' and resid 210 through 226 Processing helix chain 'Ca' and resid 66 through 72 removed outlier: 3.685A pdb=" N GLUCa 72 " --> pdb=" O GLUCa 68 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 76 through 81 Processing helix chain 'Ca' and resid 86 through 102 Processing helix chain 'Ca' and resid 107 through 123 removed outlier: 3.777A pdb=" N VALCa 111 " --> pdb=" O GLUCa 107 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNCa 151 " --> pdb=" O PROCa 147 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 155 through 161 Processing helix chain 'Ca' and resid 163 through 175 Processing helix chain 'Ca' and resid 182 through 188 Processing helix chain 'Ca' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGCa 197 " --> pdb=" O SERCa 194 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 210 through 226 Processing helix chain 'Cc' and resid 66 through 72 removed outlier: 3.684A pdb=" N GLUCc 72 " --> pdb=" O GLUCc 68 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 76 through 81 Processing helix chain 'Cc' and resid 86 through 102 Processing helix chain 'Cc' and resid 107 through 123 removed outlier: 3.778A pdb=" N VALCc 111 " --> pdb=" O GLUCc 107 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 145 through 151 removed outlier: 3.573A pdb=" N ASNCc 151 " --> pdb=" O PROCc 147 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 155 through 161 Processing helix chain 'Cc' and resid 163 through 175 Processing helix chain 'Cc' and resid 182 through 188 Processing helix chain 'Cc' and resid 192 through 197 removed outlier: 4.509A pdb=" N ARGCc 197 " --> pdb=" O SERCc 194 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 210 through 226 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 131 through 136 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'Ac' and resid 131 through 136 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'Ae' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'Ag' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'Ai' and resid 131 through 136 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'Ak' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'Am' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'Am' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'Ao' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'Ao' and resid 131 through 136 Processing sheet with id=AB8, first strand: chain 'Aq' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'Aq' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'As' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'As' and resid 131 through 136 Processing sheet with id=AC3, first strand: chain 'Au' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'Au' and resid 131 through 136 Processing sheet with id=AC5, first strand: chain 'Aw' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'Aw' and resid 131 through 136 Processing sheet with id=AC7, first strand: chain 'Ay' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'Ay' and resid 131 through 136 Processing sheet with id=AC9, first strand: chain 'Ba' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'Ba' and resid 131 through 136 Processing sheet with id=AD2, first strand: chain 'Bc' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'Bc' and resid 131 through 136 Processing sheet with id=AD4, first strand: chain 'Be' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'Be' and resid 131 through 136 Processing sheet with id=AD6, first strand: chain 'Bg' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'Bg' and resid 131 through 136 Processing sheet with id=AD8, first strand: chain 'Bi' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Bi' and resid 131 through 136 Processing sheet with id=AE1, first strand: chain 'Bk' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'Bk' and resid 131 through 136 Processing sheet with id=AE3, first strand: chain 'Bm' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'Bm' and resid 131 through 136 Processing sheet with id=AE5, first strand: chain 'Bo' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'Bo' and resid 131 through 136 Processing sheet with id=AE7, first strand: chain 'Bq' and resid 58 through 59 Processing sheet with id=AE8, first strand: chain 'Bq' and resid 131 through 136 Processing sheet with id=AE9, first strand: chain 'Bs' and resid 58 through 59 Processing sheet with id=AF1, first strand: chain 'Bs' and resid 131 through 136 Processing sheet with id=AF2, first strand: chain 'Bu' and resid 58 through 59 Processing sheet with id=AF3, first strand: chain 'Bu' and resid 131 through 136 Processing sheet with id=AF4, first strand: chain 'Bw' and resid 58 through 59 Processing sheet with id=AF5, first strand: chain 'Bw' and resid 131 through 136 Processing sheet with id=AF6, first strand: chain 'By' and resid 58 through 59 Processing sheet with id=AF7, first strand: chain 'By' and resid 131 through 136 Processing sheet with id=AF8, first strand: chain 'Ca' and resid 58 through 59 Processing sheet with id=AF9, first strand: chain 'Ca' and resid 131 through 136 Processing sheet with id=AG1, first strand: chain 'Cc' and resid 58 through 59 Processing sheet with id=AG2, first strand: chain 'Cc' and resid 131 through 136 1926 hydrogen bonds defined for protein. 5442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 13.73 Time building geometry restraints manager: 17.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11431 1.33 - 1.45: 12107 1.45 - 1.57: 29830 1.57 - 1.69: 252 1.69 - 1.81: 756 Bond restraints: 54376 Sorted by residual: bond pdb=" C ASNAi 113 " pdb=" N GLYAi 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.54e+01 bond pdb=" C ASNBa 113 " pdb=" N GLYBa 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.53e+01 bond pdb=" C ASNCc 113 " pdb=" N GLYCc 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.53e+01 bond pdb=" C ASNBs 113 " pdb=" N GLYBs 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.53e+01 bond pdb=" C ASNBm 113 " pdb=" N GLYBm 114 " ideal model delta sigma weight residual 1.334 1.273 0.061 1.21e-02 6.83e+03 2.52e+01 ... (remaining 54371 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.88: 2140 105.88 - 112.91: 28970 112.91 - 119.95: 18597 119.95 - 126.98: 23680 126.98 - 134.02: 757 Bond angle restraints: 74144 Sorted by residual: angle pdb=" N ASNAo 122 " pdb=" CA ASNAo 122 " pdb=" C ASNAo 122 " ideal model delta sigma weight residual 112.97 119.77 -6.80 1.06e+00 8.90e-01 4.11e+01 angle pdb=" N ASNAg 122 " pdb=" CA ASNAg 122 " pdb=" C ASNAg 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.11e+01 angle pdb=" N ASNAy 122 " pdb=" CA ASNAy 122 " pdb=" C ASNAy 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" N ASNAe 122 " pdb=" CA ASNAe 122 " pdb=" C ASNAe 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" N ASNBu 122 " pdb=" CA ASNBu 122 " pdb=" C ASNBu 122 " ideal model delta sigma weight residual 112.97 119.76 -6.79 1.06e+00 8.90e-01 4.10e+01 ... (remaining 74139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 27687 15.57 - 31.14: 4009 31.14 - 46.70: 1288 46.70 - 62.27: 588 62.27 - 77.84: 84 Dihedral angle restraints: 33656 sinusoidal: 15120 harmonic: 18536 Sorted by residual: dihedral pdb=" CA LEUCa 261 " pdb=" C LEUCa 261 " pdb=" N LEUCa 262 " pdb=" CA LEUCa 262 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEUBi 261 " pdb=" C LEUBi 261 " pdb=" N LEUBi 262 " pdb=" CA LEUBi 262 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEUAu 261 " pdb=" C LEUAu 261 " pdb=" N LEUAu 262 " pdb=" CA LEUAu 262 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 33653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 5077 0.030 - 0.061: 2415 0.061 - 0.091: 507 0.091 - 0.122: 252 0.122 - 0.152: 121 Chirality restraints: 8372 Sorted by residual: chirality pdb=" CA GLUAs 107 " pdb=" N GLUAs 107 " pdb=" C GLUAs 107 " pdb=" CB GLUAs 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA GLUBu 107 " pdb=" N GLUBu 107 " pdb=" C GLUBu 107 " pdb=" CB GLUBu 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA GLUCc 107 " pdb=" N GLUCc 107 " pdb=" C GLUCc 107 " pdb=" CB GLUCc 107 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 8369 not shown) Planarity restraints: 9184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA METBc 54 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C METBc 54 " 0.033 2.00e-02 2.50e+03 pdb=" O METBc 54 " -0.012 2.00e-02 2.50e+03 pdb=" N ARGBc 55 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METBi 54 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C METBi 54 " -0.033 2.00e-02 2.50e+03 pdb=" O METBi 54 " 0.012 2.00e-02 2.50e+03 pdb=" N ARGBi 55 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA METAg 54 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C METAg 54 " -0.033 2.00e-02 2.50e+03 pdb=" O METAg 54 " 0.012 2.00e-02 2.50e+03 pdb=" N ARGAg 55 " 0.011 2.00e-02 2.50e+03 ... (remaining 9181 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5307 2.74 - 3.28: 50671 3.28 - 3.82: 90924 3.82 - 4.36: 109658 4.36 - 4.90: 185749 Nonbonded interactions: 442309 Sorted by model distance: nonbonded pdb=" OH TYRAa 184 " pdb=" O2 UAb 4 " model vdw 2.198 2.440 nonbonded pdb=" OH TYRBk 184 " pdb=" O2 UBl 4 " model vdw 2.198 2.440 nonbonded pdb=" OH TYRBc 184 " pdb=" O2 UBd 4 " model vdw 2.198 2.440 nonbonded pdb=" OH TYRAo 184 " pdb=" O2 UAp 4 " model vdw 2.198 2.440 nonbonded pdb=" OH TYRAc 184 " pdb=" O2 UAd 4 " model vdw 2.198 2.440 ... (remaining 442304 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 '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 'Ba' selection = chain 'Bc' selection = chain 'Be' selection = chain 'Bg' selection = chain 'Bi' selection = chain 'Bk' selection = chain 'Bm' selection = chain 'Bo' selection = chain 'Bq' selection = chain 'Bs' selection = chain 'Bu' selection = chain 'Bw' selection = chain 'By' selection = chain 'Ca' selection = chain 'Cc' } ncs_group { reference = 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 'Bb' selection = chain 'Bd' selection = chain 'Bf' selection = chain 'Bh' selection = chain 'Bj' selection = chain 'Bl' selection = chain 'Bn' selection = chain 'Bp' selection = chain 'Br' selection = chain 'Bt' selection = chain 'Bv' selection = chain 'Bx' selection = chain 'Bz' selection = chain 'Cb' selection = chain 'Cd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.890 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 109.040 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.650 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: 0.000 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.005 0.061 54376 Z= 0.320 Angle : 0.769 8.624 74144 Z= 0.482 Chirality : 0.041 0.152 8372 Planarity : 0.005 0.038 9184 Dihedral : 17.781 77.838 21672 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.08 % Allowed : 28.01 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.10), residues: 6272 helix: 0.50 (0.11), residues: 2660 sheet: 1.04 (0.25), residues: 280 loop : -1.40 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPBg 132 HIS 0.002 0.001 HISBu 217 PHE 0.021 0.003 PHEBq 202 TYR 0.008 0.001 TYRAi 184 ARG 0.002 0.000 ARGBq 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1326 time to evaluate : 4.558 Fit side-chains REVERT: Aa 231 ARG cc_start: 0.8495 (mmm160) cc_final: 0.8128 (mmm160) REVERT: Ac 134 MET cc_start: 0.8692 (ttt) cc_final: 0.8389 (ttt) REVERT: Ac 258 MET cc_start: 0.7282 (mtt) cc_final: 0.6985 (mtt) REVERT: Ae 160 MET cc_start: 0.9521 (mmm) cc_final: 0.9283 (mmm) REVERT: Ae 267 MET cc_start: 0.4991 (OUTLIER) cc_final: 0.4502 (pp-130) REVERT: Ag 53 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7776 (mtmt) REVERT: Ag 77 GLN cc_start: 0.8575 (mt0) cc_final: 0.8335 (mt0) REVERT: Ag 134 MET cc_start: 0.8774 (ttt) cc_final: 0.8494 (ttt) REVERT: Ag 245 ASN cc_start: 0.9161 (t0) cc_final: 0.8879 (t0) REVERT: Ai 53 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7730 (mtmt) REVERT: Ai 245 ASN cc_start: 0.9144 (t0) cc_final: 0.8922 (t0) REVERT: Ai 267 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4583 (tmm) REVERT: Ak 134 MET cc_start: 0.8714 (ttt) cc_final: 0.8423 (ttt) REVERT: Ak 153 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8604 (mptt) REVERT: Ao 53 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7931 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8633 (m-30) cc_final: 0.8412 (m-30) REVERT: Ao 98 GLN cc_start: 0.8742 (tt0) cc_final: 0.8518 (tt0) REVERT: Ao 134 MET cc_start: 0.8719 (ttt) cc_final: 0.8378 (ttt) REVERT: Ao 153 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8664 (mptt) REVERT: Aq 53 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8053 (mttm) REVERT: Aq 91 ASP cc_start: 0.8695 (m-30) cc_final: 0.8360 (m-30) REVERT: Aq 160 MET cc_start: 0.9488 (mmm) cc_final: 0.9275 (mmm) REVERT: As 53 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8045 (mttp) REVERT: As 108 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8290 (tpp) REVERT: As 267 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4806 (tmm) REVERT: Au 77 GLN cc_start: 0.8518 (mt0) cc_final: 0.8297 (mt0) REVERT: Aw 134 MET cc_start: 0.8696 (ttt) cc_final: 0.8291 (ttm) REVERT: Aw 153 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8639 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8251 (mmt180) REVERT: Aw 267 MET cc_start: 0.4872 (OUTLIER) cc_final: 0.4492 (tmm) REVERT: Ay 160 MET cc_start: 0.9508 (mmm) cc_final: 0.9270 (mmp) REVERT: Ba 113 ASN cc_start: 0.9019 (m-40) cc_final: 0.8763 (m-40) REVERT: Ba 153 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8702 (mptt) REVERT: Ba 160 MET cc_start: 0.9495 (mmm) cc_final: 0.9248 (mmm) REVERT: Ba 212 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8191 (ttp80) REVERT: Ba 267 MET cc_start: 0.4895 (OUTLIER) cc_final: 0.4441 (pp-130) REVERT: Bc 53 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7926 (mttm) REVERT: Bc 267 MET cc_start: 0.4967 (OUTLIER) cc_final: 0.4421 (pp-130) REVERT: Be 153 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8579 (mptt) REVERT: Be 267 MET cc_start: 0.4751 (OUTLIER) cc_final: 0.4292 (tmm) REVERT: Bg 113 ASN cc_start: 0.9122 (m-40) cc_final: 0.8798 (m-40) REVERT: Bg 153 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8416 (mptt) REVERT: Bg 231 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8249 (mmt180) REVERT: Bi 116 MET cc_start: 0.9225 (ttp) cc_final: 0.9024 (ttt) REVERT: Bi 153 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8488 (mptt) REVERT: Bk 134 MET cc_start: 0.8725 (ttt) cc_final: 0.8494 (ttt) REVERT: Bk 153 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8483 (mttt) REVERT: Bm 53 LYS cc_start: 0.8323 (mmtt) cc_final: 0.8005 (mttp) REVERT: Bm 153 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8390 (mptt) REVERT: Bm 258 MET cc_start: 0.7170 (mtt) cc_final: 0.6953 (mtt) REVERT: Bo 54 MET cc_start: 0.8857 (ptm) cc_final: 0.8515 (ptm) REVERT: Bo 153 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8364 (mttt) REVERT: Bo 267 MET cc_start: 0.5085 (OUTLIER) cc_final: 0.4785 (tmm) REVERT: Bq 134 MET cc_start: 0.8734 (ttt) cc_final: 0.8370 (ttt) REVERT: Bq 153 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8468 (mptt) REVERT: Bq 267 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4542 (tmm) REVERT: Bs 98 GLN cc_start: 0.8733 (tt0) cc_final: 0.8521 (tt0) REVERT: Bs 153 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8263 (mttt) REVERT: Bu 53 LYS cc_start: 0.8337 (mmtt) cc_final: 0.8086 (mttm) REVERT: Bu 153 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8214 (mttt) REVERT: Bu 267 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.4317 (tmm) REVERT: Bw 53 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7840 (mtmt) REVERT: Bw 91 ASP cc_start: 0.8687 (m-30) cc_final: 0.8425 (m-30) REVERT: Bw 134 MET cc_start: 0.8646 (ttt) cc_final: 0.8379 (ttt) REVERT: Bw 160 MET cc_start: 0.9494 (mmm) cc_final: 0.9279 (mmm) REVERT: Bw 212 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8144 (ttt-90) REVERT: By 53 LYS cc_start: 0.8447 (mmtt) cc_final: 0.7888 (mtmt) REVERT: By 153 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8693 (mptt) REVERT: Ca 53 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7807 (mtmt) REVERT: Ca 134 MET cc_start: 0.8683 (ttt) cc_final: 0.8400 (ttm) REVERT: Ca 267 MET cc_start: 0.4839 (OUTLIER) cc_final: 0.4425 (tmm) REVERT: Cc 53 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7881 (mtmt) REVERT: Cc 134 MET cc_start: 0.8658 (ttt) cc_final: 0.8352 (ttt) REVERT: Cc 153 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8704 (mptt) outliers start: 59 outliers final: 10 residues processed: 1326 average time/residue: 1.4327 time to fit residues: 2346.4059 Evaluate side-chains 988 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 966 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 267 MET Chi-restraints excluded: chain Ae residue 267 MET Chi-restraints excluded: chain Ag residue 267 MET Chi-restraints excluded: chain Ai residue 267 MET Chi-restraints excluded: chain Ak residue 267 MET Chi-restraints excluded: chain Am residue 267 MET Chi-restraints excluded: chain Ao residue 267 MET Chi-restraints excluded: chain Aq residue 267 MET Chi-restraints excluded: chain As residue 108 MET Chi-restraints excluded: chain As residue 267 MET Chi-restraints excluded: chain Aw residue 267 MET Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 267 MET Chi-restraints excluded: chain Bc residue 267 MET Chi-restraints excluded: chain Be residue 267 MET Chi-restraints excluded: chain Bo residue 267 MET Chi-restraints excluded: chain Bq residue 267 MET Chi-restraints excluded: chain Bs residue 267 MET Chi-restraints excluded: chain Bu residue 267 MET Chi-restraints excluded: chain Bw residue 267 MET Chi-restraints excluded: chain By residue 267 MET Chi-restraints excluded: chain Ca residue 267 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 4.9990 chunk 466 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 314 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 482 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 chunk 359 optimal weight: 3.9990 chunk 559 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 245 ASN Ae 77 GLN Ae 82 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 82 ASN Ag 245 ASN Ai 77 GLN Ai 245 ASN Ak 77 GLN Ak 82 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN Ao 82 ASN Ao 98 GLN Aq 77 GLN Aq 82 ASN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 77 GLN Aw 82 ASN ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 245 ASN ** Bc 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 245 ASN Be 77 GLN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 245 ASN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 245 ASN Bi 113 ASN ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 245 ASN Bk 77 GLN Bm 77 GLN Bm 82 ASN Bm 245 ASN Bo 77 GLN Bo 82 ASN Bq 77 GLN Bq 82 ASN Bq 122 ASN ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 245 ASN Bs 77 GLN Bs 98 GLN ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 245 ASN Bu 77 GLN Bu 245 ASN ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 245 ASN ** By 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** By 77 GLN Ca 77 GLN ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 54376 Z= 0.311 Angle : 0.541 6.863 74144 Z= 0.276 Chirality : 0.041 0.158 8372 Planarity : 0.005 0.043 9184 Dihedral : 10.975 59.995 9166 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.21 % Allowed : 28.12 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.10), residues: 6272 helix: 0.71 (0.11), residues: 2660 sheet: 1.41 (0.26), residues: 280 loop : -1.07 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPBs 132 HIS 0.003 0.001 HISBc 259 PHE 0.015 0.003 PHEBe 202 TYR 0.016 0.001 TYRBs 198 ARG 0.003 0.000 ARGBo 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 982 time to evaluate : 4.543 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7960 (mtt-85) REVERT: Ac 113 ASN cc_start: 0.9148 (m110) cc_final: 0.8909 (m-40) REVERT: Ac 134 MET cc_start: 0.8810 (ttt) cc_final: 0.8512 (ttt) REVERT: Ag 53 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7801 (mtmt) REVERT: Ag 134 MET cc_start: 0.8867 (ttt) cc_final: 0.8655 (ttt) REVERT: Ag 153 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8064 (mptt) REVERT: Ag 177 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8111 (mttp) REVERT: Ag 191 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7769 (mtt-85) REVERT: Ag 245 ASN cc_start: 0.9164 (t0) cc_final: 0.8866 (t0) REVERT: Ai 134 MET cc_start: 0.8842 (ttt) cc_final: 0.8581 (ttt) REVERT: Ai 191 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8386 (mtt180) REVERT: Am 191 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7803 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7801 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8697 (m-30) cc_final: 0.8323 (m-30) REVERT: Ao 98 GLN cc_start: 0.8669 (tt0) cc_final: 0.8444 (tt0) REVERT: Ao 113 ASN cc_start: 0.8957 (m110) cc_final: 0.8575 (m-40) REVERT: Aq 91 ASP cc_start: 0.8715 (m-30) cc_final: 0.8248 (m-30) REVERT: Aq 135 MET cc_start: 0.8997 (mmp) cc_final: 0.8776 (mmp) REVERT: Aq 160 MET cc_start: 0.9495 (mmm) cc_final: 0.9196 (mmt) REVERT: Aq 191 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7838 (mtt-85) REVERT: As 53 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8102 (mttp) REVERT: As 113 ASN cc_start: 0.9031 (m-40) cc_final: 0.8721 (m-40) REVERT: As 191 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7755 (mtt180) REVERT: Au 191 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7960 (mtt180) REVERT: Aw 134 MET cc_start: 0.8790 (ttt) cc_final: 0.8576 (ttt) REVERT: Aw 153 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8587 (mmtt) REVERT: Aw 191 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7398 (mtt180) REVERT: Ay 113 ASN cc_start: 0.8963 (m-40) cc_final: 0.8536 (m-40) REVERT: Ay 160 MET cc_start: 0.9506 (mmm) cc_final: 0.9282 (mmp) REVERT: Ay 191 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7721 (mtt180) REVERT: Ba 113 ASN cc_start: 0.9033 (m-40) cc_final: 0.8805 (m110) REVERT: Ba 160 MET cc_start: 0.9500 (mmm) cc_final: 0.9232 (mmm) REVERT: Ba 191 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7828 (mtt90) REVERT: Ba 212 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8062 (ttp80) REVERT: Bc 113 ASN cc_start: 0.9071 (m-40) cc_final: 0.8635 (m110) REVERT: Bc 191 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7860 (mtt-85) REVERT: Bg 113 ASN cc_start: 0.9032 (m-40) cc_final: 0.8746 (m110) REVERT: Bg 153 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8396 (mttt) REVERT: Bg 191 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7710 (mtt-85) REVERT: Bi 191 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7944 (mtt180) REVERT: Bk 108 MET cc_start: 0.8988 (tpt) cc_final: 0.8766 (tpp) REVERT: Bm 153 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8406 (mptt) REVERT: Bo 153 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8329 (mttt) REVERT: Bo 191 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7646 (mtt180) REVERT: Bo 197 ARG cc_start: 0.8313 (ptm160) cc_final: 0.8006 (ptm160) REVERT: Bq 153 LYS cc_start: 0.8895 (mmtt) cc_final: 0.8405 (mptt) REVERT: Bs 54 MET cc_start: 0.9074 (ptp) cc_final: 0.8867 (ptp) REVERT: Bs 191 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7691 (mtt180) REVERT: Bw 53 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7858 (mtmt) REVERT: Bw 160 MET cc_start: 0.9486 (mmm) cc_final: 0.9257 (mmm) REVERT: By 53 LYS cc_start: 0.8470 (mmtt) cc_final: 0.7818 (mtmt) REVERT: Ca 191 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8050 (mtt-85) REVERT: Cc 53 LYS cc_start: 0.8413 (mmtt) cc_final: 0.7895 (mtmt) REVERT: Cc 134 MET cc_start: 0.8772 (ttt) cc_final: 0.8370 (ttt) REVERT: Cc 191 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7891 (mtt-85) outliers start: 231 outliers final: 113 residues processed: 1134 average time/residue: 1.3522 time to fit residues: 1916.9088 Evaluate side-chains 1040 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 905 time to evaluate : 4.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 177 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 267 MET Chi-restraints excluded: chain Aq residue 64 VAL Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 191 ARG Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 191 ARG Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 265 LYS Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Bc residue 267 MET Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 191 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 103 ILE Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 191 ARG Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bs residue 231 ARG Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Cc residue 116 MET Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Chi-restraints excluded: chain Cc residue 267 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 465 optimal weight: 8.9990 chunk 380 optimal weight: 0.0670 chunk 154 optimal weight: 10.0000 chunk 560 optimal weight: 4.9990 chunk 605 optimal weight: 9.9990 chunk 499 optimal weight: 9.9990 chunk 555 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 449 optimal weight: 1.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 245 ASN ** Ae 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 245 ASN As 82 ASN Au 98 GLN ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 82 ASN Ba 245 ASN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 245 ASN Bi 77 GLN Bi 82 ASN Bi 113 ASN ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 245 ASN Bk 82 ASN Bk 113 ASN Bk 158 GLN ** Bo 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 77 GLN Bq 122 ASN ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 245 ASN ** Bs 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 245 ASN Bu 82 ASN Bu 245 ASN ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 158 GLN By 113 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 245 ASN ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 54376 Z= 0.335 Angle : 0.545 7.450 74144 Z= 0.275 Chirality : 0.042 0.165 8372 Planarity : 0.005 0.047 9184 Dihedral : 10.804 60.089 9109 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.96 % Allowed : 27.79 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 6272 helix: 0.74 (0.11), residues: 2660 sheet: 1.57 (0.26), residues: 280 loop : -0.97 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPCc 132 HIS 0.003 0.001 HISBy 259 PHE 0.014 0.003 PHEAs 163 TYR 0.012 0.001 TYRBa 198 ARG 0.002 0.000 ARGBm 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 906 time to evaluate : 4.560 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7934 (mtt180) REVERT: Ae 53 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8008 (mmtt) REVERT: Ag 53 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7738 (mtmt) REVERT: Ag 134 MET cc_start: 0.8896 (ttt) cc_final: 0.8694 (ttt) REVERT: Ag 177 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8095 (mttp) REVERT: Ag 191 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7767 (mtt-85) REVERT: Ag 245 ASN cc_start: 0.9103 (t0) cc_final: 0.8782 (t0) REVERT: Ai 53 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7723 (mtmt) REVERT: Ai 134 MET cc_start: 0.8940 (ttt) cc_final: 0.8734 (ttm) REVERT: Ai 191 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8411 (mtt180) REVERT: Am 53 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7822 (mtmt) REVERT: Am 191 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7840 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7798 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8696 (m-30) cc_final: 0.8400 (m-30) REVERT: Ao 98 GLN cc_start: 0.8772 (tt0) cc_final: 0.8546 (tt0) REVERT: Ao 113 ASN cc_start: 0.9016 (m110) cc_final: 0.8642 (m-40) REVERT: Ao 191 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8026 (mtt90) REVERT: Aq 91 ASP cc_start: 0.8618 (m-30) cc_final: 0.8215 (m-30) REVERT: Aq 160 MET cc_start: 0.9505 (mmm) cc_final: 0.9281 (mmm) REVERT: Aq 191 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7905 (mtt-85) REVERT: As 53 LYS cc_start: 0.8266 (mmtt) cc_final: 0.8041 (mttp) REVERT: As 135 MET cc_start: 0.9046 (mmm) cc_final: 0.8482 (mmp) REVERT: As 191 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7805 (mtt180) REVERT: As 231 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8395 (mmm160) REVERT: Au 191 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8008 (mtt180) REVERT: Aw 153 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8682 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8207 (mmt180) REVERT: Ay 191 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7703 (mtt180) REVERT: Ba 53 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7539 (mmtt) REVERT: Ba 160 MET cc_start: 0.9498 (mmm) cc_final: 0.9184 (mmm) REVERT: Bc 191 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7898 (mtt-85) REVERT: Bg 113 ASN cc_start: 0.8957 (m-40) cc_final: 0.8664 (m110) REVERT: Bg 153 LYS cc_start: 0.9024 (mmpt) cc_final: 0.8401 (mttt) REVERT: Bg 191 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: Bi 191 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7930 (mtt180) REVERT: Bk 108 MET cc_start: 0.9052 (tpt) cc_final: 0.8825 (tpp) REVERT: Bk 191 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7888 (mtt-85) REVERT: Bo 191 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7619 (mtt180) REVERT: Bo 231 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8239 (mmm160) REVERT: Bq 95 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8215 (mt-10) REVERT: Bq 153 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8403 (mptt) REVERT: Bs 134 MET cc_start: 0.8907 (ttt) cc_final: 0.8640 (ttt) REVERT: Bs 191 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: Bw 53 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7854 (mtmt) REVERT: Bw 160 MET cc_start: 0.9480 (mmm) cc_final: 0.9246 (mmm) REVERT: By 53 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7844 (mtmt) REVERT: Ca 53 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7822 (mtmt) REVERT: Ca 134 MET cc_start: 0.8951 (ttt) cc_final: 0.8640 (ttt) REVERT: Ca 191 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8073 (mtt-85) REVERT: Ca 258 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6554 (mmt) REVERT: Cc 53 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7923 (mtmt) REVERT: Cc 134 MET cc_start: 0.8815 (ttt) cc_final: 0.8451 (ttt) outliers start: 272 outliers final: 136 residues processed: 1084 average time/residue: 1.4041 time to fit residues: 1891.6793 Evaluate side-chains 995 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 831 time to evaluate : 4.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ac residue 211 VAL Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 177 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 191 ARG Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 267 MET Chi-restraints excluded: chain Aq residue 64 VAL Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain As residue 231 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 267 MET Chi-restraints excluded: chain Ba residue 53 LYS Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 99 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 191 ARG Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 265 LYS Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 191 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 78 ILE Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 149 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 246 THR Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 106 THR Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 99 LEU Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 191 ARG Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 78 ILE Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bu residue 246 THR Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 149 VAL Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain By residue 267 MET Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Ca residue 258 MET Chi-restraints excluded: chain Cc residue 53 LYS Chi-restraints excluded: chain Cc residue 116 MET Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 4.9990 chunk 421 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 267 optimal weight: 0.9980 chunk 376 optimal weight: 10.0000 chunk 562 optimal weight: 6.9990 chunk 595 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 533 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 82 ASN ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 82 ASN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 82 ASN ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 77 GLN Be 77 GLN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 77 GLN Bq 122 ASN Bq 158 GLN Bs 245 ASN ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 82 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 54376 Z= 0.295 Angle : 0.524 8.687 74144 Z= 0.265 Chirality : 0.041 0.162 8372 Planarity : 0.004 0.049 9184 Dihedral : 10.704 59.954 9106 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.88 % Allowed : 27.64 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 6272 helix: 0.80 (0.11), residues: 2660 sheet: 1.60 (0.26), residues: 280 loop : -0.89 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAi 132 HIS 0.002 0.000 HISBc 259 PHE 0.014 0.002 PHEBa 202 TYR 0.012 0.001 TYRAw 180 ARG 0.002 0.000 ARGCc 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 902 time to evaluate : 4.539 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7932 (mtt180) REVERT: Ae 53 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8008 (mmtt) REVERT: Ae 197 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7740 (ptm160) REVERT: Ag 53 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7731 (mtmt) REVERT: Ag 191 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7776 (mtt-85) REVERT: Ai 53 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7728 (mtmt) REVERT: Ai 134 MET cc_start: 0.8955 (ttt) cc_final: 0.8685 (ttm) REVERT: Ai 191 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (mtt180) REVERT: Ak 108 MET cc_start: 0.9066 (tpt) cc_final: 0.8720 (tpp) REVERT: Ak 244 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: Am 53 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7815 (mtmt) REVERT: Am 191 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7934 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7792 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8699 (m-30) cc_final: 0.8407 (m-30) REVERT: Ao 113 ASN cc_start: 0.9011 (m110) cc_final: 0.8735 (m-40) REVERT: Ao 191 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8336 (mtt90) REVERT: Aq 91 ASP cc_start: 0.8587 (m-30) cc_final: 0.8209 (m-30) REVERT: Aq 160 MET cc_start: 0.9501 (mmm) cc_final: 0.9251 (mmm) REVERT: Aq 191 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7859 (mtt-85) REVERT: As 53 LYS cc_start: 0.8236 (mmtt) cc_final: 0.8013 (mttp) REVERT: As 191 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7815 (mtt180) REVERT: As 231 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8428 (mmm160) REVERT: Au 191 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8006 (mtt180) REVERT: Aw 153 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8653 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8209 (mmt180) REVERT: Ay 160 MET cc_start: 0.9486 (mmm) cc_final: 0.9192 (mmm) REVERT: Ay 191 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7684 (mtt180) REVERT: Ba 72 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7648 (mm-30) REVERT: Ba 160 MET cc_start: 0.9487 (mmm) cc_final: 0.9258 (mmm) REVERT: Bc 191 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7903 (mtt-85) REVERT: Bi 53 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8119 (mttt) REVERT: Bi 191 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7916 (mtt180) REVERT: Bk 108 MET cc_start: 0.9048 (tpt) cc_final: 0.8768 (tpp) REVERT: Bk 191 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7919 (mtt-85) REVERT: Bm 134 MET cc_start: 0.8832 (ttt) cc_final: 0.8568 (ttt) REVERT: Bm 191 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8157 (mtt-85) REVERT: Bo 191 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7729 (mtt180) REVERT: Bq 134 MET cc_start: 0.8944 (ttt) cc_final: 0.8587 (ttt) REVERT: Bq 153 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8375 (mptt) REVERT: Bs 108 MET cc_start: 0.9072 (tpt) cc_final: 0.8680 (tpt) REVERT: Bs 134 MET cc_start: 0.8982 (ttt) cc_final: 0.8677 (ttt) REVERT: Bs 191 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7711 (mtt180) REVERT: Bw 53 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7825 (mtmt) REVERT: Bw 160 MET cc_start: 0.9464 (mmm) cc_final: 0.9230 (mmm) REVERT: By 53 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7789 (mtmt) REVERT: By 191 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8027 (mtt90) REVERT: Ca 53 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7823 (mtmt) REVERT: Ca 134 MET cc_start: 0.8968 (ttt) cc_final: 0.8655 (ttt) REVERT: Ca 191 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8074 (mtt-85) REVERT: Ca 258 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6540 (mmt) REVERT: Cc 53 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7864 (mtmt) REVERT: Cc 134 MET cc_start: 0.8845 (ttt) cc_final: 0.8465 (ttt) outliers start: 268 outliers final: 149 residues processed: 1082 average time/residue: 1.4178 time to fit residues: 1902.7007 Evaluate side-chains 1005 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 826 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ac residue 211 VAL Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 197 ARG Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 244 GLU Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 191 ARG Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 64 VAL Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain As residue 231 ARG Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 103 ILE Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Ba residue 99 LEU Chi-restraints excluded: chain Ba residue 191 ARG Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 265 LYS Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 246 THR Chi-restraints excluded: chain Bi residue 53 LYS Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 78 ILE Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bi residue 257 SER Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 81 SER Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 246 THR Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bq residue 255 SER Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 99 LEU Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 173 MET Chi-restraints excluded: chain Bs residue 191 ARG Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bu residue 246 THR Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 265 LYS Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 191 ARG Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 99 LEU Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Ca residue 258 MET Chi-restraints excluded: chain Cc residue 53 LYS Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 116 MET Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 10.0000 chunk 337 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 443 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 508 optimal weight: 2.9990 chunk 411 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 534 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN Ao 77 GLN ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 82 ASN ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 82 ASN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 113 ASN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 77 GLN Bq 122 ASN ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** By 82 ASN ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 54376 Z= 0.425 Angle : 0.584 10.057 74144 Z= 0.294 Chirality : 0.044 0.179 8372 Planarity : 0.005 0.052 9184 Dihedral : 10.883 60.281 9100 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.19 % Allowed : 27.19 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 6272 helix: 0.64 (0.11), residues: 2660 sheet: 1.58 (0.26), residues: 280 loop : -0.96 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPCc 132 HIS 0.003 0.001 HISCc 259 PHE 0.017 0.003 PHEBa 163 TYR 0.016 0.002 TYRBs 198 ARG 0.003 0.000 ARGBw 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 853 time to evaluate : 4.677 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7945 (mtt180) REVERT: Ae 53 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7916 (mmtt) REVERT: Ae 197 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7865 (ptm160) REVERT: Ag 53 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7750 (mtmt) REVERT: Ag 191 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7778 (mtt-85) REVERT: Ai 53 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7697 (mtmt) REVERT: Ai 191 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8436 (mtt180) REVERT: Ak 244 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: Am 53 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7807 (mtmt) REVERT: Am 191 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7970 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7826 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8708 (m-30) cc_final: 0.8440 (m-30) REVERT: Aq 91 ASP cc_start: 0.8585 (m-30) cc_final: 0.8215 (m-30) REVERT: Aq 160 MET cc_start: 0.9504 (mmm) cc_final: 0.9247 (mmm) REVERT: Aq 191 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7895 (mtt-85) REVERT: As 53 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7995 (mttp) REVERT: As 191 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7803 (mtt180) REVERT: Au 191 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8049 (mtt180) REVERT: Aw 102 ASP cc_start: 0.8422 (t0) cc_final: 0.8213 (t0) REVERT: Aw 153 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8723 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8621 (mmm160) cc_final: 0.8252 (mmt180) REVERT: Ay 191 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7701 (mtt180) REVERT: Ba 160 MET cc_start: 0.9496 (mmm) cc_final: 0.9254 (mmm) REVERT: Bc 191 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7886 (mtt-85) REVERT: Be 95 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8182 (mt-10) REVERT: Be 134 MET cc_start: 0.8958 (ttt) cc_final: 0.8696 (ttt) REVERT: Bi 191 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7925 (mtt180) REVERT: Bk 191 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7912 (mtt-85) REVERT: Bm 191 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8155 (mtt-85) REVERT: Bm 267 MET cc_start: 0.4149 (mtp) cc_final: 0.3890 (mtp) REVERT: Bo 191 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7799 (mtt180) REVERT: Bq 134 MET cc_start: 0.8965 (ttt) cc_final: 0.8604 (ttt) REVERT: Bq 153 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8408 (mptt) REVERT: Bs 198 TYR cc_start: 0.9403 (m-80) cc_final: 0.8938 (m-80) REVERT: Bw 53 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7857 (mtmt) REVERT: Bw 160 MET cc_start: 0.9465 (mmm) cc_final: 0.9235 (mmm) REVERT: By 53 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7760 (mtmt) REVERT: Ca 53 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7841 (mtmt) REVERT: Ca 134 MET cc_start: 0.8986 (ttt) cc_final: 0.8664 (ttt) REVERT: Ca 191 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8098 (mtt-85) REVERT: Ca 258 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6388 (mmt) REVERT: Cc 53 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7846 (mtmt) REVERT: Cc 134 MET cc_start: 0.8880 (ttt) cc_final: 0.8555 (ttt) REVERT: Cc 191 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7977 (mtt-85) outliers start: 285 outliers final: 178 residues processed: 1051 average time/residue: 1.3986 time to fit residues: 1829.3052 Evaluate side-chains 1012 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 807 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 53 LYS Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Aa residue 255 SER Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ac residue 211 VAL Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 197 ARG Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 81 SER Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 81 SER Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 244 GLU Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 191 ARG Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 64 VAL Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 103 ILE Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 80 ILE Chi-restraints excluded: chain Ba residue 81 SER Chi-restraints excluded: chain Ba residue 99 LEU Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 191 ARG Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Ba residue 265 LYS Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Bc residue 255 SER Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 81 SER Chi-restraints excluded: chain Bg residue 141 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 246 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 78 ILE Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 246 THR Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bi residue 257 SER Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 81 SER Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 99 LEU Chi-restraints excluded: chain Bm residue 141 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 103 ILE Chi-restraints excluded: chain Bq residue 124 THR Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 236 ASP Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bq residue 255 SER Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 99 LEU Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 173 MET Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bs residue 231 ARG Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 78 ILE Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bu residue 246 THR Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 78 ILE Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 258 MET Chi-restraints excluded: chain Bw residue 265 LYS Chi-restraints excluded: chain By residue 53 LYS Chi-restraints excluded: chain By residue 64 VAL Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 99 LEU Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Ca residue 258 MET Chi-restraints excluded: chain Cc residue 53 LYS Chi-restraints excluded: chain Cc residue 56 MET Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 103 ILE Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 141 VAL Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Chi-restraints excluded: chain Cc residue 267 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 6.9990 chunk 536 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 349 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 596 optimal weight: 8.9990 chunk 494 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 122 ASN ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 77 GLN Be 77 GLN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 77 GLN Bq 122 ASN ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 54376 Z= 0.159 Angle : 0.484 9.736 74144 Z= 0.243 Chirality : 0.038 0.143 8372 Planarity : 0.004 0.049 9184 Dihedral : 10.353 59.567 9100 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.26 % Allowed : 29.17 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 6272 helix: 1.13 (0.11), residues: 2492 sheet: -0.16 (0.25), residues: 392 loop : -0.83 (0.11), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAq 132 HIS 0.003 0.000 HISAy 259 PHE 0.013 0.002 PHEBs 202 TYR 0.012 0.001 TYRAw 180 ARG 0.001 0.000 ARGBi 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 948 time to evaluate : 4.700 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7886 (mtt180) REVERT: Ac 113 ASN cc_start: 0.8964 (m110) cc_final: 0.8687 (m-40) REVERT: Ae 53 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8001 (mmtt) REVERT: Ag 53 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7801 (mtmt) REVERT: Ag 153 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8277 (mptt) REVERT: Ag 191 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7758 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7736 (mtmt) REVERT: Ai 191 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8424 (mtt180) REVERT: Am 53 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7824 (mtmt) REVERT: Am 191 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7800 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7821 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8671 (m-30) cc_final: 0.8434 (m-30) REVERT: Ao 191 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8064 (mtt90) REVERT: Aq 91 ASP cc_start: 0.8557 (m-30) cc_final: 0.8170 (m-30) REVERT: Aq 191 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7869 (mtt-85) REVERT: As 53 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7990 (mttp) REVERT: As 191 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7767 (mtt180) REVERT: As 231 ARG cc_start: 0.8582 (mmt180) cc_final: 0.8369 (mmm160) REVERT: Au 191 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7972 (mtt-85) REVERT: Aw 153 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8777 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8117 (mmt180) REVERT: Ay 160 MET cc_start: 0.9474 (mmm) cc_final: 0.9170 (mmm) REVERT: Ay 191 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7652 (mtt180) REVERT: Ba 160 MET cc_start: 0.9461 (mmm) cc_final: 0.9196 (mmm) REVERT: Ba 265 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7125 (mttm) REVERT: Bc 191 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: Be 134 MET cc_start: 0.8860 (ttt) cc_final: 0.8642 (ttt) REVERT: Bg 153 LYS cc_start: 0.8991 (mmpt) cc_final: 0.8297 (mttt) REVERT: Bg 231 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8205 (mmt180) REVERT: Bi 191 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7911 (mtt-85) REVERT: Bk 108 MET cc_start: 0.8983 (tpt) cc_final: 0.8665 (tpp) REVERT: Bk 191 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7993 (mtt-85) REVERT: Bm 191 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8119 (mtt-85) REVERT: Bo 191 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7761 (mtt180) REVERT: Bq 134 MET cc_start: 0.8884 (ttt) cc_final: 0.8580 (ttt) REVERT: Bq 153 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8451 (mptt) REVERT: Bs 108 MET cc_start: 0.8983 (tpt) cc_final: 0.8723 (tpt) REVERT: Bw 53 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7782 (mtmt) REVERT: Bw 160 MET cc_start: 0.9445 (mmm) cc_final: 0.9168 (mmm) REVERT: By 53 LYS cc_start: 0.8452 (mmtt) cc_final: 0.7814 (mtmt) REVERT: Ca 53 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7815 (mtmt) REVERT: Ca 134 MET cc_start: 0.8924 (ttt) cc_final: 0.8634 (ttt) REVERT: Ca 191 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8024 (mtt-85) REVERT: Ca 258 MET cc_start: 0.6848 (mtt) cc_final: 0.6279 (mmt) REVERT: Cc 53 LYS cc_start: 0.8406 (mmtt) cc_final: 0.7854 (mtmt) REVERT: Cc 134 MET cc_start: 0.8801 (ttt) cc_final: 0.8545 (ttt) REVERT: Cc 191 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7859 (mtt-85) outliers start: 179 outliers final: 86 residues processed: 1071 average time/residue: 1.4341 time to fit residues: 1902.4580 Evaluate side-chains 977 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 868 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 191 ARG Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 124 THR Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 265 LYS Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bi residue 257 SER Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 124 THR Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bq residue 255 SER Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Cc residue 56 MET Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 339 optimal weight: 10.0000 chunk 435 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 501 optimal weight: 7.9990 chunk 332 optimal weight: 0.0070 chunk 593 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 361 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 82 ASN ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ba 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Be 82 ASN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 82 ASN Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 77 GLN ** Bq 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 82 ASN ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** By 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54376 Z= 0.202 Angle : 0.500 11.227 74144 Z= 0.249 Chirality : 0.039 0.141 8372 Planarity : 0.004 0.049 9184 Dihedral : 10.494 59.664 9100 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.77 % Allowed : 28.50 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.11), residues: 6272 helix: 1.11 (0.11), residues: 2660 sheet: 0.88 (0.24), residues: 336 loop : -0.67 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAy 132 HIS 0.001 0.000 HISCc 259 PHE 0.013 0.002 PHEBg 202 TYR 0.012 0.001 TYRCc 180 ARG 0.001 0.000 ARGBg 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 903 time to evaluate : 4.633 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7884 (mtt180) REVERT: Ac 113 ASN cc_start: 0.8984 (m110) cc_final: 0.8696 (m-40) REVERT: Ac 134 MET cc_start: 0.8832 (ttt) cc_final: 0.8612 (ttt) REVERT: Ae 53 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7990 (mmtt) REVERT: Ag 53 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7888 (mtmt) REVERT: Ag 56 MET cc_start: 0.9093 (mtp) cc_final: 0.8875 (ttm) REVERT: Ag 153 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8224 (mptt) REVERT: Ag 191 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7787 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7724 (mtmt) REVERT: Ai 191 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8138 (mtt180) REVERT: Am 53 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7759 (mtmt) REVERT: Am 191 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7941 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8398 (mmtt) cc_final: 0.7786 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8699 (m-30) cc_final: 0.8448 (m-30) REVERT: Ao 113 ASN cc_start: 0.8830 (m110) cc_final: 0.8488 (m110) REVERT: Ao 191 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8258 (mtt90) REVERT: Aq 72 GLU cc_start: 0.7560 (pt0) cc_final: 0.6988 (pp20) REVERT: Aq 91 ASP cc_start: 0.8528 (m-30) cc_final: 0.8152 (m-30) REVERT: Aq 191 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7889 (mtt-85) REVERT: As 53 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7975 (mttp) REVERT: As 191 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7771 (mtt180) REVERT: As 231 ARG cc_start: 0.8653 (mmt180) cc_final: 0.8401 (mmm160) REVERT: Au 191 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7977 (mtt180) REVERT: Aw 153 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8758 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8038 (mmt180) REVERT: Ay 191 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7666 (mtt180) REVERT: Ba 160 MET cc_start: 0.9458 (mmm) cc_final: 0.9079 (mmm) REVERT: Bc 191 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7875 (mtt-85) REVERT: Bg 231 ARG cc_start: 0.8552 (mmm160) cc_final: 0.8030 (mmt180) REVERT: Bi 191 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7911 (mtt-85) REVERT: Bk 108 MET cc_start: 0.9015 (tpt) cc_final: 0.8676 (tpp) REVERT: Bk 191 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7983 (mtt-85) REVERT: Bm 191 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8069 (mtt-85) REVERT: Bo 191 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7761 (mtt180) REVERT: Bq 153 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8457 (mptt) REVERT: Bs 108 MET cc_start: 0.9030 (tpt) cc_final: 0.8694 (tpt) REVERT: Bs 134 MET cc_start: 0.8887 (ttt) cc_final: 0.8630 (ttt) REVERT: Bs 153 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8278 (mttt) REVERT: Bu 72 GLU cc_start: 0.7695 (pt0) cc_final: 0.7130 (pp20) REVERT: Bw 53 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7839 (mtmt) REVERT: Bw 160 MET cc_start: 0.9443 (mmm) cc_final: 0.9201 (mmm) REVERT: By 53 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7786 (mtmt) REVERT: By 113 ASN cc_start: 0.8205 (m110) cc_final: 0.7871 (m110) REVERT: Ca 53 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7812 (mtmt) REVERT: Ca 134 MET cc_start: 0.8934 (ttt) cc_final: 0.8669 (ttt) REVERT: Ca 191 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8029 (mtt-85) REVERT: Ca 258 MET cc_start: 0.6865 (mtt) cc_final: 0.6308 (mmt) REVERT: Cc 53 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7834 (mtmt) REVERT: Cc 134 MET cc_start: 0.8834 (ttt) cc_final: 0.8575 (ttt) REVERT: Cc 191 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7925 (mtt-85) outliers start: 207 outliers final: 127 residues processed: 1056 average time/residue: 1.4159 time to fit residues: 1860.9128 Evaluate side-chains 1020 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 871 time to evaluate : 4.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 153 LYS Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 81 SER Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 191 ARG Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 191 ARG Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 135 MET Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 81 SER Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 236 ASP Chi-restraints excluded: chain Bg residue 250 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 246 THR Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 53 LYS Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 99 LEU Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Cc residue 56 MET Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 377 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 466 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 69 HIS ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 77 GLN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 245 ASN ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 98 GLN ** Ay 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 69 HIS ** Be 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bo 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 77 GLN ** Bq 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 77 GLN ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 82 ASN ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 54376 Z= 0.375 Angle : 0.570 11.953 74144 Z= 0.285 Chirality : 0.043 0.168 8372 Planarity : 0.005 0.051 9184 Dihedral : 10.798 60.155 9100 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.28 % Allowed : 27.77 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.11), residues: 6272 helix: 0.89 (0.10), residues: 2660 sheet: 1.38 (0.25), residues: 280 loop : -0.87 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAy 132 HIS 0.003 0.001 HISBs 259 PHE 0.016 0.003 PHEBa 163 TYR 0.014 0.001 TYRAw 180 ARG 0.002 0.000 ARGBo 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 861 time to evaluate : 4.556 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7897 (mtt180) REVERT: Ac 134 MET cc_start: 0.8961 (ttt) cc_final: 0.8694 (ttt) REVERT: Ae 53 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7970 (mmtt) REVERT: Ag 53 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7838 (mtmt) REVERT: Ag 153 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8185 (mptt) REVERT: Ag 191 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7775 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7710 (mtmt) REVERT: Am 53 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7827 (mtmt) REVERT: Am 191 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7972 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7864 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8678 (m-30) cc_final: 0.8415 (m-30) REVERT: Ao 113 ASN cc_start: 0.9122 (m110) cc_final: 0.8801 (m-40) REVERT: Aq 72 GLU cc_start: 0.7639 (pt0) cc_final: 0.7176 (pp20) REVERT: Aq 91 ASP cc_start: 0.8562 (m-30) cc_final: 0.8226 (m-30) REVERT: Aq 143 TYR cc_start: 0.9053 (m-80) cc_final: 0.8762 (m-80) REVERT: Aq 191 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7883 (mtt-85) REVERT: As 53 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7979 (mttp) REVERT: As 191 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7781 (mtt180) REVERT: As 231 ARG cc_start: 0.8694 (mmt180) cc_final: 0.8344 (mmm160) REVERT: Au 191 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8011 (mtt180) REVERT: Aw 153 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8704 (mmtt) REVERT: Aw 231 ARG cc_start: 0.8547 (mmm160) cc_final: 0.8134 (mmt180) REVERT: Ay 191 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7673 (mtt180) REVERT: Ba 160 MET cc_start: 0.9491 (mmm) cc_final: 0.9132 (mmm) REVERT: Bc 191 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: Bi 191 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7918 (mtt180) REVERT: Bk 72 GLU cc_start: 0.7707 (pt0) cc_final: 0.7364 (pp20) REVERT: Bk 191 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7915 (mtt-85) REVERT: Bm 191 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8169 (mtt-85) REVERT: Bo 72 GLU cc_start: 0.7594 (pt0) cc_final: 0.7146 (pp20) REVERT: Bo 191 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7778 (mtt180) REVERT: Bq 153 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8427 (mptt) REVERT: Bs 72 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7235 (pp20) REVERT: Bs 134 MET cc_start: 0.8971 (ttt) cc_final: 0.8648 (ttt) REVERT: Bu 72 GLU cc_start: 0.7763 (pt0) cc_final: 0.7267 (pp20) REVERT: Bw 72 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7012 (pp20) REVERT: Bw 160 MET cc_start: 0.9459 (mmm) cc_final: 0.9238 (mmm) REVERT: By 53 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7767 (mtmt) REVERT: By 191 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8244 (mtt180) REVERT: Ca 72 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: Ca 134 MET cc_start: 0.8975 (ttt) cc_final: 0.8647 (ttt) REVERT: Ca 191 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8077 (mtt-85) REVERT: Ca 258 MET cc_start: 0.6975 (mtt) cc_final: 0.6415 (mmt) REVERT: Cc 134 MET cc_start: 0.8887 (ttt) cc_final: 0.8607 (ttt) REVERT: Cc 191 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7931 (mtt-85) outliers start: 235 outliers final: 156 residues processed: 1034 average time/residue: 1.3993 time to fit residues: 1803.7784 Evaluate side-chains 1011 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 831 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 153 LYS Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 53 LYS Chi-restraints excluded: chain Ae residue 64 VAL Chi-restraints excluded: chain Ae residue 81 SER Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 53 LYS Chi-restraints excluded: chain Ag residue 64 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 164 SER Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 207 SER Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 81 SER Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ai residue 211 VAL Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 81 SER Chi-restraints excluded: chain Ak residue 164 SER Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 53 LYS Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 54 MET Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 81 SER Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 191 ARG Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Ao residue 255 SER Chi-restraints excluded: chain Aq residue 81 SER Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 211 VAL Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 81 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 124 THR Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 141 VAL Chi-restraints excluded: chain Ba residue 207 SER Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 135 MET Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 211 VAL Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 81 SER Chi-restraints excluded: chain Bg residue 99 LEU Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 211 VAL Chi-restraints excluded: chain Bg residue 246 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 78 ILE Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 191 ARG Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bi residue 246 THR Chi-restraints excluded: chain Bi residue 255 SER Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 191 ARG Chi-restraints excluded: chain Bk residue 207 SER Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bk residue 246 THR Chi-restraints excluded: chain Bm residue 64 VAL Chi-restraints excluded: chain Bm residue 81 SER Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 64 VAL Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 255 SER Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 81 SER Chi-restraints excluded: chain Bq residue 103 ILE Chi-restraints excluded: chain Bq residue 124 THR Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 236 ASP Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bq residue 255 SER Chi-restraints excluded: chain Bs residue 64 VAL Chi-restraints excluded: chain Bs residue 72 GLU Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 103 ILE Chi-restraints excluded: chain Bs residue 141 VAL Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bu residue 64 VAL Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 64 VAL Chi-restraints excluded: chain Bw residue 72 GLU Chi-restraints excluded: chain Bw residue 78 ILE Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 141 VAL Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain Bw residue 258 MET Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 191 ARG Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 64 VAL Chi-restraints excluded: chain Ca residue 72 GLU Chi-restraints excluded: chain Ca residue 191 ARG Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Ca residue 255 SER Chi-restraints excluded: chain Cc residue 56 MET Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 103 ILE Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 5.9990 chunk 568 optimal weight: 0.9990 chunk 518 optimal weight: 0.9990 chunk 553 optimal weight: 1.9990 chunk 333 optimal weight: 4.9990 chunk 241 optimal weight: 0.7980 chunk 434 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 499 optimal weight: 5.9990 chunk 523 optimal weight: 1.9990 chunk 551 optimal weight: 0.0040 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 245 ASN ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 77 GLN Am 113 ASN ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 113 ASN Ba 245 ASN Bc 77 GLN Be 77 GLN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 82 ASN ** Bo 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bs 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 54376 Z= 0.135 Angle : 0.484 12.519 74144 Z= 0.241 Chirality : 0.038 0.140 8372 Planarity : 0.004 0.049 9184 Dihedral : 10.252 59.376 9100 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.13 % Allowed : 29.85 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.11), residues: 6272 helix: 1.23 (0.10), residues: 2660 sheet: 0.89 (0.24), residues: 336 loop : -0.71 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAq 132 HIS 0.002 0.000 HISAk 69 PHE 0.012 0.002 PHEAq 202 TYR 0.012 0.001 TYRAk 198 ARG 0.001 0.000 ARGBa 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 965 time to evaluate : 5.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 191 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7874 (mtt180) REVERT: Ac 113 ASN cc_start: 0.8908 (m110) cc_final: 0.8611 (m110) REVERT: Ag 153 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8275 (mptt) REVERT: Ag 191 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7700 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7762 (mtmt) REVERT: Am 53 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7758 (mtmt) REVERT: Am 191 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7838 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8424 (mmtt) cc_final: 0.7827 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8659 (m-30) cc_final: 0.8435 (m-30) REVERT: Ao 112 MET cc_start: 0.9232 (mmp) cc_final: 0.8985 (mmp) REVERT: Ao 113 ASN cc_start: 0.8677 (m110) cc_final: 0.8395 (m110) REVERT: Aq 72 GLU cc_start: 0.7591 (pt0) cc_final: 0.7126 (pp20) REVERT: Aq 91 ASP cc_start: 0.8556 (m-30) cc_final: 0.8170 (m-30) REVERT: Aq 191 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7896 (mtt180) REVERT: As 53 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7976 (mttp) REVERT: As 191 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7526 (mtt180) REVERT: As 231 ARG cc_start: 0.8656 (mmt180) cc_final: 0.8347 (mmm160) REVERT: Au 191 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7923 (mtt180) REVERT: Aw 72 GLU cc_start: 0.7516 (pp20) cc_final: 0.6912 (pp20) REVERT: Aw 231 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8016 (mmt180) REVERT: Ay 160 MET cc_start: 0.9448 (mmm) cc_final: 0.9198 (mmm) REVERT: Ay 191 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7678 (mtt180) REVERT: Ba 113 ASN cc_start: 0.8741 (m-40) cc_final: 0.8479 (m110) REVERT: Ba 160 MET cc_start: 0.9446 (mmm) cc_final: 0.9164 (mmm) REVERT: Bc 191 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7874 (mtt180) REVERT: Be 181 MET cc_start: 0.9319 (tpp) cc_final: 0.9095 (tpp) REVERT: Bg 231 ARG cc_start: 0.8528 (mmm160) cc_final: 0.8022 (mmt180) REVERT: Bi 82 ASN cc_start: 0.8348 (t0) cc_final: 0.8112 (t0) REVERT: Bk 108 MET cc_start: 0.8960 (tpt) cc_final: 0.8611 (tpp) REVERT: Bm 82 ASN cc_start: 0.7690 (t0) cc_final: 0.7439 (t0) REVERT: Bm 191 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8049 (mtt-85) REVERT: Bo 72 GLU cc_start: 0.7650 (pt0) cc_final: 0.7208 (pp20) REVERT: Bo 191 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7746 (mtt180) REVERT: Bo 231 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8025 (mmm160) REVERT: Bo 267 MET cc_start: 0.5090 (OUTLIER) cc_final: 0.4808 (pp-130) REVERT: Bq 153 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8396 (mptt) REVERT: Bu 72 GLU cc_start: 0.7734 (pt0) cc_final: 0.7297 (pp20) REVERT: Bu 113 ASN cc_start: 0.8485 (m110) cc_final: 0.8121 (m110) REVERT: Bw 53 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7781 (mtmt) REVERT: Bw 160 MET cc_start: 0.9422 (mmm) cc_final: 0.9145 (mmm) REVERT: Bw 212 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8037 (ttt-90) REVERT: By 53 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7786 (mtmt) REVERT: By 72 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7077 (pp20) REVERT: By 113 ASN cc_start: 0.7931 (m110) cc_final: 0.7710 (m110) REVERT: By 191 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8165 (mtt180) REVERT: Ca 72 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6982 (pp20) REVERT: Ca 113 ASN cc_start: 0.8151 (m110) cc_final: 0.7860 (m110) REVERT: Ca 134 MET cc_start: 0.8911 (ttt) cc_final: 0.8647 (ttt) REVERT: Ca 258 MET cc_start: 0.6779 (mtt) cc_final: 0.6244 (mmt) REVERT: Cc 53 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7769 (mtmt) REVERT: Cc 134 MET cc_start: 0.8788 (ttt) cc_final: 0.8562 (ttt) REVERT: Cc 191 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7888 (mtt-85) outliers start: 117 outliers final: 79 residues processed: 1055 average time/residue: 1.4110 time to fit residues: 1851.2049 Evaluate side-chains 1001 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 904 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ak residue 164 SER Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 81 SER Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 250 THR Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bk residue 54 MET Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bo residue 267 MET Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 72 GLU Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 191 ARG Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 72 GLU Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Cc residue 56 MET Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 10.0000 chunk 585 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 chunk 277 optimal weight: 3.9990 chunk 406 optimal weight: 5.9990 chunk 613 optimal weight: 10.0000 chunk 564 optimal weight: 0.8980 chunk 488 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 377 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 69 HIS ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 69 HIS Be 113 ASN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 69 HIS ** Bq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN Bw 82 ASN ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** By 189 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 189 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 54376 Z= 0.302 Angle : 0.553 13.247 74144 Z= 0.274 Chirality : 0.041 0.152 8372 Planarity : 0.004 0.050 9184 Dihedral : 10.685 59.918 9100 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.61 % Allowed : 29.45 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 6272 helix: 1.10 (0.10), residues: 2660 sheet: 0.71 (0.23), residues: 336 loop : -0.75 (0.11), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAu 132 HIS 0.003 0.000 HISAg 259 PHE 0.014 0.002 PHEBa 163 TYR 0.027 0.001 TYRBs 198 ARG 0.003 0.000 ARGAi 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12544 Ramachandran restraints generated. 6272 Oldfield, 0 Emsley, 6272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1028 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 885 time to evaluate : 4.694 Fit side-chains REVERT: Aa 191 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7900 (mtt180) REVERT: Ac 113 ASN cc_start: 0.9069 (m110) cc_final: 0.8767 (m-40) REVERT: Ag 153 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8194 (mptt) REVERT: Ag 191 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7764 (mtt180) REVERT: Ai 53 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7719 (mtmt) REVERT: Ak 244 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: Am 53 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7833 (mtmt) REVERT: Am 191 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7946 (mtt180) REVERT: Ao 53 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7794 (mtmt) REVERT: Ao 91 ASP cc_start: 0.8680 (m-30) cc_final: 0.8402 (m-30) REVERT: Ao 113 ASN cc_start: 0.8995 (m110) cc_final: 0.8727 (m-40) REVERT: Ao 191 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8033 (mtt90) REVERT: Aq 72 GLU cc_start: 0.7644 (pt0) cc_final: 0.7180 (pp20) REVERT: Aq 91 ASP cc_start: 0.8524 (m-30) cc_final: 0.8185 (m-30) REVERT: Aq 191 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7856 (mtt-85) REVERT: As 53 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7967 (mttp) REVERT: As 191 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7775 (mtt180) REVERT: As 231 ARG cc_start: 0.8685 (mmt180) cc_final: 0.8343 (mmm160) REVERT: Au 191 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: Aw 72 GLU cc_start: 0.7591 (pp20) cc_final: 0.6982 (pp20) REVERT: Aw 231 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8085 (mmt180) REVERT: Ay 113 ASN cc_start: 0.8895 (m110) cc_final: 0.8556 (m-40) REVERT: Ay 191 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7661 (mtt180) REVERT: Ba 160 MET cc_start: 0.9471 (mmm) cc_final: 0.9094 (mmm) REVERT: Ba 231 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8193 (mmt180) REVERT: Bc 191 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7875 (mtt-85) REVERT: Bg 231 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8067 (mmt180) REVERT: Bm 191 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8155 (mtt-85) REVERT: Bo 72 GLU cc_start: 0.7648 (pt0) cc_final: 0.7251 (pp20) REVERT: Bo 191 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7759 (mtt180) REVERT: Bo 231 ARG cc_start: 0.8529 (mmm160) cc_final: 0.8211 (mmm160) REVERT: Bq 153 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8466 (mptt) REVERT: Bs 153 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8261 (mttt) REVERT: Bs 198 TYR cc_start: 0.9258 (m-10) cc_final: 0.8936 (m-80) REVERT: Bw 53 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: Bw 72 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6932 (pp20) REVERT: Bw 160 MET cc_start: 0.9459 (mmm) cc_final: 0.9245 (mmm) REVERT: By 53 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7753 (mtmt) REVERT: By 72 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6944 (pp20) REVERT: By 191 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8172 (mtt90) REVERT: Ca 72 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7023 (pp20) REVERT: Ca 134 MET cc_start: 0.8958 (ttt) cc_final: 0.8700 (ttt) REVERT: Ca 258 MET cc_start: 0.6947 (mtt) cc_final: 0.6390 (mmt) REVERT: Cc 134 MET cc_start: 0.8859 (ttt) cc_final: 0.8623 (ttt) REVERT: Cc 191 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7949 (mtt-85) outliers start: 143 outliers final: 103 residues processed: 998 average time/residue: 1.4251 time to fit residues: 1766.8606 Evaluate side-chains 987 residues out of total 5488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 863 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 64 VAL Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 191 ARG Chi-restraints excluded: chain Aa residue 207 SER Chi-restraints excluded: chain Aa residue 211 VAL Chi-restraints excluded: chain Ac residue 64 VAL Chi-restraints excluded: chain Ac residue 81 SER Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 207 SER Chi-restraints excluded: chain Ae residue 153 LYS Chi-restraints excluded: chain Ae residue 207 SER Chi-restraints excluded: chain Ae residue 211 VAL Chi-restraints excluded: chain Ag residue 153 LYS Chi-restraints excluded: chain Ag residue 191 ARG Chi-restraints excluded: chain Ag residue 211 VAL Chi-restraints excluded: chain Ag residue 255 SER Chi-restraints excluded: chain Ai residue 53 LYS Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 81 SER Chi-restraints excluded: chain Ai residue 207 SER Chi-restraints excluded: chain Ak residue 81 SER Chi-restraints excluded: chain Ak residue 164 SER Chi-restraints excluded: chain Ak residue 207 SER Chi-restraints excluded: chain Ak residue 211 VAL Chi-restraints excluded: chain Ak residue 244 GLU Chi-restraints excluded: chain Ak residue 255 SER Chi-restraints excluded: chain Am residue 64 VAL Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 191 ARG Chi-restraints excluded: chain Am residue 207 SER Chi-restraints excluded: chain Am residue 255 SER Chi-restraints excluded: chain Ao residue 53 LYS Chi-restraints excluded: chain Ao residue 64 VAL Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 191 ARG Chi-restraints excluded: chain Ao residue 207 SER Chi-restraints excluded: chain Ao residue 211 VAL Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 191 ARG Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain Aq residue 246 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 191 ARG Chi-restraints excluded: chain As residue 207 SER Chi-restraints excluded: chain As residue 211 VAL Chi-restraints excluded: chain Au residue 64 VAL Chi-restraints excluded: chain Au residue 81 SER Chi-restraints excluded: chain Au residue 191 ARG Chi-restraints excluded: chain Au residue 207 SER Chi-restraints excluded: chain Au residue 211 VAL Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 81 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 207 SER Chi-restraints excluded: chain Aw residue 211 VAL Chi-restraints excluded: chain Aw residue 255 SER Chi-restraints excluded: chain Ay residue 64 VAL Chi-restraints excluded: chain Ay residue 106 THR Chi-restraints excluded: chain Ay residue 124 THR Chi-restraints excluded: chain Ay residue 191 ARG Chi-restraints excluded: chain Ay residue 207 SER Chi-restraints excluded: chain Ay residue 211 VAL Chi-restraints excluded: chain Ay residue 255 SER Chi-restraints excluded: chain Ba residue 64 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 191 ARG Chi-restraints excluded: chain Bc residue 207 SER Chi-restraints excluded: chain Bc residue 211 VAL Chi-restraints excluded: chain Be residue 81 SER Chi-restraints excluded: chain Be residue 207 SER Chi-restraints excluded: chain Be residue 255 SER Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 81 SER Chi-restraints excluded: chain Bg residue 197 ARG Chi-restraints excluded: chain Bg residue 207 SER Chi-restraints excluded: chain Bg residue 246 THR Chi-restraints excluded: chain Bg residue 250 THR Chi-restraints excluded: chain Bi residue 141 VAL Chi-restraints excluded: chain Bi residue 207 SER Chi-restraints excluded: chain Bi residue 211 VAL Chi-restraints excluded: chain Bi residue 231 ARG Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 211 VAL Chi-restraints excluded: chain Bm residue 191 ARG Chi-restraints excluded: chain Bm residue 207 SER Chi-restraints excluded: chain Bm residue 211 VAL Chi-restraints excluded: chain Bm residue 255 SER Chi-restraints excluded: chain Bo residue 103 ILE Chi-restraints excluded: chain Bo residue 124 THR Chi-restraints excluded: chain Bo residue 191 ARG Chi-restraints excluded: chain Bo residue 207 SER Chi-restraints excluded: chain Bo residue 211 VAL Chi-restraints excluded: chain Bq residue 64 VAL Chi-restraints excluded: chain Bq residue 141 VAL Chi-restraints excluded: chain Bq residue 207 SER Chi-restraints excluded: chain Bq residue 211 VAL Chi-restraints excluded: chain Bq residue 246 THR Chi-restraints excluded: chain Bs residue 81 SER Chi-restraints excluded: chain Bs residue 207 SER Chi-restraints excluded: chain Bs residue 211 VAL Chi-restraints excluded: chain Bu residue 141 VAL Chi-restraints excluded: chain Bu residue 207 SER Chi-restraints excluded: chain Bu residue 211 VAL Chi-restraints excluded: chain Bw residue 53 LYS Chi-restraints excluded: chain Bw residue 72 GLU Chi-restraints excluded: chain Bw residue 81 SER Chi-restraints excluded: chain Bw residue 103 ILE Chi-restraints excluded: chain Bw residue 207 SER Chi-restraints excluded: chain Bw residue 211 VAL Chi-restraints excluded: chain Bw residue 231 ARG Chi-restraints excluded: chain By residue 72 GLU Chi-restraints excluded: chain By residue 99 LEU Chi-restraints excluded: chain By residue 191 ARG Chi-restraints excluded: chain By residue 207 SER Chi-restraints excluded: chain By residue 211 VAL Chi-restraints excluded: chain Ca residue 72 GLU Chi-restraints excluded: chain Ca residue 207 SER Chi-restraints excluded: chain Ca residue 211 VAL Chi-restraints excluded: chain Cc residue 56 MET Chi-restraints excluded: chain Cc residue 81 SER Chi-restraints excluded: chain Cc residue 106 THR Chi-restraints excluded: chain Cc residue 191 ARG Chi-restraints excluded: chain Cc residue 207 SER Chi-restraints excluded: chain Cc residue 211 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 1.9990 chunk 520 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 450 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 489 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 502 optimal weight: 0.0070 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 77 GLN ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 77 GLN ** Be 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 98 GLN ** Bg 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bq 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bs 98 GLN ** Bs 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** By 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** By 189 ASN ** Ca 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 189 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.115068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.093409 restraints weight = 68392.101| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.95 r_work: 0.2798 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54376 Z= 0.193 Angle : 0.518 12.964 74144 Z= 0.256 Chirality : 0.039 0.143 8372 Planarity : 0.004 0.050 9184 Dihedral : 10.459 59.592 9100 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.50 % Allowed : 29.85 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.11), residues: 6272 helix: 1.21 (0.10), residues: 2660 sheet: 1.21 (0.25), residues: 280 loop : -0.78 (0.11), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAu 132 HIS 0.001 0.000 HISAk 69 PHE 0.013 0.002 PHEBs 202 TYR 0.023 0.001 TYRBs 198 ARG 0.002 0.000 ARGAi 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23428.17 seconds wall clock time: 404 minutes 24.31 seconds (24264.31 seconds total)