Starting phenix.real_space_refine on Mon Apr 15 02:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ope_17050/04_2024/8ope_17050.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ope_17050/04_2024/8ope_17050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ope_17050/04_2024/8ope_17050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ope_17050/04_2024/8ope_17050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ope_17050/04_2024/8ope_17050.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ope_17050/04_2024/8ope_17050.pdb" } resolution = 3.09 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= 0.001 sd= 0.059 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 105 5.49 5 S 252 5.16 5 C 20727 2.51 5 N 5670 2.21 5 O 6657 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 GLU 139": "OE1" <-> "OE2" Residue "Ac GLU 107": "OE1" <-> "OE2" Residue "Ac GLU 139": "OE1" <-> "OE2" Residue "Ae GLU 107": "OE1" <-> "OE2" Residue "Ae GLU 139": "OE1" <-> "OE2" Residue "Ag GLU 107": "OE1" <-> "OE2" Residue "Ag GLU 139": "OE1" <-> "OE2" Residue "Ai GLU 107": "OE1" <-> "OE2" Residue "Ai GLU 139": "OE1" <-> "OE2" Residue "Ak GLU 107": "OE1" <-> "OE2" Residue "Ak GLU 139": "OE1" <-> "OE2" Residue "Am GLU 107": "OE1" <-> "OE2" Residue "Am GLU 139": "OE1" <-> "OE2" Residue "Ao GLU 107": "OE1" <-> "OE2" Residue "Ao GLU 139": "OE1" <-> "OE2" Residue "Aq GLU 107": "OE1" <-> "OE2" Residue "Aq GLU 139": "OE1" <-> "OE2" Residue "As GLU 107": "OE1" <-> "OE2" Residue "As GLU 139": "OE1" <-> "OE2" Residue "Au GLU 107": "OE1" <-> "OE2" Residue "Au GLU 139": "OE1" <-> "OE2" Residue "Aw GLU 107": "OE1" <-> "OE2" Residue "Aw GLU 139": "OE1" <-> "OE2" Residue "Ay GLU 107": "OE1" <-> "OE2" Residue "Ay GLU 139": "OE1" <-> "OE2" Residue "Ba GLU 107": "OE1" <-> "OE2" Residue "Ba GLU 139": "OE1" <-> "OE2" Residue "Bc GLU 107": "OE1" <-> "OE2" Residue "Bc GLU 139": "OE1" <-> "OE2" Residue "Be GLU 107": "OE1" <-> "OE2" Residue "Be GLU 139": "OE1" <-> "OE2" Residue "Bg GLU 107": "OE1" <-> "OE2" Residue "Bg GLU 139": "OE1" <-> "OE2" Residue "Bi GLU 107": "OE1" <-> "OE2" Residue "Bi GLU 139": "OE1" <-> "OE2" Residue "Bk GLU 107": "OE1" <-> "OE2" Residue "Bk GLU 139": "OE1" <-> "OE2" Residue "Bm GLU 107": "OE1" <-> "OE2" Residue "Bm GLU 139": "OE1" <-> "OE2" Residue "Bo GLU 107": "OE1" <-> "OE2" Residue "Bo GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33411 Number of models: 1 Model: "" Number of chains: 42 Chain: "Aa" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1491 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 174} 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} Time building chain proxies: 16.80, per 1000 atoms: 0.50 Number of scatterers: 33411 At special positions: 0 Unit cell: (142.442, 141.379, 155.198, 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 252 16.00 P 105 15.00 O 6657 8.00 N 5670 7.00 C 20727 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: 14.50 Conformation dependent library (CDL) restraints added in 5.6 seconds 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 42 sheets defined 56.5% alpha, 5.4% beta 0 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 11.07 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAa 72 " --> pdb=" O GLUAa 68 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAa 80 " --> pdb=" O GLNAa 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAa 81 " --> pdb=" O ILEAa 78 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 152 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 176 Processing helix chain 'Aa' and resid 182 through 188 Processing helix chain 'Aa' and resid 195 through 199 Processing helix chain 'Aa' and resid 210 through 226 Processing helix chain 'Ac' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAc 72 " --> pdb=" O GLUAc 68 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAc 80 " --> pdb=" O GLNAc 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAc 81 " --> pdb=" O ILEAc 78 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 152 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 176 Processing helix chain 'Ac' and resid 182 through 188 Processing helix chain 'Ac' and resid 195 through 199 Processing helix chain 'Ac' and resid 210 through 226 Processing helix chain 'Ae' and resid 66 through 73 removed outlier: 3.740A pdb=" N GLUAe 72 " --> pdb=" O GLUAe 68 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAe 80 " --> pdb=" O GLNAe 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAe 81 " --> pdb=" O ILEAe 78 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 152 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 176 Processing helix chain 'Ae' and resid 182 through 188 Processing helix chain 'Ae' and resid 195 through 199 Processing helix chain 'Ae' and resid 210 through 226 Processing helix chain 'Ag' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAg 72 " --> pdb=" O GLUAg 68 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAg 80 " --> pdb=" O GLNAg 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERAg 81 " --> pdb=" O ILEAg 78 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.551A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 152 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 176 Processing helix chain 'Ag' and resid 182 through 188 Processing helix chain 'Ag' and resid 195 through 199 Processing helix chain 'Ag' and resid 210 through 226 Processing helix chain 'Ai' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAi 72 " --> pdb=" O GLUAi 68 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAi 80 " --> pdb=" O GLNAi 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERAi 81 " --> pdb=" O ILEAi 78 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 152 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 176 Processing helix chain 'Ai' and resid 182 through 188 Processing helix chain 'Ai' and resid 195 through 199 Processing helix chain 'Ai' and resid 210 through 226 Processing helix chain 'Ak' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAk 72 " --> pdb=" O GLUAk 68 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAk 80 " --> pdb=" O GLNAk 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAk 81 " --> pdb=" O ILEAk 78 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 152 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 176 Processing helix chain 'Ak' and resid 182 through 188 Processing helix chain 'Ak' and resid 195 through 199 Processing helix chain 'Ak' and resid 210 through 226 Processing helix chain 'Am' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAm 72 " --> pdb=" O GLUAm 68 " (cutoff:3.500A) Processing helix chain 'Am' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAm 80 " --> pdb=" O GLNAm 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAm 81 " --> pdb=" O ILEAm 78 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 152 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 176 Processing helix chain 'Am' and resid 182 through 188 Processing helix chain 'Am' and resid 195 through 199 Processing helix chain 'Am' and resid 210 through 226 Processing helix chain 'Ao' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAo 72 " --> pdb=" O GLUAo 68 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAo 80 " --> pdb=" O GLNAo 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAo 81 " --> pdb=" O ILEAo 78 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 152 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 176 Processing helix chain 'Ao' and resid 182 through 188 Processing helix chain 'Ao' and resid 195 through 199 Processing helix chain 'Ao' and resid 210 through 226 Processing helix chain 'Aq' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAq 72 " --> pdb=" O GLUAq 68 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 76 through 81 removed outlier: 3.595A pdb=" N ILEAq 80 " --> pdb=" O GLNAq 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERAq 81 " --> pdb=" O ILEAq 78 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 Processing helix chain 'Aq' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 152 Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 176 Processing helix chain 'Aq' and resid 182 through 188 Processing helix chain 'Aq' and resid 195 through 199 Processing helix chain 'Aq' and resid 210 through 226 Processing helix chain 'As' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAs 72 " --> pdb=" O GLUAs 68 " (cutoff:3.500A) Processing helix chain 'As' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAs 80 " --> pdb=" O GLNAs 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAs 81 " --> pdb=" O ILEAs 78 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 Processing helix chain 'As' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 152 Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 176 Processing helix chain 'As' and resid 182 through 188 Processing helix chain 'As' and resid 195 through 199 Processing helix chain 'As' and resid 210 through 226 Processing helix chain 'Au' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAu 72 " --> pdb=" O GLUAu 68 " (cutoff:3.500A) Processing helix chain 'Au' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAu 80 " --> pdb=" O GLNAu 77 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SERAu 81 " --> pdb=" O ILEAu 78 " (cutoff:3.500A) Processing helix chain 'Au' and resid 86 through 102 Processing helix chain 'Au' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 152 Processing helix chain 'Au' and resid 155 through 161 Processing helix chain 'Au' and resid 163 through 176 Processing helix chain 'Au' and resid 182 through 188 Processing helix chain 'Au' and resid 195 through 199 Processing helix chain 'Au' and resid 210 through 226 Processing helix chain 'Aw' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUAw 72 " --> pdb=" O GLUAw 68 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAw 80 " --> pdb=" O GLNAw 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAw 81 " --> pdb=" O ILEAw 78 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 86 through 102 Processing helix chain 'Aw' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 152 Processing helix chain 'Aw' and resid 155 through 161 Processing helix chain 'Aw' and resid 163 through 176 Processing helix chain 'Aw' and resid 182 through 188 Processing helix chain 'Aw' and resid 195 through 199 Processing helix chain 'Aw' and resid 210 through 226 Processing helix chain 'Ay' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUAy 72 " --> pdb=" O GLUAy 68 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEAy 80 " --> pdb=" O GLNAy 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERAy 81 " --> pdb=" O ILEAy 78 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 86 through 102 Processing helix chain 'Ay' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALAy 111 " --> pdb=" O GLUAy 107 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 145 through 152 Processing helix chain 'Ay' and resid 155 through 161 Processing helix chain 'Ay' and resid 163 through 176 Processing helix chain 'Ay' and resid 182 through 188 Processing helix chain 'Ay' and resid 195 through 199 Processing helix chain 'Ay' and resid 210 through 226 Processing helix chain 'Ba' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBa 72 " --> pdb=" O GLUBa 68 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBa 80 " --> pdb=" O GLNBa 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBa 81 " --> pdb=" O ILEBa 78 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 86 through 102 Processing helix chain 'Ba' and resid 107 through 122 removed outlier: 3.552A pdb=" N VALBa 111 " --> pdb=" O GLUBa 107 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 145 through 152 Processing helix chain 'Ba' and resid 155 through 161 Processing helix chain 'Ba' and resid 163 through 176 Processing helix chain 'Ba' and resid 182 through 188 Processing helix chain 'Ba' and resid 195 through 199 Processing helix chain 'Ba' and resid 210 through 226 Processing helix chain 'Bc' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBc 72 " --> pdb=" O GLUBc 68 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 76 through 81 removed outlier: 3.595A pdb=" N ILEBc 80 " --> pdb=" O GLNBc 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBc 81 " --> pdb=" O ILEBc 78 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 86 through 102 Processing helix chain 'Bc' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBc 111 " --> pdb=" O GLUBc 107 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 145 through 152 Processing helix chain 'Bc' and resid 155 through 161 Processing helix chain 'Bc' and resid 163 through 176 Processing helix chain 'Bc' and resid 182 through 188 Processing helix chain 'Bc' and resid 195 through 199 Processing helix chain 'Bc' and resid 210 through 226 Processing helix chain 'Be' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBe 72 " --> pdb=" O GLUBe 68 " (cutoff:3.500A) Processing helix chain 'Be' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBe 80 " --> pdb=" O GLNBe 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERBe 81 " --> pdb=" O ILEBe 78 " (cutoff:3.500A) Processing helix chain 'Be' and resid 86 through 102 Processing helix chain 'Be' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBe 111 " --> pdb=" O GLUBe 107 " (cutoff:3.500A) Processing helix chain 'Be' and resid 145 through 152 Processing helix chain 'Be' and resid 155 through 161 Processing helix chain 'Be' and resid 163 through 176 Processing helix chain 'Be' and resid 182 through 188 Processing helix chain 'Be' and resid 195 through 199 Processing helix chain 'Be' and resid 210 through 226 Processing helix chain 'Bg' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBg 72 " --> pdb=" O GLUBg 68 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBg 80 " --> pdb=" O GLNBg 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SERBg 81 " --> pdb=" O ILEBg 78 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 86 through 102 Processing helix chain 'Bg' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBg 111 " --> pdb=" O GLUBg 107 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 145 through 152 Processing helix chain 'Bg' and resid 155 through 161 Processing helix chain 'Bg' and resid 163 through 176 Processing helix chain 'Bg' and resid 182 through 188 Processing helix chain 'Bg' and resid 195 through 199 Processing helix chain 'Bg' and resid 210 through 226 Processing helix chain 'Bi' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUBi 72 " --> pdb=" O GLUBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBi 80 " --> pdb=" O GLNBi 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBi 81 " --> pdb=" O ILEBi 78 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 86 through 102 Processing helix chain 'Bi' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBi 111 " --> pdb=" O GLUBi 107 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 145 through 152 Processing helix chain 'Bi' and resid 155 through 161 Processing helix chain 'Bi' and resid 163 through 176 Processing helix chain 'Bi' and resid 182 through 188 Processing helix chain 'Bi' and resid 195 through 199 Processing helix chain 'Bi' and resid 210 through 226 Processing helix chain 'Bk' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUBk 72 " --> pdb=" O GLUBk 68 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBk 80 " --> pdb=" O GLNBk 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBk 81 " --> pdb=" O ILEBk 78 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 86 through 102 Processing helix chain 'Bk' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBk 111 " --> pdb=" O GLUBk 107 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 145 through 152 Processing helix chain 'Bk' and resid 155 through 161 Processing helix chain 'Bk' and resid 163 through 176 Processing helix chain 'Bk' and resid 182 through 188 Processing helix chain 'Bk' and resid 195 through 199 Processing helix chain 'Bk' and resid 210 through 226 Processing helix chain 'Bm' and resid 66 through 73 removed outlier: 3.739A pdb=" N GLUBm 72 " --> pdb=" O GLUBm 68 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBm 80 " --> pdb=" O GLNBm 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBm 81 " --> pdb=" O ILEBm 78 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 86 through 102 Processing helix chain 'Bm' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBm 111 " --> pdb=" O GLUBm 107 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 145 through 152 Processing helix chain 'Bm' and resid 155 through 161 Processing helix chain 'Bm' and resid 163 through 176 Processing helix chain 'Bm' and resid 182 through 188 Processing helix chain 'Bm' and resid 195 through 199 Processing helix chain 'Bm' and resid 210 through 226 Processing helix chain 'Bo' and resid 66 through 73 removed outlier: 3.738A pdb=" N GLUBo 72 " --> pdb=" O GLUBo 68 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 76 through 81 removed outlier: 3.596A pdb=" N ILEBo 80 " --> pdb=" O GLNBo 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SERBo 81 " --> pdb=" O ILEBo 78 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 86 through 102 Processing helix chain 'Bo' and resid 107 through 122 removed outlier: 3.553A pdb=" N VALBo 111 " --> pdb=" O GLUBo 107 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 145 through 152 Processing helix chain 'Bo' and resid 155 through 161 Processing helix chain 'Bo' and resid 163 through 176 Processing helix chain 'Bo' and resid 182 through 188 Processing helix chain 'Bo' and resid 195 through 199 Processing helix chain 'Bo' 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 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 135 1449 hydrogen bonds defined for protein. 4095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 12.65 Time building geometry restraints manager: 15.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6226 1.32 - 1.45: 8662 1.45 - 1.57: 18733 1.57 - 1.69: 189 1.69 - 1.81: 483 Bond restraints: 34293 Sorted by residual: bond pdb=" C ALAAo 196 " pdb=" N ARGAo 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.22e+01 bond pdb=" C ALAAm 196 " pdb=" N ARGAm 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" C ALABc 196 " pdb=" N ARGBc 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" C ALABe 196 " pdb=" N ARGBe 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.20e+01 bond pdb=" C ALABo 196 " pdb=" N ARGBo 197 " ideal model delta sigma weight residual 1.335 1.288 0.047 1.35e-02 5.49e+03 1.20e+01 ... (remaining 34288 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.11: 1540 106.11 - 113.11: 18387 113.11 - 120.11: 12186 120.11 - 127.12: 14316 127.12 - 134.12: 422 Bond angle restraints: 46851 Sorted by residual: angle pdb=" C PROAa 45 " pdb=" CA PROAa 45 " pdb=" CB PROAa 45 " ideal model delta sigma weight residual 111.40 104.95 6.45 9.10e-01 1.21e+00 5.02e+01 angle pdb=" C PROBg 45 " pdb=" CA PROBg 45 " pdb=" CB PROBg 45 " ideal model delta sigma weight residual 111.40 104.96 6.44 9.10e-01 1.21e+00 5.01e+01 angle pdb=" C PROAy 45 " pdb=" CA PROAy 45 " pdb=" CB PROAy 45 " ideal model delta sigma weight residual 111.40 104.97 6.43 9.10e-01 1.21e+00 5.00e+01 angle pdb=" C PROAe 45 " pdb=" CA PROAe 45 " pdb=" CB PROAe 45 " ideal model delta sigma weight residual 111.40 104.97 6.43 9.10e-01 1.21e+00 5.00e+01 angle pdb=" C PROBk 45 " pdb=" CA PROBk 45 " pdb=" CB PROBk 45 " ideal model delta sigma weight residual 111.40 104.97 6.43 9.10e-01 1.21e+00 4.99e+01 ... (remaining 46846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 20177 34.16 - 68.32: 1075 68.32 - 102.47: 21 102.47 - 136.63: 0 136.63 - 170.79: 21 Dihedral angle restraints: 21294 sinusoidal: 9744 harmonic: 11550 Sorted by residual: dihedral pdb=" O4' UAl 4 " pdb=" C1' UAl 4 " pdb=" N1 UAl 4 " pdb=" C2 UAl 4 " ideal model delta sinusoidal sigma weight residual -128.00 42.79 -170.79 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' UBh 4 " pdb=" C1' UBh 4 " pdb=" N1 UBh 4 " pdb=" C2 UBh 4 " ideal model delta sinusoidal sigma weight residual -128.00 42.78 -170.78 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" O4' UAz 4 " pdb=" C1' UAz 4 " pdb=" N1 UAz 4 " pdb=" C2 UAz 4 " ideal model delta sinusoidal sigma weight residual -128.00 42.77 -170.77 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 21291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2933 0.026 - 0.052: 1567 0.052 - 0.078: 335 0.078 - 0.103: 257 0.103 - 0.129: 179 Chirality restraints: 5271 Sorted by residual: chirality pdb=" CA ILEBo 50 " pdb=" N ILEBo 50 " pdb=" C ILEBo 50 " pdb=" CB ILEBo 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" C1' UAz 2 " pdb=" O4' UAz 2 " pdb=" C2' UAz 2 " pdb=" N1 UAz 2 " both_signs ideal model delta sigma weight residual False 2.47 2.34 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILEBi 50 " pdb=" N ILEBi 50 " pdb=" C ILEBi 50 " pdb=" CB ILEBi 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 5268 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PROBm 45 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C PROBm 45 " 0.035 2.00e-02 2.50e+03 pdb=" O PROBm 45 " -0.013 2.00e-02 2.50e+03 pdb=" N ARGBm 46 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROAo 45 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C PROAo 45 " 0.035 2.00e-02 2.50e+03 pdb=" O PROAo 45 " -0.013 2.00e-02 2.50e+03 pdb=" N ARGAo 46 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROBg 45 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C PROBg 45 " -0.035 2.00e-02 2.50e+03 pdb=" O PROBg 45 " 0.013 2.00e-02 2.50e+03 pdb=" N ARGBg 46 " 0.012 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.94: 15661 2.94 - 3.43: 35800 3.43 - 3.92: 58418 3.92 - 4.41: 70627 4.41 - 4.90: 108364 Nonbonded interactions: 288870 Sorted by model distance: nonbonded pdb=" OE2 GLUBe 121 " pdb=" OH TYRBe 180 " model vdw 2.456 2.440 nonbonded pdb=" OE2 GLUBg 121 " pdb=" OH TYRBg 180 " model vdw 2.456 2.440 nonbonded pdb=" OE2 GLUBo 121 " pdb=" OH TYRBo 180 " model vdw 2.456 2.440 nonbonded pdb=" OE2 GLUAu 121 " pdb=" OH TYRAu 180 " model vdw 2.456 2.440 nonbonded pdb=" OE2 GLUAc 121 " pdb=" OH TYRAc 180 " model vdw 2.456 2.440 ... (remaining 288865 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' } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 7.620 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 94.620 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 0.047 34293 Z= 0.338 Angle : 0.695 9.646 46851 Z= 0.456 Chirality : 0.040 0.129 5271 Planarity : 0.007 0.076 5712 Dihedral : 18.434 170.791 13818 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.24 % Allowed : 19.05 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.16 (0.13), residues: 3864 helix: 1.19 (0.12), residues: 1890 sheet: 0.57 (0.32), residues: 252 loop : -1.21 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAo 132 HIS 0.004 0.001 HISAu 217 PHE 0.011 0.002 PHEAe 163 TYR 0.018 0.002 TYRAi 143 ARG 0.005 0.001 ARGAg 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1064 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7117 (mt-10) REVERT: Ac 95 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7380 (mt-10) REVERT: Ae 134 MET cc_start: 0.7317 (ttt) cc_final: 0.7085 (ttt) REVERT: Ae 146 LYS cc_start: 0.8477 (ttpp) cc_final: 0.8113 (ttmm) REVERT: Ak 60 LYS cc_start: 0.8503 (mmtp) cc_final: 0.7944 (mmtp) REVERT: Am 60 LYS cc_start: 0.8585 (mmtp) cc_final: 0.8075 (mmtp) REVERT: Ao 112 MET cc_start: 0.8393 (mmm) cc_final: 0.8120 (mmp) REVERT: Aq 95 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7580 (mt-10) REVERT: Aq 134 MET cc_start: 0.8073 (ttt) cc_final: 0.7589 (ttt) REVERT: As 54 MET cc_start: 0.7579 (ttp) cc_final: 0.7364 (ttp) REVERT: As 134 MET cc_start: 0.7625 (ttt) cc_final: 0.7371 (ttt) REVERT: As 146 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8144 (tppt) REVERT: As 151 ASN cc_start: 0.8959 (m-40) cc_final: 0.8565 (m110) REVERT: Au 46 ARG cc_start: 0.9015 (mpt180) cc_final: 0.8798 (mpt180) REVERT: Au 173 MET cc_start: 0.7871 (ttp) cc_final: 0.7591 (tmm) REVERT: Aw 134 MET cc_start: 0.7437 (ttt) cc_final: 0.7158 (ttt) REVERT: Ay 60 LYS cc_start: 0.8464 (mmtp) cc_final: 0.8218 (mmtp) REVERT: Ay 134 MET cc_start: 0.7868 (ttt) cc_final: 0.7341 (ttt) REVERT: Ba 50 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7913 (tt) REVERT: Ba 60 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8456 (mmtm) REVERT: Ba 125 SER cc_start: 0.8812 (p) cc_final: 0.8541 (p) REVERT: Be 89 GLN cc_start: 0.8478 (mt0) cc_final: 0.8090 (mt0) REVERT: Be 95 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6680 (mt-10) REVERT: Be 191 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.7618 (mtp-110) REVERT: Bi 50 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7800 (mt) REVERT: Bi 60 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8419 (mmtm) REVERT: Bi 121 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8218 (mm-30) REVERT: Bi 134 MET cc_start: 0.8016 (ttt) cc_final: 0.7767 (ttt) REVERT: Bi 208 ARG cc_start: 0.8411 (ptm160) cc_final: 0.8185 (ptm160) REVERT: Bk 121 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8051 (mm-30) REVERT: Bm 55 ARG cc_start: 0.8313 (tpt-90) cc_final: 0.7951 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6723 (mt-10) REVERT: Bm 191 ARG cc_start: 0.7798 (mtp-110) cc_final: 0.7502 (mtp-110) outliers start: 8 outliers final: 2 residues processed: 1068 average time/residue: 0.5110 time to fit residues: 842.7024 Evaluate side-chains 962 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 958 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 50 ILE Chi-restraints excluded: chain Ba residue 50 ILE Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bo residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.1980 chunk 286 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 180 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 151 ASN Ae 66 ASN Ae 129 ASN Ae 151 ASN Ag 129 ASN Ag 151 ASN Ao 87 GLN Aq 66 ASN Aq 77 GLN Aq 151 ASN Au 151 ASN Ay 151 ASN Bc 66 ASN Be 66 ASN ** Be 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 98 GLN Bk 98 GLN Bm 66 ASN Bo 77 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34293 Z= 0.156 Angle : 0.488 5.681 46851 Z= 0.253 Chirality : 0.038 0.129 5271 Planarity : 0.005 0.048 5712 Dihedral : 15.333 179.011 5951 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.48 % Allowed : 19.34 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.45 (0.13), residues: 3864 helix: 1.19 (0.12), residues: 2016 sheet: 0.99 (0.30), residues: 210 loop : -0.91 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAg 93 HIS 0.005 0.001 HISAy 217 PHE 0.017 0.002 PHEAo 200 TYR 0.010 0.001 TYRAc 184 ARG 0.009 0.001 ARGAm 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 996 time to evaluate : 3.629 Fit side-chains REVERT: Aa 55 ARG cc_start: 0.8612 (mtp180) cc_final: 0.8376 (tpt-90) REVERT: Aa 95 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7277 (mt-10) REVERT: Ac 95 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7509 (mt-10) REVERT: Ae 134 MET cc_start: 0.7971 (ttt) cc_final: 0.7648 (ttt) REVERT: Ae 146 LYS cc_start: 0.8289 (ttpp) cc_final: 0.7987 (ttmm) REVERT: Ag 113 ASN cc_start: 0.8884 (m-40) cc_final: 0.8671 (m-40) REVERT: Ai 46 ARG cc_start: 0.8539 (mpt180) cc_final: 0.8245 (mpt180) REVERT: Ai 158 GLN cc_start: 0.9166 (mt0) cc_final: 0.8822 (mt0) REVERT: Ai 181 MET cc_start: 0.8004 (tpt) cc_final: 0.7685 (tpt) REVERT: Ai 204 GLU cc_start: 0.8616 (tt0) cc_final: 0.8381 (tt0) REVERT: Ai 208 ARG cc_start: 0.8391 (ptm160) cc_final: 0.8110 (mtp85) REVERT: Ak 180 TYR cc_start: 0.8661 (t80) cc_final: 0.8450 (t80) REVERT: Ak 208 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8308 (ptp-110) REVERT: Aq 95 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7606 (mt-10) REVERT: Aq 134 MET cc_start: 0.8569 (ttt) cc_final: 0.7974 (ttt) REVERT: Aq 212 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7565 (ttp-170) REVERT: Aq 220 MET cc_start: 0.8750 (mtp) cc_final: 0.8534 (mtm) REVERT: As 55 ARG cc_start: 0.8271 (tpt-90) cc_final: 0.7946 (tpt-90) REVERT: As 134 MET cc_start: 0.8386 (ttt) cc_final: 0.8044 (ttt) REVERT: As 139 GLU cc_start: 0.7551 (tp30) cc_final: 0.7159 (tm-30) REVERT: As 148 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7900 (mt) REVERT: As 151 ASN cc_start: 0.8491 (m-40) cc_final: 0.8067 (m110) REVERT: As 212 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7572 (ttp-170) REVERT: Au 46 ARG cc_start: 0.9056 (mpt180) cc_final: 0.8783 (mpt180) REVERT: Aw 134 MET cc_start: 0.7847 (ttt) cc_final: 0.7437 (ttt) REVERT: Aw 204 GLU cc_start: 0.8750 (tt0) cc_final: 0.8349 (pt0) REVERT: Ay 108 MET cc_start: 0.8314 (tpt) cc_final: 0.7666 (tpt) REVERT: Bc 50 ILE cc_start: 0.8353 (mt) cc_final: 0.8141 (mt) REVERT: Bc 95 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6867 (mt-10) REVERT: Bc 121 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8428 (mm-30) REVERT: Be 95 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7108 (mt-10) REVERT: Be 177 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7656 (ttmm) REVERT: Be 180 TYR cc_start: 0.8737 (t80) cc_final: 0.8317 (t80) REVERT: Bg 56 MET cc_start: 0.8055 (mmm) cc_final: 0.7801 (mmt) REVERT: Bg 160 MET cc_start: 0.9410 (mmp) cc_final: 0.9119 (mmp) REVERT: Bg 204 GLU cc_start: 0.8702 (tt0) cc_final: 0.7904 (pt0) REVERT: Bi 121 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8427 (mm-30) REVERT: Bi 135 MET cc_start: 0.7893 (mmm) cc_final: 0.7577 (mmm) REVERT: Bi 168 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8237 (mt-10) REVERT: Bi 177 LYS cc_start: 0.8348 (mttt) cc_final: 0.7854 (ttmm) REVERT: Bi 191 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7466 (mtp-110) REVERT: Bi 201 ASP cc_start: 0.8458 (t0) cc_final: 0.8232 (t0) REVERT: Bk 153 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8867 (mmtt) REVERT: Bm 55 ARG cc_start: 0.8414 (tpt-90) cc_final: 0.8141 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7095 (mt-10) REVERT: Bm 158 GLN cc_start: 0.9083 (mt0) cc_final: 0.8839 (mt0) REVERT: Bm 208 ARG cc_start: 0.8384 (ptm160) cc_final: 0.8153 (ptp-110) REVERT: Bo 95 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7212 (mt-10) REVERT: Bo 141 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8794 (t) REVERT: Bo 204 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8357 (tt0) outliers start: 84 outliers final: 35 residues processed: 1023 average time/residue: 0.4939 time to fit residues: 814.5956 Evaluate side-chains 1008 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 969 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 159 ILE Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 122 ASN Chi-restraints excluded: chain Ak residue 208 ARG Chi-restraints excluded: chain Am residue 122 ASN Chi-restraints excluded: chain Am residue 194 SER Chi-restraints excluded: chain Ao residue 65 LEU Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain As residue 50 ILE Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 148 ILE Chi-restraints excluded: chain Au residue 107 GLU Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Ay residue 107 GLU Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ba residue 50 ILE Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Be residue 67 LEU Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bk residue 50 ILE Chi-restraints excluded: chain Bm residue 68 GLU Chi-restraints excluded: chain Bo residue 67 LEU Chi-restraints excluded: chain Bo residue 141 VAL Chi-restraints excluded: chain Bo residue 204 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 285 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 343 optimal weight: 0.5980 chunk 371 optimal weight: 0.7980 chunk 306 optimal weight: 0.0670 chunk 341 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 275 optimal weight: 10.0000 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 151 ASN Ag 151 ASN Am 151 ASN Ao 87 GLN Ao 158 GLN Aq 77 GLN ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 77 GLN Ba 151 ASN Be 87 GLN Bk 77 GLN Bk 98 GLN Bo 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34293 Z= 0.169 Angle : 0.484 6.970 46851 Z= 0.247 Chirality : 0.038 0.168 5271 Planarity : 0.005 0.047 5712 Dihedral : 15.234 179.377 5945 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.72 % Allowed : 19.08 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.65 (0.13), residues: 3864 helix: 1.25 (0.12), residues: 2058 sheet: 1.21 (0.30), residues: 210 loop : -0.73 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAe 132 HIS 0.004 0.001 HISAs 217 PHE 0.016 0.002 PHEAc 200 TYR 0.014 0.001 TYRAs 184 ARG 0.006 0.001 ARGBi 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1182 time to evaluate : 3.797 Fit side-chains revert: symmetry clash REVERT: Aa 55 ARG cc_start: 0.8573 (mtp180) cc_final: 0.8317 (tpt-90) REVERT: Aa 95 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7528 (mt-10) REVERT: Aa 215 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7615 (mt-10) REVERT: Ac 55 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8072 (tpt-90) REVERT: Ac 95 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7808 (mt-10) REVERT: Ac 191 ARG cc_start: 0.7842 (mtp-110) cc_final: 0.7590 (mtp-110) REVERT: Ae 108 MET cc_start: 0.9374 (tpt) cc_final: 0.8480 (tpt) REVERT: Ae 177 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8274 (ttmm) REVERT: Ae 191 ARG cc_start: 0.7484 (mtp-110) cc_final: 0.7153 (mtp-110) REVERT: Ag 95 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7706 (mt-10) REVERT: Ag 151 ASN cc_start: 0.8690 (m-40) cc_final: 0.8476 (m110) REVERT: Ag 212 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.7896 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7649 (mt-10) REVERT: Ai 204 GLU cc_start: 0.8939 (tt0) cc_final: 0.8563 (tt0) REVERT: Ai 212 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7750 (ttp-170) REVERT: Ak 181 MET cc_start: 0.7967 (tpt) cc_final: 0.7409 (tpt) REVERT: Ak 183 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8742 (ttp80) REVERT: Ak 191 ARG cc_start: 0.7606 (mtp-110) cc_final: 0.7324 (mtp-110) REVERT: Ak 208 ARG cc_start: 0.8825 (ptp-170) cc_final: 0.8540 (ptp-110) REVERT: Ak 212 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7528 (ptm-80) REVERT: Ao 176 LYS cc_start: 0.8249 (ttmm) cc_final: 0.7769 (ttmt) REVERT: Aq 55 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.7937 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7783 (mt-10) REVERT: Aq 168 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: Aq 191 ARG cc_start: 0.7867 (mtp-110) cc_final: 0.7574 (mtp-110) REVERT: Aq 212 ARG cc_start: 0.8336 (ttp-110) cc_final: 0.7713 (ttp-170) REVERT: Aq 220 MET cc_start: 0.8765 (mtp) cc_final: 0.8480 (mtm) REVERT: As 67 LEU cc_start: 0.8709 (mt) cc_final: 0.8507 (mp) REVERT: As 95 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7659 (mt-10) REVERT: As 148 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8382 (mt) REVERT: As 160 MET cc_start: 0.9562 (mmm) cc_final: 0.9231 (mmt) REVERT: As 220 MET cc_start: 0.8791 (mtm) cc_final: 0.8560 (mtp) REVERT: Au 175 ASN cc_start: 0.8950 (m-40) cc_final: 0.8701 (m-40) REVERT: Au 177 LYS cc_start: 0.8669 (mmmm) cc_final: 0.8390 (ttmm) REVERT: Au 191 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.7069 (mtp-110) REVERT: Au 204 GLU cc_start: 0.9099 (tt0) cc_final: 0.8849 (tt0) REVERT: Au 208 ARG cc_start: 0.8236 (ptm160) cc_final: 0.8024 (mtp85) REVERT: Aw 95 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7667 (mt-10) REVERT: Aw 110 THR cc_start: 0.8999 (m) cc_final: 0.8648 (m) REVERT: Aw 134 MET cc_start: 0.8580 (ttt) cc_final: 0.8128 (ttt) REVERT: Aw 180 TYR cc_start: 0.9316 (t80) cc_final: 0.9074 (t80) REVERT: Aw 215 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7315 (mt-10) REVERT: Ay 95 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7808 (mt-10) REVERT: Ba 56 MET cc_start: 0.8192 (mmm) cc_final: 0.7970 (mmt) REVERT: Ba 191 ARG cc_start: 0.7833 (mtp-110) cc_final: 0.7539 (mtp-110) REVERT: Ba 204 GLU cc_start: 0.9023 (tt0) cc_final: 0.8728 (tt0) REVERT: Ba 212 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7531 (ptm-80) REVERT: Ba 220 MET cc_start: 0.8550 (mtm) cc_final: 0.8165 (mtm) REVERT: Bc 95 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7434 (mt-10) REVERT: Bc 136 ASP cc_start: 0.8508 (t0) cc_final: 0.8301 (t0) REVERT: Bc 206 THR cc_start: 0.9359 (p) cc_final: 0.9140 (t) REVERT: Bc 212 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7301 (ttp-170) REVERT: Bc 220 MET cc_start: 0.8677 (mtm) cc_final: 0.8431 (mtm) REVERT: Be 79 ASP cc_start: 0.9006 (m-30) cc_final: 0.8630 (m-30) REVERT: Be 89 GLN cc_start: 0.9255 (mt0) cc_final: 0.9028 (mt0) REVERT: Be 95 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7559 (mt-10) REVERT: Be 177 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8137 (ttmm) REVERT: Be 191 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7745 (mtp-110) REVERT: Bg 212 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7581 (ttp-170) REVERT: Bi 50 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8152 (mt) REVERT: Bi 79 ASP cc_start: 0.8794 (m-30) cc_final: 0.8487 (m-30) REVERT: Bi 135 MET cc_start: 0.8428 (mmm) cc_final: 0.8148 (mmm) REVERT: Bi 177 LYS cc_start: 0.8577 (mttt) cc_final: 0.8169 (ttmm) REVERT: Bi 191 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7532 (mtp-110) REVERT: Bi 201 ASP cc_start: 0.8706 (t0) cc_final: 0.8494 (t0) REVERT: Bi 206 THR cc_start: 0.9309 (p) cc_final: 0.9041 (t) REVERT: Bi 212 ARG cc_start: 0.7865 (ttp-110) cc_final: 0.7346 (ttp-170) REVERT: Bi 215 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7215 (mt-10) REVERT: Bk 134 MET cc_start: 0.8515 (ttt) cc_final: 0.7905 (ttt) REVERT: Bk 201 ASP cc_start: 0.8542 (t0) cc_final: 0.8334 (t0) REVERT: Bk 206 THR cc_start: 0.9396 (p) cc_final: 0.9182 (t) REVERT: Bk 212 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7727 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8391 (tpt-90) cc_final: 0.8065 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7529 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8108 (ttmt) REVERT: Bm 215 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7163 (mt-10) REVERT: Bo 95 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7474 (mt-10) REVERT: Bo 108 MET cc_start: 0.9290 (tpt) cc_final: 0.8651 (tpt) REVERT: Bo 151 ASN cc_start: 0.9342 (m110) cc_final: 0.9130 (m110) REVERT: Bo 190 LEU cc_start: 0.9067 (tp) cc_final: 0.8842 (mp) REVERT: Bo 191 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7415 (mtp-110) REVERT: Bo 214 ARG cc_start: 0.8819 (ttp80) cc_final: 0.8606 (ttp-170) outliers start: 92 outliers final: 48 residues processed: 1217 average time/residue: 0.4991 time to fit residues: 943.8117 Evaluate side-chains 1164 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1113 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 107 GLU Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ai residue 124 THR Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 142 GLU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 122 ASN Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 168 GLU Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 148 ILE Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 178 GLU Chi-restraints excluded: chain Aw residue 54 MET Chi-restraints excluded: chain Aw residue 103 ILE Chi-restraints excluded: chain Aw residue 159 ILE Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 141 VAL Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 72 GLU Chi-restraints excluded: chain Bc residue 122 ASN Chi-restraints excluded: chain Bc residue 129 ASN Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 68 GLU Chi-restraints excluded: chain Be residue 122 ASN Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bk residue 142 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 8.9990 chunk 258 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 345 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 180 optimal weight: 0.0170 chunk 327 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Ac 158 GLN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN Ae 158 GLN ** Ag 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 129 ASN Ai 151 ASN ** Ak 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 151 ASN Ao 151 ASN Ao 158 GLN Aq 151 ASN ** As 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 129 ASN Aw 151 ASN Ay 158 GLN ** Ba 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 129 ASN ** Be 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 98 GLN ** Bg 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 151 ASN Bk 77 GLN ** Bm 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 69 HIS Bo 77 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 34293 Z= 0.444 Angle : 0.597 6.530 46851 Z= 0.312 Chirality : 0.045 0.180 5271 Planarity : 0.005 0.058 5712 Dihedral : 15.318 174.747 5943 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.79 % Allowed : 19.61 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.38 (0.13), residues: 3864 helix: 1.11 (0.12), residues: 1890 sheet: 0.86 (0.29), residues: 252 loop : -0.78 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPBe 132 HIS 0.005 0.001 HISBo 217 PHE 0.020 0.003 PHEBa 200 TYR 0.014 0.002 TYRBg 184 ARG 0.014 0.001 ARGAk 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1224 time to evaluate : 3.393 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8688 (mt0) cc_final: 0.8481 (mt0) REVERT: Aa 79 ASP cc_start: 0.9055 (m-30) cc_final: 0.8821 (m-30) REVERT: Aa 95 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7791 (mt-10) REVERT: Aa 206 THR cc_start: 0.9448 (p) cc_final: 0.9223 (t) REVERT: Ac 55 ARG cc_start: 0.8604 (mmm160) cc_final: 0.7923 (tpt-90) REVERT: Ac 89 GLN cc_start: 0.9465 (mt0) cc_final: 0.9262 (mt0) REVERT: Ac 91 ASP cc_start: 0.8864 (m-30) cc_final: 0.8548 (m-30) REVERT: Ac 95 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8041 (mt-10) REVERT: Ac 153 LYS cc_start: 0.9127 (mptt) cc_final: 0.8745 (mmtm) REVERT: Ac 181 MET cc_start: 0.9033 (tpp) cc_final: 0.8728 (tpp) REVERT: Ac 191 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7520 (mtp-110) REVERT: Ac 206 THR cc_start: 0.9498 (p) cc_final: 0.9254 (t) REVERT: Ae 129 ASN cc_start: 0.9180 (p0) cc_final: 0.8943 (p0) REVERT: Ae 177 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8464 (ttmm) REVERT: Ae 191 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7405 (mtp-110) REVERT: Ag 95 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7867 (mt-10) REVERT: Ag 204 GLU cc_start: 0.9335 (tt0) cc_final: 0.9066 (tt0) REVERT: Ag 212 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.8060 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7692 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9148 (m-40) cc_final: 0.8695 (m110) REVERT: Ai 172 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7758 (mt-10) REVERT: Ai 175 ASN cc_start: 0.8979 (m-40) cc_final: 0.8172 (m110) REVERT: Ai 212 ARG cc_start: 0.8493 (ttp-110) cc_final: 0.7950 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7443 (mt-10) REVERT: Ak 79 ASP cc_start: 0.9207 (m-30) cc_final: 0.8944 (m-30) REVERT: Ak 134 MET cc_start: 0.9115 (ttt) cc_final: 0.8818 (ttt) REVERT: Ak 191 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7111 (mtp-110) REVERT: Ak 206 THR cc_start: 0.9576 (p) cc_final: 0.9317 (t) REVERT: Ak 208 ARG cc_start: 0.8929 (ptp-170) cc_final: 0.8719 (ptp-110) REVERT: Ak 212 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8170 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7620 (mt-10) REVERT: Am 67 LEU cc_start: 0.8654 (mt) cc_final: 0.8433 (mm) REVERT: Am 92 THR cc_start: 0.9510 (m) cc_final: 0.9284 (m) REVERT: Am 191 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7638 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.7987 (ttp-170) REVERT: Ao 110 THR cc_start: 0.9204 (m) cc_final: 0.8937 (m) REVERT: Ao 129 ASN cc_start: 0.9169 (p0) cc_final: 0.8965 (p0) REVERT: Ao 134 MET cc_start: 0.9084 (ttt) cc_final: 0.8527 (ttt) REVERT: Ao 180 TYR cc_start: 0.9185 (t80) cc_final: 0.8744 (t80) REVERT: Ao 204 GLU cc_start: 0.9119 (tt0) cc_final: 0.8572 (tt0) REVERT: Ao 212 ARG cc_start: 0.8585 (ttp-110) cc_final: 0.8061 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8737 (tpt-90) cc_final: 0.8235 (tpt-90) REVERT: Aq 88 SER cc_start: 0.9278 (p) cc_final: 0.9053 (p) REVERT: Aq 95 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7867 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.7790 (ttp-170) REVERT: As 71 LEU cc_start: 0.8856 (mm) cc_final: 0.8617 (mm) REVERT: As 79 ASP cc_start: 0.9008 (m-30) cc_final: 0.8769 (m-30) REVERT: As 95 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7812 (mt-10) REVERT: As 142 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8402 (mt-10) REVERT: As 160 MET cc_start: 0.9558 (mmm) cc_final: 0.9333 (mmt) REVERT: As 212 ARG cc_start: 0.8560 (ttp-110) cc_final: 0.7969 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9074 (m-30) cc_final: 0.8744 (m-30) REVERT: Au 95 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7617 (mt-10) REVERT: Au 175 ASN cc_start: 0.8974 (m-40) cc_final: 0.8706 (m-40) REVERT: Au 177 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8471 (ttmm) REVERT: Au 208 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7885 (ptm160) REVERT: Aw 67 LEU cc_start: 0.8812 (mt) cc_final: 0.8458 (mm) REVERT: Aw 110 THR cc_start: 0.9347 (m) cc_final: 0.9061 (m) REVERT: Aw 134 MET cc_start: 0.9060 (ttt) cc_final: 0.8455 (ttt) REVERT: Aw 191 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.7517 (mtp-110) REVERT: Aw 208 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7691 (ptm160) REVERT: Ay 56 MET cc_start: 0.9011 (mtt) cc_final: 0.8585 (mtt) REVERT: Ay 95 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7829 (mt-10) REVERT: Ba 54 MET cc_start: 0.8598 (ptp) cc_final: 0.8380 (ptp) REVERT: Ba 157 ARG cc_start: 0.9259 (ttm110) cc_final: 0.8674 (ttm110) REVERT: Ba 212 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8099 (ttp-170) REVERT: Ba 220 MET cc_start: 0.9077 (mtm) cc_final: 0.8810 (mtm) REVERT: Bc 95 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7794 (mt-10) REVERT: Bc 206 THR cc_start: 0.9494 (p) cc_final: 0.9218 (t) REVERT: Bc 212 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.7977 (ttp-170) REVERT: Be 79 ASP cc_start: 0.9035 (m-30) cc_final: 0.8667 (m-30) REVERT: Be 89 GLN cc_start: 0.9399 (mt0) cc_final: 0.9148 (mt0) REVERT: Be 95 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7703 (mt-10) REVERT: Be 158 GLN cc_start: 0.9403 (mt0) cc_final: 0.9047 (mt0) REVERT: Be 177 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8415 (ttmm) REVERT: Be 215 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7733 (mt-10) REVERT: Bg 99 LEU cc_start: 0.8722 (tp) cc_final: 0.8507 (tp) REVERT: Bg 135 MET cc_start: 0.9030 (mmm) cc_final: 0.8628 (mmm) REVERT: Bg 212 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8154 (ttp-170) REVERT: Bi 135 MET cc_start: 0.9082 (mmm) cc_final: 0.8869 (mmt) REVERT: Bi 177 LYS cc_start: 0.8628 (mttt) cc_final: 0.8198 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9192 (tt0) cc_final: 0.8856 (tt0) REVERT: Bi 206 THR cc_start: 0.9484 (p) cc_final: 0.9191 (t) REVERT: Bi 208 ARG cc_start: 0.8792 (ptp-110) cc_final: 0.8556 (ptp-110) REVERT: Bi 212 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.7988 (ttp-170) REVERT: Bi 220 MET cc_start: 0.8863 (mtm) cc_final: 0.8522 (mtp) REVERT: Bk 67 LEU cc_start: 0.8662 (mt) cc_final: 0.8442 (mm) REVERT: Bk 102 ASP cc_start: 0.8251 (t70) cc_final: 0.7934 (t0) REVERT: Bk 110 THR cc_start: 0.9086 (m) cc_final: 0.8866 (m) REVERT: Bk 134 MET cc_start: 0.8941 (ttt) cc_final: 0.8507 (ttt) REVERT: Bk 203 TYR cc_start: 0.9456 (t80) cc_final: 0.9207 (t80) REVERT: Bk 212 ARG cc_start: 0.8485 (ttp-110) cc_final: 0.8063 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7829 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8331 (ttmt) REVERT: Bo 95 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7622 (mt-10) REVERT: Bo 158 GLN cc_start: 0.9468 (mt0) cc_final: 0.9257 (mt0) outliers start: 128 outliers final: 81 residues processed: 1287 average time/residue: 0.4779 time to fit residues: 970.3528 Evaluate side-chains 1248 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1165 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 159 ILE Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ai residue 129 ASN Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 54 MET Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 103 ILE Chi-restraints excluded: chain Ay residue 110 THR Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ba residue 50 ILE Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 206 THR Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 54 MET Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 186 LEU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 103 ILE Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bg residue 209 THR Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 68 GLU Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 311 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 189 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN Ag 66 ASN ** Ag 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 66 ASN ** Ai 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN Aq 151 ASN As 77 GLN Au 77 GLN ** Ay 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Be 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 77 GLN Bi 66 ASN Bi 151 ASN ** Bk 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 77 GLN Bm 151 ASN Bo 77 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34293 Z= 0.328 Angle : 0.539 6.370 46851 Z= 0.278 Chirality : 0.041 0.152 5271 Planarity : 0.005 0.046 5712 Dihedral : 15.250 175.460 5943 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.67 % Allowed : 19.96 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.14 (0.13), residues: 3864 helix: 1.07 (0.12), residues: 1764 sheet: 1.30 (0.28), residues: 210 loop : -1.01 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAc 132 HIS 0.004 0.001 HISAa 217 PHE 0.016 0.002 PHEBa 200 TYR 0.016 0.001 TYRAw 198 ARG 0.006 0.001 ARGAu 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1195 time to evaluate : 3.632 Fit side-chains REVERT: Aa 79 ASP cc_start: 0.9088 (m-30) cc_final: 0.8839 (m-30) REVERT: Aa 95 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7762 (mt-10) REVERT: Aa 172 GLU cc_start: 0.8175 (tt0) cc_final: 0.7531 (mt-10) REVERT: Aa 206 THR cc_start: 0.9503 (p) cc_final: 0.9256 (t) REVERT: Ac 55 ARG cc_start: 0.8602 (mmm160) cc_final: 0.7991 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8863 (m-30) cc_final: 0.8549 (m-30) REVERT: Ac 181 MET cc_start: 0.9061 (tpp) cc_final: 0.8748 (tpp) REVERT: Ae 108 MET cc_start: 0.9385 (tpt) cc_final: 0.8900 (tpt) REVERT: Ag 95 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7861 (mt-10) REVERT: Ag 204 GLU cc_start: 0.9300 (tt0) cc_final: 0.9053 (tt0) REVERT: Ag 212 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.8028 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7710 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9189 (m-40) cc_final: 0.8899 (m110) REVERT: Ai 175 ASN cc_start: 0.8957 (m-40) cc_final: 0.8255 (m110) REVERT: Ai 215 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7385 (mt-10) REVERT: Ai 220 MET cc_start: 0.9072 (mtm) cc_final: 0.8791 (mtm) REVERT: Ak 134 MET cc_start: 0.9064 (ttt) cc_final: 0.8817 (ttt) REVERT: Ak 191 ARG cc_start: 0.7897 (mtp-110) cc_final: 0.7632 (mtp-110) REVERT: Ak 212 ARG cc_start: 0.8541 (ttp-110) cc_final: 0.8191 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7577 (mt-10) REVERT: Am 92 THR cc_start: 0.9506 (m) cc_final: 0.9274 (m) REVERT: Am 191 ARG cc_start: 0.7979 (mtp-110) cc_final: 0.7485 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7987 (ttp-170) REVERT: Ao 110 THR cc_start: 0.9157 (m) cc_final: 0.8830 (m) REVERT: Ao 129 ASN cc_start: 0.9170 (p0) cc_final: 0.8932 (p0) REVERT: Ao 134 MET cc_start: 0.9060 (ttt) cc_final: 0.8435 (ttt) REVERT: Ao 180 TYR cc_start: 0.9225 (t80) cc_final: 0.8883 (t80) REVERT: Ao 204 GLU cc_start: 0.9097 (tt0) cc_final: 0.8514 (tt0) REVERT: Ao 212 ARG cc_start: 0.8570 (ttp-110) cc_final: 0.8019 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8673 (tpt-90) cc_final: 0.8137 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7911 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.7852 (ttp-170) REVERT: As 79 ASP cc_start: 0.8939 (m-30) cc_final: 0.8698 (m-30) REVERT: As 95 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7806 (mt-10) REVERT: As 116 MET cc_start: 0.9510 (ttp) cc_final: 0.9099 (ttp) REVERT: As 160 MET cc_start: 0.9562 (mmm) cc_final: 0.9265 (mmt) REVERT: As 172 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7742 (mm-30) REVERT: As 212 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.7981 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9055 (m-30) cc_final: 0.8728 (m-30) REVERT: Au 95 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7489 (mt-10) REVERT: Au 175 ASN cc_start: 0.8922 (m-40) cc_final: 0.8634 (m-40) REVERT: Au 177 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8450 (ttmm) REVERT: Au 208 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7971 (ptm160) REVERT: Aw 67 LEU cc_start: 0.8825 (mt) cc_final: 0.8587 (mm) REVERT: Aw 110 THR cc_start: 0.9350 (m) cc_final: 0.8997 (m) REVERT: Aw 134 MET cc_start: 0.9054 (ttt) cc_final: 0.8418 (ttt) REVERT: Aw 190 LEU cc_start: 0.8900 (tp) cc_final: 0.8583 (mp) REVERT: Aw 208 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8015 (ptm160) REVERT: Ay 56 MET cc_start: 0.8945 (mtt) cc_final: 0.8500 (mtt) REVERT: Ay 95 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7838 (mt-10) REVERT: Ba 212 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8006 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7820 (mt-10) REVERT: Bc 97 VAL cc_start: 0.9301 (t) cc_final: 0.9024 (t) REVERT: Bc 212 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8041 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7531 (mt-10) REVERT: Be 55 ARG cc_start: 0.8809 (tpt-90) cc_final: 0.8416 (tpt-90) REVERT: Be 79 ASP cc_start: 0.9029 (m-30) cc_final: 0.8668 (m-30) REVERT: Be 95 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7720 (mt-10) REVERT: Be 177 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8370 (ttmm) REVERT: Be 191 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.7696 (mtp-110) REVERT: Bg 99 LEU cc_start: 0.8783 (tp) cc_final: 0.8576 (tp) REVERT: Bg 212 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8176 (ttp-170) REVERT: Bi 55 ARG cc_start: 0.8476 (tpt-90) cc_final: 0.8086 (tpt-90) REVERT: Bi 151 ASN cc_start: 0.9125 (m-40) cc_final: 0.8809 (m110) REVERT: Bi 177 LYS cc_start: 0.8621 (mttt) cc_final: 0.8197 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9130 (tt0) cc_final: 0.8839 (tt0) REVERT: Bi 206 THR cc_start: 0.9518 (p) cc_final: 0.9180 (t) REVERT: Bi 212 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.7975 (ttp-170) REVERT: Bi 220 MET cc_start: 0.8983 (mtm) cc_final: 0.8644 (mtp) REVERT: Bk 67 LEU cc_start: 0.8657 (mt) cc_final: 0.8446 (mm) REVERT: Bk 79 ASP cc_start: 0.8996 (m-30) cc_final: 0.8637 (m-30) REVERT: Bk 102 ASP cc_start: 0.8265 (t70) cc_final: 0.7933 (t0) REVERT: Bk 110 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8927 (m) REVERT: Bk 134 MET cc_start: 0.8938 (ttt) cc_final: 0.8492 (ttt) REVERT: Bk 191 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7529 (mtp-110) REVERT: Bk 212 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.7896 (ttp-170) REVERT: Bm 55 ARG cc_start: 0.8640 (tpt-90) cc_final: 0.8195 (tpt-90) REVERT: Bm 95 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7820 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8327 (ttmt) REVERT: Bo 95 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7554 (mt-10) outliers start: 124 outliers final: 91 residues processed: 1256 average time/residue: 0.4762 time to fit residues: 948.1532 Evaluate side-chains 1257 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1162 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 122 ASN Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 172 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 50 ILE Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 122 ASN Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 107 GLU Chi-restraints excluded: chain Ao residue 142 GLU Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 65 LEU Chi-restraints excluded: chain Au residue 84 ARG Chi-restraints excluded: chain Au residue 103 ILE Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 54 MET Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 103 ILE Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Bc residue 50 ILE Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 178 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Be residue 186 LEU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 64 VAL Chi-restraints excluded: chain Bg residue 103 ILE Chi-restraints excluded: chain Bg residue 107 GLU Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 50 ILE Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 0.0040 chunk 329 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN Ac 66 ASN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN Ag 77 GLN Ai 77 GLN Ak 66 ASN Am 113 ASN As 66 ASN Aw 66 ASN Ay 66 ASN ** Ay 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 158 GLN ** Bc 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 77 GLN Bg 66 ASN Bk 66 ASN ** Bm 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 151 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34293 Z= 0.209 Angle : 0.498 7.246 46851 Z= 0.255 Chirality : 0.039 0.211 5271 Planarity : 0.005 0.046 5712 Dihedral : 15.179 176.330 5943 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.61 % Allowed : 20.20 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.19 (0.13), residues: 3864 helix: 0.91 (0.12), residues: 1890 sheet: -0.09 (0.29), residues: 252 loop : -0.66 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAc 132 HIS 0.003 0.001 HISAa 217 PHE 0.015 0.002 PHEBa 200 TYR 0.017 0.001 TYRBo 198 ARG 0.007 0.001 ARGBa 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1202 time to evaluate : 3.595 Fit side-chains revert: symmetry clash REVERT: Aa 55 ARG cc_start: 0.8670 (tpt-90) cc_final: 0.8392 (tpt-90) REVERT: Aa 79 ASP cc_start: 0.9047 (m-30) cc_final: 0.8752 (m-30) REVERT: Aa 95 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7744 (mt-10) REVERT: Aa 172 GLU cc_start: 0.8164 (tt0) cc_final: 0.7504 (mt-10) REVERT: Aa 206 THR cc_start: 0.9498 (p) cc_final: 0.9241 (t) REVERT: Ac 55 ARG cc_start: 0.8522 (mmm160) cc_final: 0.7871 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8837 (m-30) cc_final: 0.8509 (m-30) REVERT: Ac 190 LEU cc_start: 0.9028 (tp) cc_final: 0.8745 (mp) REVERT: Ae 108 MET cc_start: 0.9366 (tpt) cc_final: 0.8929 (tpt) REVERT: Ae 212 ARG cc_start: 0.8538 (ttp-110) cc_final: 0.7778 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7831 (mt-10) REVERT: Ag 212 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.7952 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7693 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9153 (m-40) cc_final: 0.8871 (m-40) REVERT: Ai 172 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7782 (mt-10) REVERT: Ai 175 ASN cc_start: 0.8962 (m-40) cc_final: 0.8265 (m110) REVERT: Ai 215 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7384 (mt-10) REVERT: Ai 220 MET cc_start: 0.8997 (mtm) cc_final: 0.8721 (mtm) REVERT: Ak 79 ASP cc_start: 0.9035 (m-30) cc_final: 0.8755 (m-30) REVERT: Ak 191 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7417 (mtp-110) REVERT: Ak 212 ARG cc_start: 0.8520 (ttp-110) cc_final: 0.8166 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7492 (mt-10) REVERT: Am 92 THR cc_start: 0.9518 (m) cc_final: 0.9315 (m) REVERT: Am 191 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7424 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8417 (ttp-110) cc_final: 0.7957 (ttp-170) REVERT: Ao 54 MET cc_start: 0.7679 (ptt) cc_final: 0.7342 (ptt) REVERT: Ao 110 THR cc_start: 0.9131 (m) cc_final: 0.8771 (m) REVERT: Ao 129 ASN cc_start: 0.9145 (p0) cc_final: 0.8915 (p0) REVERT: Ao 134 MET cc_start: 0.8993 (ttt) cc_final: 0.8365 (ttt) REVERT: Ao 180 TYR cc_start: 0.9214 (t80) cc_final: 0.8859 (t80) REVERT: Ao 204 GLU cc_start: 0.9060 (tt0) cc_final: 0.8506 (tt0) REVERT: Ao 212 ARG cc_start: 0.8532 (ttp-110) cc_final: 0.7933 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8666 (tpt-90) cc_final: 0.8110 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7832 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.7846 (ttp-170) REVERT: As 79 ASP cc_start: 0.8961 (m-30) cc_final: 0.8735 (m-30) REVERT: As 95 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7781 (mt-10) REVERT: As 136 ASP cc_start: 0.8661 (t0) cc_final: 0.8412 (t0) REVERT: As 172 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: As 212 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.7952 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9025 (m-30) cc_final: 0.8717 (m-30) REVERT: Au 95 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7563 (mt-10) REVERT: Au 175 ASN cc_start: 0.8866 (m-40) cc_final: 0.8582 (m-40) REVERT: Au 177 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8445 (ttmm) REVERT: Au 208 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7943 (ptm160) REVERT: Aw 67 LEU cc_start: 0.8783 (mt) cc_final: 0.8579 (mm) REVERT: Aw 110 THR cc_start: 0.9340 (m) cc_final: 0.8943 (m) REVERT: Aw 134 MET cc_start: 0.9016 (ttt) cc_final: 0.8433 (ttt) REVERT: Aw 190 LEU cc_start: 0.8922 (tp) cc_final: 0.8566 (mp) REVERT: Aw 208 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7844 (ptm160) REVERT: Ay 56 MET cc_start: 0.8862 (mtt) cc_final: 0.8399 (mtt) REVERT: Ay 95 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7832 (mt-10) REVERT: Ba 212 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8076 (ttp-170) REVERT: Bc 95 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7788 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.7965 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7568 (mt-10) REVERT: Be 65 LEU cc_start: 0.9525 (mt) cc_final: 0.9227 (mt) REVERT: Be 79 ASP cc_start: 0.9005 (m-30) cc_final: 0.8635 (m-30) REVERT: Be 95 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7700 (mt-10) REVERT: Be 177 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8343 (ttmm) REVERT: Bg 99 LEU cc_start: 0.8777 (tp) cc_final: 0.8566 (tp) REVERT: Bg 212 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8119 (ttp-170) REVERT: Bi 177 LYS cc_start: 0.8546 (mttt) cc_final: 0.8122 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9113 (tt0) cc_final: 0.8821 (tt0) REVERT: Bi 212 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.7947 (ttp-170) REVERT: Bk 102 ASP cc_start: 0.8268 (t70) cc_final: 0.7922 (t0) REVERT: Bk 110 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8928 (m) REVERT: Bk 134 MET cc_start: 0.8900 (ttt) cc_final: 0.8680 (ttt) REVERT: Bk 142 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: Bk 212 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.8021 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7768 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8344 (ttmt) REVERT: Bo 95 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7540 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8972 (tp) cc_final: 0.8754 (mp) outliers start: 122 outliers final: 93 residues processed: 1258 average time/residue: 0.4735 time to fit residues: 944.5098 Evaluate side-chains 1260 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1162 time to evaluate : 3.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 51 THR Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 107 GLU Chi-restraints excluded: chain Ai residue 177 LYS Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 142 GLU Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 178 GLU Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 83 THR Chi-restraints excluded: chain Au residue 84 ARG Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 50 ILE Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 72 GLU Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 178 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 67 LEU Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Be residue 186 LEU Chi-restraints excluded: chain Bg residue 103 ILE Chi-restraints excluded: chain Bg residue 107 GLU Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 72 GLU Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 142 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 71 LEU Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 206 optimal weight: 8.9990 chunk 307 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 364 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN Ai 77 GLN Aq 151 ASN As 77 GLN Ay 158 GLN Ba 158 GLN ** Bc 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 77 GLN Be 89 GLN Bi 151 ASN ** Bk 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 69 HIS Bm 151 ASN Bo 158 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34293 Z= 0.210 Angle : 0.499 6.869 46851 Z= 0.254 Chirality : 0.039 0.213 5271 Planarity : 0.005 0.048 5712 Dihedral : 15.191 176.540 5943 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.31 % Allowed : 20.97 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.29 (0.13), residues: 3864 helix: 0.98 (0.12), residues: 1890 sheet: -0.14 (0.29), residues: 252 loop : -0.57 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAc 132 HIS 0.003 0.001 HISAa 217 PHE 0.014 0.002 PHEBm 200 TYR 0.016 0.001 TYRBo 198 ARG 0.008 0.001 ARGBi 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1180 time to evaluate : 3.768 Fit side-chains revert: symmetry clash REVERT: Aa 55 ARG cc_start: 0.8654 (tpt-90) cc_final: 0.8400 (tpt-90) REVERT: Aa 77 GLN cc_start: 0.8795 (mt0) cc_final: 0.8587 (mt0) REVERT: Aa 95 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7754 (mt-10) REVERT: Aa 107 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8273 (pt0) REVERT: Aa 172 GLU cc_start: 0.8152 (tt0) cc_final: 0.7486 (mt-10) REVERT: Aa 206 THR cc_start: 0.9500 (p) cc_final: 0.9267 (t) REVERT: Ac 55 ARG cc_start: 0.8556 (mmm160) cc_final: 0.7900 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8825 (m-30) cc_final: 0.8499 (m-30) REVERT: Ae 56 MET cc_start: 0.9001 (mtt) cc_final: 0.8554 (mtt) REVERT: Ae 108 MET cc_start: 0.9367 (tpt) cc_final: 0.8940 (tpt) REVERT: Ae 212 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.7753 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7800 (mt-10) REVERT: Ag 212 ARG cc_start: 0.8545 (ttp-110) cc_final: 0.7831 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7698 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9162 (m-40) cc_final: 0.8902 (m-40) REVERT: Ai 175 ASN cc_start: 0.8967 (m-40) cc_final: 0.8279 (m110) REVERT: Ai 212 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7925 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7389 (mt-10) REVERT: Ai 220 MET cc_start: 0.8998 (mtm) cc_final: 0.8731 (mtm) REVERT: Ak 55 ARG cc_start: 0.8488 (tpt-90) cc_final: 0.8207 (tpt-90) REVERT: Ak 79 ASP cc_start: 0.9019 (m-30) cc_final: 0.8738 (m-30) REVERT: Ak 190 LEU cc_start: 0.8947 (tp) cc_final: 0.8497 (mp) REVERT: Ak 191 ARG cc_start: 0.7700 (mtp-110) cc_final: 0.7345 (mtp-110) REVERT: Ak 212 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8192 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7504 (mt-10) REVERT: Am 50 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8047 (tt) REVERT: Am 191 ARG cc_start: 0.7960 (mtp-110) cc_final: 0.7473 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.7896 (ttp-170) REVERT: Ao 107 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8216 (mt-10) REVERT: Ao 129 ASN cc_start: 0.9119 (p0) cc_final: 0.8910 (p0) REVERT: Ao 180 TYR cc_start: 0.9231 (t80) cc_final: 0.8938 (t80) REVERT: Ao 204 GLU cc_start: 0.9064 (tt0) cc_final: 0.8521 (tt0) REVERT: Ao 212 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.7870 (ttp-170) REVERT: Aq 55 ARG cc_start: 0.8678 (tpt-90) cc_final: 0.8089 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7940 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7887 (ttp-170) REVERT: As 55 ARG cc_start: 0.8800 (tpt-90) cc_final: 0.8205 (tpt-90) REVERT: As 79 ASP cc_start: 0.8950 (m-30) cc_final: 0.8561 (m-30) REVERT: As 95 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7780 (mt-10) REVERT: As 136 ASP cc_start: 0.8682 (t0) cc_final: 0.8456 (t0) REVERT: As 172 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: As 212 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.7938 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9034 (m-30) cc_final: 0.8727 (m-30) REVERT: Au 95 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7571 (mt-10) REVERT: Au 175 ASN cc_start: 0.8875 (m-40) cc_final: 0.8593 (m-40) REVERT: Au 177 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8427 (ttmm) REVERT: Au 208 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7920 (ptm160) REVERT: Aw 50 ILE cc_start: 0.8385 (mt) cc_final: 0.8055 (tt) REVERT: Aw 110 THR cc_start: 0.9340 (m) cc_final: 0.8950 (m) REVERT: Aw 134 MET cc_start: 0.9003 (ttt) cc_final: 0.8504 (ttt) REVERT: Aw 190 LEU cc_start: 0.8910 (tp) cc_final: 0.8579 (mp) REVERT: Aw 208 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7774 (ptm160) REVERT: Ay 56 MET cc_start: 0.8890 (mtt) cc_final: 0.8429 (mtt) REVERT: Ay 95 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7839 (mt-10) REVERT: Ba 180 TYR cc_start: 0.9123 (t80) cc_final: 0.8760 (t80) REVERT: Ba 212 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8107 (ttp-170) REVERT: Ba 219 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7729 (tt0) REVERT: Bc 95 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7787 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.7961 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7598 (mt-10) REVERT: Be 68 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: Be 79 ASP cc_start: 0.8997 (m-30) cc_final: 0.8634 (m-30) REVERT: Be 95 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7700 (mt-10) REVERT: Be 177 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8342 (ttmm) REVERT: Bg 99 LEU cc_start: 0.8766 (tp) cc_final: 0.8562 (tp) REVERT: Bg 212 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8145 (ttp-170) REVERT: Bi 151 ASN cc_start: 0.9085 (m-40) cc_final: 0.8852 (m110) REVERT: Bi 177 LYS cc_start: 0.8536 (mttt) cc_final: 0.8136 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9115 (tt0) cc_final: 0.8834 (tt0) REVERT: Bi 212 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8006 (ttp-170) REVERT: Bk 102 ASP cc_start: 0.8264 (t70) cc_final: 0.7910 (t0) REVERT: Bk 110 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8883 (m) REVERT: Bk 134 MET cc_start: 0.8901 (ttt) cc_final: 0.8454 (ttt) REVERT: Bk 212 ARG cc_start: 0.8447 (ttp-110) cc_final: 0.8025 (ttp-170) REVERT: Bm 95 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7739 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8336 (ttmt) REVERT: Bo 95 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7552 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8984 (tp) cc_final: 0.8725 (mp) outliers start: 112 outliers final: 87 residues processed: 1233 average time/residue: 0.4650 time to fit residues: 917.9722 Evaluate side-chains 1254 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1161 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 122 ASN Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Am residue 50 ILE Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain Aq residue 178 GLU Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 83 THR Chi-restraints excluded: chain Au residue 84 ARG Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Bc residue 178 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 68 GLU Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Be residue 186 LEU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 107 GLU Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 72 GLU Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 71 LEU Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 109 optimal weight: 0.0770 chunk 71 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 286 optimal weight: 0.0470 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN Ag 77 GLN Aq 77 GLN As 77 GLN Ba 158 GLN ** Bc 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 77 GLN ** Bk 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 151 ASN ** Bo 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 158 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34293 Z= 0.229 Angle : 0.509 7.216 46851 Z= 0.258 Chirality : 0.039 0.211 5271 Planarity : 0.005 0.047 5712 Dihedral : 15.203 176.223 5943 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.46 % Allowed : 20.97 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.50 (0.13), residues: 3864 helix: 1.34 (0.12), residues: 1764 sheet: -0.15 (0.29), residues: 252 loop : -0.56 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAk 132 HIS 0.003 0.001 HISAa 217 PHE 0.014 0.002 PHEBo 163 TYR 0.019 0.001 TYRAk 198 ARG 0.008 0.001 ARGAi 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1181 time to evaluate : 3.547 Fit side-chains revert: symmetry clash REVERT: Aa 79 ASP cc_start: 0.8861 (m-30) cc_final: 0.8577 (m-30) REVERT: Aa 95 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7763 (mt-10) REVERT: Aa 172 GLU cc_start: 0.8183 (tt0) cc_final: 0.7527 (mt-10) REVERT: Aa 206 THR cc_start: 0.9501 (p) cc_final: 0.9277 (t) REVERT: Ac 55 ARG cc_start: 0.8584 (mmm160) cc_final: 0.7857 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8825 (m-30) cc_final: 0.8511 (m-30) REVERT: Ae 56 MET cc_start: 0.9049 (mtt) cc_final: 0.8599 (mtt) REVERT: Ae 108 MET cc_start: 0.9363 (tpt) cc_final: 0.8931 (tpt) REVERT: Ae 212 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.7818 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7808 (mt-10) REVERT: Ag 212 ARG cc_start: 0.8542 (ttp-110) cc_final: 0.7831 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7700 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9170 (m-40) cc_final: 0.8913 (m-40) REVERT: Ai 172 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7815 (mt-10) REVERT: Ai 175 ASN cc_start: 0.8957 (m-40) cc_final: 0.8265 (m110) REVERT: Ai 212 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.7880 (ttp-170) REVERT: Ai 215 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7400 (mt-10) REVERT: Ak 55 ARG cc_start: 0.8534 (tpt-90) cc_final: 0.8252 (tpt-90) REVERT: Ak 79 ASP cc_start: 0.9020 (m-30) cc_final: 0.8741 (m-30) REVERT: Ak 190 LEU cc_start: 0.8939 (tp) cc_final: 0.8506 (mp) REVERT: Ak 191 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7330 (mtp-110) REVERT: Ak 212 ARG cc_start: 0.8541 (ttp-110) cc_final: 0.8211 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7500 (mt-10) REVERT: Am 107 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: Am 116 MET cc_start: 0.9577 (ttp) cc_final: 0.9314 (ttp) REVERT: Am 172 GLU cc_start: 0.8071 (tt0) cc_final: 0.7833 (tt0) REVERT: Am 191 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7477 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.7893 (ttp-170) REVERT: Ao 180 TYR cc_start: 0.9228 (t80) cc_final: 0.8916 (t80) REVERT: Ao 204 GLU cc_start: 0.9069 (tt0) cc_final: 0.8530 (tt0) REVERT: Aq 55 ARG cc_start: 0.8649 (tpt-90) cc_final: 0.8303 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7928 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7895 (ttp-170) REVERT: As 55 ARG cc_start: 0.8792 (tpt-90) cc_final: 0.8207 (tpt-90) REVERT: As 79 ASP cc_start: 0.8956 (m-30) cc_final: 0.8629 (m-30) REVERT: As 95 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7777 (mt-10) REVERT: As 136 ASP cc_start: 0.8694 (t0) cc_final: 0.8468 (t0) REVERT: As 172 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: As 212 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.7920 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9045 (m-30) cc_final: 0.8731 (m-30) REVERT: Au 95 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7575 (mt-10) REVERT: Au 175 ASN cc_start: 0.8875 (m-40) cc_final: 0.8596 (m-40) REVERT: Au 177 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8418 (ttmm) REVERT: Au 208 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7890 (ptm160) REVERT: Aw 110 THR cc_start: 0.9341 (m) cc_final: 0.8961 (m) REVERT: Aw 134 MET cc_start: 0.9012 (ttt) cc_final: 0.8511 (ttt) REVERT: Aw 190 LEU cc_start: 0.8885 (tp) cc_final: 0.8569 (mp) REVERT: Aw 208 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7769 (ptm160) REVERT: Ay 56 MET cc_start: 0.8910 (mtt) cc_final: 0.8434 (mtt) REVERT: Ay 95 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7835 (mt-10) REVERT: Ay 177 LYS cc_start: 0.8710 (mttt) cc_final: 0.8394 (mtpt) REVERT: Ba 180 TYR cc_start: 0.9159 (t80) cc_final: 0.8841 (t80) REVERT: Ba 212 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8129 (ttp-170) REVERT: Ba 219 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7731 (tt0) REVERT: Bc 95 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7798 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8441 (ttp-110) cc_final: 0.7983 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7579 (mt-10) REVERT: Be 68 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: Be 79 ASP cc_start: 0.9002 (m-30) cc_final: 0.8667 (m-30) REVERT: Be 95 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7705 (mt-10) REVERT: Be 177 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8344 (ttmm) REVERT: Bg 99 LEU cc_start: 0.8786 (tp) cc_final: 0.8568 (tp) REVERT: Bg 212 ARG cc_start: 0.8543 (ttp-110) cc_final: 0.8145 (ttp-170) REVERT: Bi 151 ASN cc_start: 0.9049 (m-40) cc_final: 0.8724 (m110) REVERT: Bi 177 LYS cc_start: 0.8525 (mttt) cc_final: 0.8129 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9114 (tt0) cc_final: 0.8830 (tt0) REVERT: Bi 212 ARG cc_start: 0.8529 (ttp-110) cc_final: 0.7997 (ttp-170) REVERT: Bk 46 ARG cc_start: 0.9143 (mpt180) cc_final: 0.8695 (mpt180) REVERT: Bk 55 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8244 (tpt-90) REVERT: Bk 102 ASP cc_start: 0.8265 (t70) cc_final: 0.7909 (t0) REVERT: Bk 110 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8896 (m) REVERT: Bk 134 MET cc_start: 0.8909 (ttt) cc_final: 0.8467 (ttt) REVERT: Bk 142 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: Bk 212 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.7989 (ttp-170) REVERT: Bm 68 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: Bm 95 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7750 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8339 (ttmt) REVERT: Bo 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7563 (mt-10) REVERT: Bo 190 LEU cc_start: 0.8949 (tp) cc_final: 0.8735 (mp) outliers start: 117 outliers final: 98 residues processed: 1238 average time/residue: 0.4715 time to fit residues: 936.7738 Evaluate side-chains 1269 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1163 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 172 GLU Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 122 ASN Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 172 GLU Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 150 GLU Chi-restraints excluded: chain Aq residue 178 GLU Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 51 THR Chi-restraints excluded: chain Au residue 83 THR Chi-restraints excluded: chain Au residue 84 ARG Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 67 LEU Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Aw residue 186 LEU Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 107 GLU Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 68 GLU Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Be residue 166 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Be residue 186 LEU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 103 ILE Chi-restraints excluded: chain Bg residue 107 GLU Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 142 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 68 GLU Chi-restraints excluded: chain Bm residue 71 LEU Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 5.9990 chunk 349 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 339 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 77 GLN ** Ae 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN ** Ag 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 158 GLN ** Ai 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 77 GLN Aq 151 ASN As 77 GLN Au 77 GLN Ba 158 GLN ** Bc 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 151 ASN ** Bo 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 158 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34293 Z= 0.260 Angle : 0.524 7.574 46851 Z= 0.266 Chirality : 0.040 0.181 5271 Planarity : 0.005 0.047 5712 Dihedral : 15.231 175.414 5943 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.52 % Allowed : 21.30 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.47 (0.13), residues: 3864 helix: 1.30 (0.12), residues: 1764 sheet: -0.12 (0.29), residues: 252 loop : -0.56 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAk 132 HIS 0.004 0.001 HISAa 217 PHE 0.014 0.002 PHEBa 200 TYR 0.021 0.001 TYRAk 198 ARG 0.008 0.001 ARGBm 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1169 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7759 (mt-10) REVERT: Aa 172 GLU cc_start: 0.8216 (tt0) cc_final: 0.7563 (mt-10) REVERT: Aa 206 THR cc_start: 0.9510 (p) cc_final: 0.9250 (t) REVERT: Ac 55 ARG cc_start: 0.8578 (mmm160) cc_final: 0.7799 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8832 (m-30) cc_final: 0.8525 (m-30) REVERT: Ac 181 MET cc_start: 0.9065 (tpp) cc_final: 0.8683 (tpp) REVERT: Ae 56 MET cc_start: 0.9052 (mtt) cc_final: 0.8623 (mtt) REVERT: Ae 108 MET cc_start: 0.9374 (tpt) cc_final: 0.8927 (tpt) REVERT: Ae 212 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.7823 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7883 (mt-10) REVERT: Ag 212 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.7787 (ttp-170) REVERT: Ai 79 ASP cc_start: 0.9089 (m-30) cc_final: 0.8836 (m-30) REVERT: Ai 95 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7693 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9188 (m-40) cc_final: 0.8942 (m-40) REVERT: Ai 172 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7743 (mt-10) REVERT: Ai 175 ASN cc_start: 0.8955 (m-40) cc_final: 0.8270 (m110) REVERT: Ai 212 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.7909 (ttp-170) REVERT: Ak 79 ASP cc_start: 0.9036 (m-30) cc_final: 0.8756 (m-30) REVERT: Ak 134 MET cc_start: 0.9011 (ttt) cc_final: 0.8722 (ttt) REVERT: Ak 148 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8544 (mm) REVERT: Ak 190 LEU cc_start: 0.8939 (tp) cc_final: 0.8496 (mp) REVERT: Ak 191 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7424 (mtp-110) REVERT: Ak 212 ARG cc_start: 0.8530 (ttp-110) cc_final: 0.8215 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7515 (mt-10) REVERT: Ak 225 LEU cc_start: 0.8678 (mt) cc_final: 0.8425 (mp) REVERT: Am 56 MET cc_start: 0.9070 (mmt) cc_final: 0.8703 (mmm) REVERT: Am 107 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: Am 116 MET cc_start: 0.9568 (ttp) cc_final: 0.9320 (ttp) REVERT: Am 172 GLU cc_start: 0.8102 (tt0) cc_final: 0.7856 (tt0) REVERT: Am 191 ARG cc_start: 0.7882 (mtp-110) cc_final: 0.7472 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7922 (ttp-170) REVERT: Ao 107 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8226 (mp0) REVERT: Ao 180 TYR cc_start: 0.9236 (t80) cc_final: 0.8970 (t80) REVERT: Ao 204 GLU cc_start: 0.9070 (tt0) cc_final: 0.8483 (tt0) REVERT: Aq 55 ARG cc_start: 0.8656 (tpt-90) cc_final: 0.8303 (tpt-90) REVERT: Aq 95 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7915 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8393 (ttp-110) cc_final: 0.7897 (ttp-170) REVERT: As 55 ARG cc_start: 0.8854 (tpt-90) cc_final: 0.8247 (tpt-90) REVERT: As 79 ASP cc_start: 0.8956 (m-30) cc_final: 0.8639 (m-30) REVERT: As 95 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7779 (mt-10) REVERT: As 136 ASP cc_start: 0.8679 (t0) cc_final: 0.8477 (t0) REVERT: As 212 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.7916 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9057 (m-30) cc_final: 0.8738 (m-30) REVERT: Au 95 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7575 (mt-10) REVERT: Au 175 ASN cc_start: 0.8890 (m-40) cc_final: 0.8618 (m-40) REVERT: Au 177 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8427 (ttmm) REVERT: Au 208 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7916 (ptm160) REVERT: Aw 110 THR cc_start: 0.9334 (m) cc_final: 0.8966 (m) REVERT: Aw 134 MET cc_start: 0.9028 (ttt) cc_final: 0.8515 (ttt) REVERT: Aw 190 LEU cc_start: 0.8914 (tp) cc_final: 0.8576 (mp) REVERT: Ay 56 MET cc_start: 0.8960 (mtt) cc_final: 0.8483 (mtt) REVERT: Ay 95 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7887 (mt-10) REVERT: Ay 177 LYS cc_start: 0.8739 (mttt) cc_final: 0.8446 (mtpt) REVERT: Ba 180 TYR cc_start: 0.9165 (t80) cc_final: 0.8857 (t80) REVERT: Ba 212 ARG cc_start: 0.8598 (ttp-110) cc_final: 0.8147 (ttp-170) REVERT: Ba 219 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7745 (tt0) REVERT: Bc 95 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7813 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8008 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7637 (mt-10) REVERT: Be 68 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: Be 79 ASP cc_start: 0.9028 (m-30) cc_final: 0.8668 (m-30) REVERT: Be 95 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7713 (mt-10) REVERT: Be 177 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8345 (ttmm) REVERT: Bg 99 LEU cc_start: 0.8799 (tp) cc_final: 0.8573 (tp) REVERT: Bg 212 ARG cc_start: 0.8539 (ttp-110) cc_final: 0.8138 (ttp-170) REVERT: Bi 71 LEU cc_start: 0.8958 (mm) cc_final: 0.8707 (mm) REVERT: Bi 177 LYS cc_start: 0.8524 (mttt) cc_final: 0.8127 (ttmm) REVERT: Bi 204 GLU cc_start: 0.9118 (tt0) cc_final: 0.8841 (tt0) REVERT: Bi 212 ARG cc_start: 0.8524 (ttp-110) cc_final: 0.8002 (ttp-170) REVERT: Bk 46 ARG cc_start: 0.9110 (mpt180) cc_final: 0.8686 (mpt180) REVERT: Bk 55 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8254 (tpt-90) REVERT: Bk 102 ASP cc_start: 0.8260 (t70) cc_final: 0.7903 (t0) REVERT: Bk 110 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8884 (m) REVERT: Bk 134 MET cc_start: 0.8927 (ttt) cc_final: 0.8488 (ttt) REVERT: Bk 142 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: Bk 212 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.8031 (ttp-170) REVERT: Bk 225 LEU cc_start: 0.8774 (mt) cc_final: 0.8556 (mm) REVERT: Bm 95 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7743 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8328 (ttmt) REVERT: Bo 95 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7561 (mt-10) outliers start: 119 outliers final: 103 residues processed: 1227 average time/residue: 0.4910 time to fit residues: 969.1596 Evaluate side-chains 1265 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1156 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 122 ASN Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 122 ASN Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ai residue 64 VAL Chi-restraints excluded: chain Ai residue 122 ASN Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 148 ILE Chi-restraints excluded: chain Ak residue 172 GLU Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 177 LYS Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 150 GLU Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain Aq residue 178 GLU Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 64 VAL Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 122 ASN Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 83 THR Chi-restraints excluded: chain Au residue 84 ARG Chi-restraints excluded: chain Au residue 103 ILE Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 67 LEU Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Ay residue 107 GLU Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 133 VAL Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Be residue 64 VAL Chi-restraints excluded: chain Be residue 68 GLU Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 124 THR Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Be residue 166 VAL Chi-restraints excluded: chain Be residue 178 GLU Chi-restraints excluded: chain Be residue 186 LEU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 103 ILE Chi-restraints excluded: chain Bg residue 107 GLU Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bg residue 178 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 122 ASN Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 142 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 50 ILE Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 71 LEU Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 122 ASN Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 122 ASN Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 359 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 376 optimal weight: 0.8980 chunk 346 optimal weight: 0.4980 chunk 299 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 77 GLN Ae 151 ASN Ai 77 GLN Am 66 ASN As 77 GLN Au 77 GLN Ba 158 GLN Be 77 GLN Bi 151 ASN ** Bo 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 158 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34293 Z= 0.153 Angle : 0.492 7.585 46851 Z= 0.247 Chirality : 0.038 0.235 5271 Planarity : 0.005 0.048 5712 Dihedral : 15.151 178.257 5943 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.93 % Allowed : 21.92 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.83 (0.13), residues: 3864 helix: 1.50 (0.13), residues: 1806 sheet: 1.20 (0.26), residues: 210 loop : -0.45 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAm 132 HIS 0.003 0.001 HISAm 217 PHE 0.015 0.002 PHEAw 200 TYR 0.017 0.001 TYRAk 198 ARG 0.009 0.001 ARGBm 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1168 time to evaluate : 3.737 Fit side-chains revert: symmetry clash REVERT: Aa 95 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7735 (mt-10) REVERT: Aa 172 GLU cc_start: 0.8174 (tt0) cc_final: 0.7539 (mt-10) REVERT: Aa 190 LEU cc_start: 0.8984 (tp) cc_final: 0.8680 (mp) REVERT: Aa 206 THR cc_start: 0.9514 (p) cc_final: 0.9263 (t) REVERT: Ac 55 ARG cc_start: 0.8562 (mmm160) cc_final: 0.7876 (tpt-90) REVERT: Ac 91 ASP cc_start: 0.8784 (m-30) cc_final: 0.8462 (m-30) REVERT: Ac 190 LEU cc_start: 0.8984 (tp) cc_final: 0.8767 (mp) REVERT: Ae 56 MET cc_start: 0.8971 (mtt) cc_final: 0.8550 (mtt) REVERT: Ae 108 MET cc_start: 0.9328 (tpt) cc_final: 0.9022 (tpt) REVERT: Ae 212 ARG cc_start: 0.8470 (ttp-110) cc_final: 0.7904 (ttp-170) REVERT: Ag 95 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7778 (mt-10) REVERT: Ag 212 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.7810 (ttp-170) REVERT: Ai 95 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7726 (mt-10) REVERT: Ai 151 ASN cc_start: 0.9113 (m-40) cc_final: 0.8873 (m-40) REVERT: Ai 172 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7634 (mt-10) REVERT: Ai 175 ASN cc_start: 0.8925 (m-40) cc_final: 0.8280 (m110) REVERT: Ai 212 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.7934 (ttp-170) REVERT: Ak 55 ARG cc_start: 0.8485 (tpt-90) cc_final: 0.8139 (tpt-90) REVERT: Ak 79 ASP cc_start: 0.8995 (m-30) cc_final: 0.8687 (m-30) REVERT: Ak 139 GLU cc_start: 0.8127 (tp30) cc_final: 0.7835 (tp30) REVERT: Ak 148 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8493 (mm) REVERT: Ak 190 LEU cc_start: 0.8880 (tp) cc_final: 0.8577 (mp) REVERT: Ak 212 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.8188 (ttp-170) REVERT: Ak 215 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7478 (mt-10) REVERT: Ak 225 LEU cc_start: 0.8552 (mt) cc_final: 0.8311 (mm) REVERT: Am 107 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: Am 136 ASP cc_start: 0.8757 (t0) cc_final: 0.8549 (t0) REVERT: Am 177 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8340 (ttmm) REVERT: Am 191 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7360 (mtp-110) REVERT: Am 212 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7874 (ttp-170) REVERT: Ao 180 TYR cc_start: 0.9159 (t80) cc_final: 0.8842 (t80) REVERT: Ao 204 GLU cc_start: 0.9051 (tt0) cc_final: 0.8507 (tt0) REVERT: Ao 212 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.7735 (ttp-170) REVERT: Aq 95 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7951 (mt-10) REVERT: Aq 212 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.7906 (ttp-170) REVERT: As 55 ARG cc_start: 0.8823 (tpt-90) cc_final: 0.8253 (tpt-90) REVERT: As 79 ASP cc_start: 0.8912 (m-30) cc_final: 0.8676 (m-30) REVERT: As 95 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7757 (mt-10) REVERT: As 136 ASP cc_start: 0.8643 (t0) cc_final: 0.8442 (t0) REVERT: As 172 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: As 212 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.7852 (ttp-170) REVERT: Au 79 ASP cc_start: 0.9034 (m-30) cc_final: 0.8722 (m-30) REVERT: Au 95 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7562 (mt-10) REVERT: Au 175 ASN cc_start: 0.8847 (m-40) cc_final: 0.8571 (m-40) REVERT: Au 177 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8412 (ttmm) REVERT: Au 208 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7916 (ptm160) REVERT: Aw 110 THR cc_start: 0.9319 (m) cc_final: 0.8926 (m) REVERT: Aw 134 MET cc_start: 0.8922 (ttt) cc_final: 0.8311 (ttt) REVERT: Aw 177 LYS cc_start: 0.8676 (mttt) cc_final: 0.8272 (ttmm) REVERT: Ay 56 MET cc_start: 0.8831 (mtt) cc_final: 0.8362 (mtt) REVERT: Ay 95 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7841 (mt-10) REVERT: Ba 177 LYS cc_start: 0.8665 (mttt) cc_final: 0.8342 (ttmm) REVERT: Ba 180 TYR cc_start: 0.9122 (t80) cc_final: 0.8800 (t80) REVERT: Ba 212 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8139 (ttp-170) REVERT: Ba 219 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7716 (tt0) REVERT: Bc 95 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7798 (mt-10) REVERT: Bc 212 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.7939 (ttp-170) REVERT: Bc 215 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7626 (mt-10) REVERT: Be 68 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: Be 79 ASP cc_start: 0.9011 (m-30) cc_final: 0.8678 (m-30) REVERT: Be 95 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7695 (mt-10) REVERT: Be 177 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8364 (ttmm) REVERT: Bg 99 LEU cc_start: 0.8758 (tp) cc_final: 0.8545 (tp) REVERT: Bg 212 ARG cc_start: 0.8484 (ttp-110) cc_final: 0.8078 (ttp-170) REVERT: Bg 220 MET cc_start: 0.9123 (mtm) cc_final: 0.8836 (mtp) REVERT: Bi 71 LEU cc_start: 0.8862 (mm) cc_final: 0.8594 (mm) REVERT: Bi 139 GLU cc_start: 0.8098 (tp30) cc_final: 0.7838 (tp30) REVERT: Bi 177 LYS cc_start: 0.8491 (mttt) cc_final: 0.8138 (ttmm) REVERT: Bi 212 ARG cc_start: 0.8525 (ttp-110) cc_final: 0.8013 (ttp-170) REVERT: Bk 46 ARG cc_start: 0.9101 (mpt180) cc_final: 0.8627 (mpt180) REVERT: Bk 55 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8161 (tpt-90) REVERT: Bk 102 ASP cc_start: 0.8246 (t70) cc_final: 0.7897 (t0) REVERT: Bk 110 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (m) REVERT: Bk 115 LEU cc_start: 0.9345 (tp) cc_final: 0.9055 (tp) REVERT: Bk 142 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: Bk 212 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.8042 (ttp-170) REVERT: Bm 68 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: Bm 95 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7780 (mt-10) REVERT: Bm 177 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8321 (ttmt) REVERT: Bm 190 LEU cc_start: 0.9002 (tp) cc_final: 0.8758 (mp) REVERT: Bo 95 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7558 (mt-10) outliers start: 99 outliers final: 83 residues processed: 1212 average time/residue: 0.4696 time to fit residues: 927.0802 Evaluate side-chains 1238 residues out of total 3381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1147 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 51 THR Chi-restraints excluded: chain Aa residue 178 GLU Chi-restraints excluded: chain Ac residue 107 GLU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ae residue 51 THR Chi-restraints excluded: chain Ae residue 122 ASN Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ag residue 51 THR Chi-restraints excluded: chain Ag residue 107 GLU Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 208 ARG Chi-restraints excluded: chain Ai residue 51 THR Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Ak residue 148 ILE Chi-restraints excluded: chain Ak residue 178 GLU Chi-restraints excluded: chain Am residue 51 THR Chi-restraints excluded: chain Am residue 54 MET Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 178 GLU Chi-restraints excluded: chain Am residue 186 LEU Chi-restraints excluded: chain Ao residue 51 THR Chi-restraints excluded: chain Ao residue 172 GLU Chi-restraints excluded: chain Ao residue 177 LYS Chi-restraints excluded: chain Aq residue 51 THR Chi-restraints excluded: chain Aq residue 122 ASN Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Aq residue 150 GLU Chi-restraints excluded: chain Aq residue 178 GLU Chi-restraints excluded: chain Aq residue 207 SER Chi-restraints excluded: chain As residue 51 THR Chi-restraints excluded: chain As residue 107 GLU Chi-restraints excluded: chain As residue 172 GLU Chi-restraints excluded: chain Au residue 84 ARG Chi-restraints excluded: chain Au residue 107 GLU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Au residue 159 ILE Chi-restraints excluded: chain Au residue 172 GLU Chi-restraints excluded: chain Au residue 208 ARG Chi-restraints excluded: chain Aw residue 64 VAL Chi-restraints excluded: chain Aw residue 107 GLU Chi-restraints excluded: chain Aw residue 186 LEU Chi-restraints excluded: chain Aw residue 208 ARG Chi-restraints excluded: chain Ay residue 51 THR Chi-restraints excluded: chain Ay residue 107 GLU Chi-restraints excluded: chain Ay residue 122 ASN Chi-restraints excluded: chain Ay residue 172 GLU Chi-restraints excluded: chain Ba residue 107 GLU Chi-restraints excluded: chain Ba residue 122 ASN Chi-restraints excluded: chain Ba residue 133 VAL Chi-restraints excluded: chain Ba residue 211 VAL Chi-restraints excluded: chain Bc residue 51 THR Chi-restraints excluded: chain Bc residue 64 VAL Chi-restraints excluded: chain Bc residue 107 GLU Chi-restraints excluded: chain Be residue 68 GLU Chi-restraints excluded: chain Be residue 107 GLU Chi-restraints excluded: chain Be residue 141 VAL Chi-restraints excluded: chain Be residue 142 GLU Chi-restraints excluded: chain Be residue 186 LEU Chi-restraints excluded: chain Bg residue 51 THR Chi-restraints excluded: chain Bg residue 103 ILE Chi-restraints excluded: chain Bg residue 107 GLU Chi-restraints excluded: chain Bg residue 122 ASN Chi-restraints excluded: chain Bg residue 142 GLU Chi-restraints excluded: chain Bg residue 172 GLU Chi-restraints excluded: chain Bi residue 63 THR Chi-restraints excluded: chain Bi residue 64 VAL Chi-restraints excluded: chain Bi residue 107 GLU Chi-restraints excluded: chain Bi residue 178 GLU Chi-restraints excluded: chain Bk residue 51 THR Chi-restraints excluded: chain Bk residue 64 VAL Chi-restraints excluded: chain Bk residue 107 GLU Chi-restraints excluded: chain Bk residue 110 THR Chi-restraints excluded: chain Bk residue 142 GLU Chi-restraints excluded: chain Bk residue 172 GLU Chi-restraints excluded: chain Bk residue 208 ARG Chi-restraints excluded: chain Bm residue 51 THR Chi-restraints excluded: chain Bm residue 68 GLU Chi-restraints excluded: chain Bm residue 71 LEU Chi-restraints excluded: chain Bm residue 107 GLU Chi-restraints excluded: chain Bm residue 133 VAL Chi-restraints excluded: chain Bo residue 51 THR Chi-restraints excluded: chain Bo residue 54 MET Chi-restraints excluded: chain Bo residue 107 GLU Chi-restraints excluded: chain Bo residue 172 GLU Chi-restraints excluded: chain Bo residue 178 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 319 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 308 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 77 GLN Ae 151 ASN ** Ag 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 77 GLN Ao 158 GLN Aq 151 ASN Au 189 ASN Aw 113 ASN Ba 158 GLN ** Bc 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 77 GLN ** Bk 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 113 ASN Bm 151 ASN ** Bo 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 158 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.102345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.083283 restraints weight = 40066.855| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 1.90 r_work: 0.2490 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2329 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 34293 Z= 0.386 Angle : 0.583 7.930 46851 Z= 0.296 Chirality : 0.043 0.241 5271 Planarity : 0.005 0.047 5712 Dihedral : 15.323 174.220 5943 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.19 % Allowed : 21.98 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.43 (0.13), residues: 3864 helix: 1.55 (0.13), residues: 1638 sheet: -0.09 (0.30), residues: 252 loop : -0.75 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAk 132 HIS 0.005 0.001 HISAa 217 PHE 0.018 0.002 PHEBo 163 TYR 0.024 0.002 TYRAk 198 ARG 0.009 0.001 ARGAy 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13004.91 seconds wall clock time: 233 minutes 12.41 seconds (13992.41 seconds total)