Starting phenix.real_space_refine on Wed Feb 21 02:13:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdr_9104/02_2024/6mdr_9104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdr_9104/02_2024/6mdr_9104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdr_9104/02_2024/6mdr_9104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdr_9104/02_2024/6mdr_9104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdr_9104/02_2024/6mdr_9104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mdr_9104/02_2024/6mdr_9104.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 18688 2.51 5 N 5232 2.21 5 O 5456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ARG 74": "NH1" <-> "NH2" Residue "a ARG 81": "NH1" <-> "NH2" Residue "a ARG 110": "NH1" <-> "NH2" Residue "a ARG 129": "NH1" <-> "NH2" Residue "a ARG 143": "NH1" <-> "NH2" Residue "a ARG 216": "NH1" <-> "NH2" Residue "b ARG 32": "NH1" <-> "NH2" Residue "b TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 111": "NH1" <-> "NH2" Residue "b TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 217": "NH1" <-> "NH2" Residue "c ARG 74": "NH1" <-> "NH2" Residue "c ARG 81": "NH1" <-> "NH2" Residue "c ARG 110": "NH1" <-> "NH2" Residue "c ARG 129": "NH1" <-> "NH2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "d TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 217": "NH1" <-> "NH2" Residue "e ARG 74": "NH1" <-> "NH2" Residue "e ARG 81": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e ARG 129": "NH1" <-> "NH2" Residue "e ARG 143": "NH1" <-> "NH2" Residue "e ARG 216": "NH1" <-> "NH2" Residue "f ARG 32": "NH1" <-> "NH2" Residue "f TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 111": "NH1" <-> "NH2" Residue "f TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 217": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g ARG 81": "NH1" <-> "NH2" Residue "g ARG 110": "NH1" <-> "NH2" Residue "g ARG 129": "NH1" <-> "NH2" Residue "g ARG 143": "NH1" <-> "NH2" Residue "g ARG 216": "NH1" <-> "NH2" Residue "h ARG 32": "NH1" <-> "NH2" Residue "h TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 111": "NH1" <-> "NH2" Residue "h TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 217": "NH1" <-> "NH2" Residue "i ARG 74": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i ARG 110": "NH1" <-> "NH2" Residue "i ARG 129": "NH1" <-> "NH2" Residue "i ARG 143": "NH1" <-> "NH2" Residue "i ARG 216": "NH1" <-> "NH2" Residue "j ARG 32": "NH1" <-> "NH2" Residue "j TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 111": "NH1" <-> "NH2" Residue "j TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 217": "NH1" <-> "NH2" Residue "k ARG 74": "NH1" <-> "NH2" Residue "k ARG 81": "NH1" <-> "NH2" Residue "k ARG 110": "NH1" <-> "NH2" Residue "k ARG 129": "NH1" <-> "NH2" Residue "k ARG 143": "NH1" <-> "NH2" Residue "k ARG 216": "NH1" <-> "NH2" Residue "l ARG 32": "NH1" <-> "NH2" Residue "l TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 111": "NH1" <-> "NH2" Residue "l TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 217": "NH1" <-> "NH2" Residue "m ARG 74": "NH1" <-> "NH2" Residue "m ARG 81": "NH1" <-> "NH2" Residue "m ARG 110": "NH1" <-> "NH2" Residue "m ARG 129": "NH1" <-> "NH2" Residue "m ARG 143": "NH1" <-> "NH2" Residue "m ARG 216": "NH1" <-> "NH2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "n TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "n TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 217": "NH1" <-> "NH2" Residue "o ARG 74": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 110": "NH1" <-> "NH2" Residue "o ARG 129": "NH1" <-> "NH2" Residue "o ARG 143": "NH1" <-> "NH2" Residue "o ARG 216": "NH1" <-> "NH2" Residue "p ARG 32": "NH1" <-> "NH2" Residue "p TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 111": "NH1" <-> "NH2" Residue "p TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 217": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29456 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "b" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "c" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "d" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "e" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "f" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "g" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "h" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "i" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "j" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "k" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "l" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "m" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "n" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain: "o" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1852 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain: "p" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1830 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Time building chain proxies: 15.94, per 1000 atoms: 0.54 Number of scatterers: 29456 At special positions: 0 Unit cell: (155.1, 155.1, 100.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 5456 8.00 N 5232 7.00 C 18688 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: 10.44 Conformation dependent library (CDL) restraints added in 5.6 seconds 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6672 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 11.7% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'a' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG a 10 " --> pdb=" O ARG a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 60 Processing helix chain 'a' and resid 61 through 66 Processing helix chain 'a' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER a 87 " --> pdb=" O ASP a 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE b 10 " --> pdb=" O GLU b 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR b 11 " --> pdb=" O GLU b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL b 63 " --> pdb=" O PRO b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE b 73 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS b 81 " --> pdb=" O ASP b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 89 removed outlier: 3.629A pdb=" N SER b 88 " --> pdb=" O ASP b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 161 Processing helix chain 'c' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG c 10 " --> pdb=" O ARG c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 60 Processing helix chain 'c' and resid 61 through 66 Processing helix chain 'c' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE d 10 " --> pdb=" O GLU d 7 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR d 11 " --> pdb=" O GLU d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL d 63 " --> pdb=" O PRO d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE d 73 " --> pdb=" O VAL d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS d 81 " --> pdb=" O ASP d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER d 88 " --> pdb=" O ASP d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 158 through 161 Processing helix chain 'e' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG e 10 " --> pdb=" O ARG e 7 " (cutoff:3.500A) Processing helix chain 'e' and resid 57 through 60 Processing helix chain 'e' and resid 61 through 66 Processing helix chain 'e' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER e 87 " --> pdb=" O ASP e 83 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE f 10 " --> pdb=" O GLU f 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR f 11 " --> pdb=" O GLU f 8 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL f 63 " --> pdb=" O PRO f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE f 73 " --> pdb=" O VAL f 70 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 81 removed outlier: 3.870A pdb=" N LYS f 81 " --> pdb=" O ASP f 78 " (cutoff:3.500A) Processing helix chain 'f' and resid 84 through 89 removed outlier: 3.629A pdb=" N SER f 88 " --> pdb=" O ASP f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 158 through 161 Processing helix chain 'g' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG g 10 " --> pdb=" O ARG g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 60 Processing helix chain 'g' and resid 61 through 66 Processing helix chain 'g' and resid 83 through 88 removed outlier: 3.776A pdb=" N SER g 87 " --> pdb=" O ASP g 83 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 11 removed outlier: 3.532A pdb=" N PHE h 10 " --> pdb=" O GLU h 7 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR h 11 " --> pdb=" O GLU h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL h 63 " --> pdb=" O PRO h 60 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE h 73 " --> pdb=" O VAL h 70 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS h 81 " --> pdb=" O ASP h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 89 removed outlier: 3.629A pdb=" N SER h 88 " --> pdb=" O ASP h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 161 Processing helix chain 'i' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG i 10 " --> pdb=" O ARG i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 57 through 60 Processing helix chain 'i' and resid 61 through 66 Processing helix chain 'i' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER i 87 " --> pdb=" O ASP i 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE j 10 " --> pdb=" O GLU j 7 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR j 11 " --> pdb=" O GLU j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 63 removed outlier: 3.594A pdb=" N VAL j 63 " --> pdb=" O PRO j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE j 73 " --> pdb=" O VAL j 70 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS j 81 " --> pdb=" O ASP j 78 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER j 88 " --> pdb=" O ASP j 84 " (cutoff:3.500A) Processing helix chain 'j' and resid 158 through 161 Processing helix chain 'k' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG k 10 " --> pdb=" O ARG k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 60 Processing helix chain 'k' and resid 61 through 66 Processing helix chain 'k' and resid 83 through 88 removed outlier: 3.774A pdb=" N SER k 87 " --> pdb=" O ASP k 83 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 11 removed outlier: 3.533A pdb=" N PHE l 10 " --> pdb=" O GLU l 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR l 11 " --> pdb=" O GLU l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL l 63 " --> pdb=" O PRO l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE l 73 " --> pdb=" O VAL l 70 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS l 81 " --> pdb=" O ASP l 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER l 88 " --> pdb=" O ASP l 84 " (cutoff:3.500A) Processing helix chain 'l' and resid 158 through 161 Processing helix chain 'm' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG m 10 " --> pdb=" O ARG m 7 " (cutoff:3.500A) Processing helix chain 'm' and resid 57 through 60 Processing helix chain 'm' and resid 61 through 66 Processing helix chain 'm' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER m 87 " --> pdb=" O ASP m 83 " (cutoff:3.500A) Processing helix chain 'n' and resid 6 through 11 removed outlier: 3.532A pdb=" N PHE n 10 " --> pdb=" O GLU n 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR n 11 " --> pdb=" O GLU n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL n 63 " --> pdb=" O PRO n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 70 through 74 removed outlier: 4.184A pdb=" N PHE n 73 " --> pdb=" O VAL n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 77 through 81 removed outlier: 3.870A pdb=" N LYS n 81 " --> pdb=" O ASP n 78 " (cutoff:3.500A) Processing helix chain 'n' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER n 88 " --> pdb=" O ASP n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 158 through 161 Processing helix chain 'o' and resid 5 through 10 removed outlier: 3.723A pdb=" N ARG o 10 " --> pdb=" O ARG o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 57 through 60 Processing helix chain 'o' and resid 61 through 66 Processing helix chain 'o' and resid 83 through 88 removed outlier: 3.775A pdb=" N SER o 87 " --> pdb=" O ASP o 83 " (cutoff:3.500A) Processing helix chain 'p' and resid 6 through 11 removed outlier: 3.532A pdb=" N PHE p 10 " --> pdb=" O GLU p 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR p 11 " --> pdb=" O GLU p 8 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 63 removed outlier: 3.593A pdb=" N VAL p 63 " --> pdb=" O PRO p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 74 removed outlier: 4.185A pdb=" N PHE p 73 " --> pdb=" O VAL p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 77 through 81 removed outlier: 3.871A pdb=" N LYS p 81 " --> pdb=" O ASP p 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 84 through 89 removed outlier: 3.630A pdb=" N SER p 88 " --> pdb=" O ASP p 84 " (cutoff:3.500A) Processing helix chain 'p' and resid 158 through 161 Processing sheet with id=AA1, first strand: chain 'a' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER a 148 " --> pdb=" O ARG a 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG a 169 " --> pdb=" O SER a 148 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS a 150 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS a 167 " --> pdb=" O LYS a 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR a 152 " --> pdb=" O LYS a 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR a 183 " --> pdb=" O THR a 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR a 119 " --> pdb=" O GLU a 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN a 122 " --> pdb=" O PRO a 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU a 16 " --> pdb=" O ASN a 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE a 124 " --> pdb=" O LEU a 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU a 18 " --> pdb=" O ILE a 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU a 126 " --> pdb=" O GLU a 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS a 20 " --> pdb=" O LEU a 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY a 128 " --> pdb=" O LYS a 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP a 22 " --> pdb=" O GLY a 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN b 123 " --> pdb=" O PRO b 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU b 17 " --> pdb=" O ASN b 123 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE b 125 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU b 19 " --> pdb=" O ILE b 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR b 120 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG b 124 " --> pdb=" O GLU b 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 178 through 189 current: chain 'b' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL b 221 " --> pdb=" O SER b 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU b 151 " --> pdb=" O LYS b 168 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS b 168 " --> pdb=" O GLU b 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR b 153 " --> pdb=" O GLU b 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU b 166 " --> pdb=" O TYR b 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE b 167 " --> pdb=" O HIS b 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 178 through 189 current: chain 'b' and resid 107 through 109 Processing sheet with id=AA3, first strand: chain 'c' and resid 13 through 23 removed outlier: 6.122A pdb=" N SER c 148 " --> pdb=" O ARG c 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG c 169 " --> pdb=" O SER c 148 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS c 150 " --> pdb=" O LYS c 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS c 167 " --> pdb=" O LYS c 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR c 152 " --> pdb=" O LYS c 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR c 183 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR c 119 " --> pdb=" O GLU c 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN c 122 " --> pdb=" O PRO c 14 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU c 16 " --> pdb=" O ASN c 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE c 124 " --> pdb=" O LEU c 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU c 18 " --> pdb=" O ILE c 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU c 126 " --> pdb=" O GLU c 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS c 20 " --> pdb=" O LEU c 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY c 128 " --> pdb=" O LYS c 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP c 22 " --> pdb=" O GLY c 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 14 through 24 removed outlier: 7.974A pdb=" N ASN d 123 " --> pdb=" O PRO d 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU d 17 " --> pdb=" O ASN d 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE d 125 " --> pdb=" O LEU d 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU d 19 " --> pdb=" O ILE d 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR d 120 " --> pdb=" O GLU d 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG d 124 " --> pdb=" O GLU d 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 178 through 189 current: chain 'd' and resid 27 through 37 removed outlier: 3.538A pdb=" N VAL d 221 " --> pdb=" O SER d 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU d 151 " --> pdb=" O LYS d 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS d 168 " --> pdb=" O GLU d 151 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR d 153 " --> pdb=" O GLU d 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU d 166 " --> pdb=" O TYR d 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE d 167 " --> pdb=" O HIS d 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 178 through 189 current: chain 'd' and resid 107 through 109 Processing sheet with id=AA5, first strand: chain 'e' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER e 148 " --> pdb=" O ARG e 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG e 169 " --> pdb=" O SER e 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS e 150 " --> pdb=" O LYS e 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS e 167 " --> pdb=" O LYS e 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR e 152 " --> pdb=" O LYS e 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR e 183 " --> pdb=" O THR e 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR e 119 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN e 122 " --> pdb=" O PRO e 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU e 16 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE e 124 " --> pdb=" O LEU e 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU e 18 " --> pdb=" O ILE e 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU e 126 " --> pdb=" O GLU e 18 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS e 20 " --> pdb=" O LEU e 126 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLY e 128 " --> pdb=" O LYS e 20 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP e 22 " --> pdb=" O GLY e 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN f 123 " --> pdb=" O PRO f 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU f 17 " --> pdb=" O ASN f 123 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE f 125 " --> pdb=" O LEU f 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU f 19 " --> pdb=" O ILE f 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR f 120 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG f 124 " --> pdb=" O GLU f 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 178 through 189 current: chain 'f' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL f 221 " --> pdb=" O SER f 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU f 151 " --> pdb=" O LYS f 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS f 168 " --> pdb=" O GLU f 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR f 153 " --> pdb=" O GLU f 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU f 166 " --> pdb=" O TYR f 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE f 167 " --> pdb=" O HIS f 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 178 through 189 current: chain 'f' and resid 107 through 109 Processing sheet with id=AA7, first strand: chain 'g' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER g 148 " --> pdb=" O ARG g 169 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG g 169 " --> pdb=" O SER g 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS g 150 " --> pdb=" O LYS g 167 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS g 167 " --> pdb=" O LYS g 150 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR g 152 " --> pdb=" O LYS g 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR g 183 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR g 119 " --> pdb=" O GLU g 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN g 122 " --> pdb=" O PRO g 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU g 16 " --> pdb=" O ASN g 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE g 124 " --> pdb=" O LEU g 16 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU g 18 " --> pdb=" O ILE g 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU g 126 " --> pdb=" O GLU g 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS g 20 " --> pdb=" O LEU g 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY g 128 " --> pdb=" O LYS g 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP g 22 " --> pdb=" O GLY g 128 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN h 123 " --> pdb=" O PRO h 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU h 17 " --> pdb=" O ASN h 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE h 125 " --> pdb=" O LEU h 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU h 19 " --> pdb=" O ILE h 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR h 120 " --> pdb=" O GLU h 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG h 124 " --> pdb=" O GLU h 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 178 through 189 current: chain 'h' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL h 221 " --> pdb=" O SER h 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU h 151 " --> pdb=" O LYS h 168 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS h 168 " --> pdb=" O GLU h 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR h 153 " --> pdb=" O GLU h 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU h 166 " --> pdb=" O TYR h 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE h 167 " --> pdb=" O HIS h 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 178 through 189 current: chain 'h' and resid 107 through 109 Processing sheet with id=AA9, first strand: chain 'i' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER i 148 " --> pdb=" O ARG i 169 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG i 169 " --> pdb=" O SER i 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS i 150 " --> pdb=" O LYS i 167 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS i 167 " --> pdb=" O LYS i 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR i 152 " --> pdb=" O LYS i 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR i 183 " --> pdb=" O THR i 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR i 119 " --> pdb=" O GLU i 116 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN i 122 " --> pdb=" O PRO i 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU i 16 " --> pdb=" O ASN i 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE i 124 " --> pdb=" O LEU i 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU i 18 " --> pdb=" O ILE i 124 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU i 126 " --> pdb=" O GLU i 18 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS i 20 " --> pdb=" O LEU i 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY i 128 " --> pdb=" O LYS i 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP i 22 " --> pdb=" O GLY i 128 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 14 through 24 removed outlier: 7.974A pdb=" N ASN j 123 " --> pdb=" O PRO j 15 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU j 17 " --> pdb=" O ASN j 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE j 125 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU j 19 " --> pdb=" O ILE j 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR j 120 " --> pdb=" O GLU j 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG j 124 " --> pdb=" O GLU j 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 178 through 189 current: chain 'j' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL j 221 " --> pdb=" O SER j 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU j 151 " --> pdb=" O LYS j 168 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LYS j 168 " --> pdb=" O GLU j 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR j 153 " --> pdb=" O GLU j 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU j 166 " --> pdb=" O TYR j 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE j 167 " --> pdb=" O HIS j 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 178 through 189 current: chain 'j' and resid 107 through 109 Processing sheet with id=AB2, first strand: chain 'k' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER k 148 " --> pdb=" O ARG k 169 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG k 169 " --> pdb=" O SER k 148 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS k 150 " --> pdb=" O LYS k 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS k 167 " --> pdb=" O LYS k 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR k 152 " --> pdb=" O LYS k 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR k 183 " --> pdb=" O THR k 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR k 119 " --> pdb=" O GLU k 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN k 122 " --> pdb=" O PRO k 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU k 16 " --> pdb=" O ASN k 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE k 124 " --> pdb=" O LEU k 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU k 18 " --> pdb=" O ILE k 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU k 126 " --> pdb=" O GLU k 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS k 20 " --> pdb=" O LEU k 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY k 128 " --> pdb=" O LYS k 20 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP k 22 " --> pdb=" O GLY k 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 14 through 24 removed outlier: 7.974A pdb=" N ASN l 123 " --> pdb=" O PRO l 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU l 17 " --> pdb=" O ASN l 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE l 125 " --> pdb=" O LEU l 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU l 19 " --> pdb=" O ILE l 125 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR l 120 " --> pdb=" O GLU l 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG l 124 " --> pdb=" O GLU l 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 178 through 189 current: chain 'l' and resid 27 through 37 removed outlier: 3.538A pdb=" N VAL l 221 " --> pdb=" O SER l 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU l 151 " --> pdb=" O LYS l 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS l 168 " --> pdb=" O GLU l 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR l 153 " --> pdb=" O GLU l 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU l 166 " --> pdb=" O TYR l 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE l 167 " --> pdb=" O HIS l 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 178 through 189 current: chain 'l' and resid 107 through 109 Processing sheet with id=AB4, first strand: chain 'm' and resid 13 through 23 removed outlier: 6.121A pdb=" N SER m 148 " --> pdb=" O ARG m 169 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG m 169 " --> pdb=" O SER m 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS m 150 " --> pdb=" O LYS m 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS m 167 " --> pdb=" O LYS m 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR m 152 " --> pdb=" O LYS m 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR m 183 " --> pdb=" O THR m 98 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR m 119 " --> pdb=" O GLU m 116 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN m 122 " --> pdb=" O PRO m 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU m 16 " --> pdb=" O ASN m 122 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE m 124 " --> pdb=" O LEU m 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU m 18 " --> pdb=" O ILE m 124 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU m 126 " --> pdb=" O GLU m 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS m 20 " --> pdb=" O LEU m 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY m 128 " --> pdb=" O LYS m 20 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP m 22 " --> pdb=" O GLY m 128 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN n 123 " --> pdb=" O PRO n 15 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU n 17 " --> pdb=" O ASN n 123 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE n 125 " --> pdb=" O LEU n 17 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU n 19 " --> pdb=" O ILE n 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR n 120 " --> pdb=" O GLU n 117 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG n 124 " --> pdb=" O GLU n 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 178 through 189 current: chain 'n' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL n 221 " --> pdb=" O SER n 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU n 151 " --> pdb=" O LYS n 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS n 168 " --> pdb=" O GLU n 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR n 153 " --> pdb=" O GLU n 166 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU n 166 " --> pdb=" O TYR n 153 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE n 167 " --> pdb=" O HIS n 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 178 through 189 current: chain 'n' and resid 107 through 109 Processing sheet with id=AB6, first strand: chain 'o' and resid 13 through 23 removed outlier: 6.122A pdb=" N SER o 148 " --> pdb=" O ARG o 169 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG o 169 " --> pdb=" O SER o 148 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LYS o 150 " --> pdb=" O LYS o 167 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS o 167 " --> pdb=" O LYS o 150 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR o 152 " --> pdb=" O LYS o 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR o 183 " --> pdb=" O THR o 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR o 119 " --> pdb=" O GLU o 116 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN o 122 " --> pdb=" O PRO o 14 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU o 16 " --> pdb=" O ASN o 122 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE o 124 " --> pdb=" O LEU o 16 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU o 18 " --> pdb=" O ILE o 124 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU o 126 " --> pdb=" O GLU o 18 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LYS o 20 " --> pdb=" O LEU o 126 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY o 128 " --> pdb=" O LYS o 20 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP o 22 " --> pdb=" O GLY o 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'p' and resid 14 through 24 removed outlier: 7.973A pdb=" N ASN p 123 " --> pdb=" O PRO p 15 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU p 17 " --> pdb=" O ASN p 123 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE p 125 " --> pdb=" O LEU p 17 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU p 19 " --> pdb=" O ILE p 125 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR p 120 " --> pdb=" O GLU p 117 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG p 124 " --> pdb=" O GLU p 113 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 178 through 189 current: chain 'p' and resid 27 through 37 removed outlier: 3.539A pdb=" N VAL p 221 " --> pdb=" O SER p 210 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU p 151 " --> pdb=" O LYS p 168 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS p 168 " --> pdb=" O GLU p 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR p 153 " --> pdb=" O GLU p 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU p 166 " --> pdb=" O TYR p 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE p 167 " --> pdb=" O HIS p 183 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 178 through 189 current: chain 'p' and resid 107 through 109 1232 hydrogen bonds defined for protein. 3144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.58 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8946 1.33 - 1.45: 4164 1.45 - 1.57: 16858 1.57 - 1.68: 0 1.68 - 1.80: 128 Bond restraints: 30096 Sorted by residual: bond pdb=" CA TYR j 68 " pdb=" C TYR j 68 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.14e-02 7.69e+03 3.38e+00 bond pdb=" CA TYR d 68 " pdb=" C TYR d 68 " ideal model delta sigma weight residual 1.521 1.501 0.021 1.14e-02 7.69e+03 3.24e+00 bond pdb=" CA TYR n 68 " pdb=" C TYR n 68 " ideal model delta sigma weight residual 1.521 1.501 0.020 1.14e-02 7.69e+03 3.19e+00 bond pdb=" CA TYR h 68 " pdb=" C TYR h 68 " ideal model delta sigma weight residual 1.521 1.501 0.020 1.14e-02 7.69e+03 3.09e+00 bond pdb=" CA TYR f 68 " pdb=" C TYR f 68 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.25e-02 6.40e+03 2.99e+00 ... (remaining 30091 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.55: 908 106.55 - 113.40: 16397 113.40 - 120.26: 10557 120.26 - 127.11: 12272 127.11 - 133.96: 354 Bond angle restraints: 40488 Sorted by residual: angle pdb=" C ASP h 157 " pdb=" N ASP h 158 " pdb=" CA ASP h 158 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C ASP f 157 " pdb=" N ASP f 158 " pdb=" CA ASP f 158 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 angle pdb=" C ASP d 157 " pdb=" N ASP d 158 " pdb=" CA ASP d 158 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C ASP b 157 " pdb=" N ASP b 158 " pdb=" CA ASP b 158 " ideal model delta sigma weight residual 121.54 129.76 -8.22 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C ASP l 157 " pdb=" N ASP l 158 " pdb=" CA ASP l 158 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+01 ... (remaining 40483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 17229 15.63 - 31.27: 683 31.27 - 46.90: 168 46.90 - 62.53: 0 62.53 - 78.16: 16 Dihedral angle restraints: 18096 sinusoidal: 7624 harmonic: 10472 Sorted by residual: dihedral pdb=" CA THR o 109 " pdb=" C THR o 109 " pdb=" N ARG o 110 " pdb=" CA ARG o 110 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA THR a 109 " pdb=" C THR a 109 " pdb=" N ARG a 110 " pdb=" CA ARG a 110 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA THR i 109 " pdb=" C THR i 109 " pdb=" N ARG i 110 " pdb=" CA ARG i 110 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 18093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2667 0.049 - 0.099: 1207 0.099 - 0.148: 424 0.148 - 0.197: 38 0.197 - 0.247: 8 Chirality restraints: 4344 Sorted by residual: chirality pdb=" CB ILE i 147 " pdb=" CA ILE i 147 " pdb=" CG1 ILE i 147 " pdb=" CG2 ILE i 147 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE a 147 " pdb=" CA ILE a 147 " pdb=" CG1 ILE a 147 " pdb=" CG2 ILE a 147 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE c 147 " pdb=" CA ILE c 147 " pdb=" CG1 ILE c 147 " pdb=" CG2 ILE c 147 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 4341 not shown) Planarity restraints: 5240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 67 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.09e+01 pdb=" CG TRP c 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP c 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP c 67 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP c 67 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP c 67 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP c 67 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 67 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 67 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP c 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP e 67 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP e 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP e 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP e 67 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP e 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP e 67 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP e 67 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 67 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 67 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP e 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP k 67 " -0.028 2.00e-02 2.50e+03 2.08e-02 1.08e+01 pdb=" CG TRP k 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP k 67 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP k 67 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP k 67 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP k 67 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP k 67 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 67 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 67 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP k 67 " -0.011 2.00e-02 2.50e+03 ... (remaining 5237 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 9370 2.86 - 3.37: 22932 3.37 - 3.88: 46523 3.88 - 4.39: 50273 4.39 - 4.90: 95399 Nonbonded interactions: 224497 Sorted by model distance: nonbonded pdb=" O THR b 64 " pdb=" NH1 ARG b 98 " model vdw 2.349 2.520 nonbonded pdb=" O THR n 64 " pdb=" NH1 ARG n 98 " model vdw 2.350 2.520 nonbonded pdb=" O THR f 64 " pdb=" NH1 ARG f 98 " model vdw 2.350 2.520 nonbonded pdb=" O THR d 64 " pdb=" NH1 ARG d 98 " model vdw 2.350 2.520 nonbonded pdb=" O THR h 64 " pdb=" NH1 ARG h 98 " model vdw 2.350 2.520 ... (remaining 224492 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 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.380 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 76.220 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.210 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.007 0.067 30096 Z= 0.486 Angle : 0.929 12.264 40488 Z= 0.486 Chirality : 0.059 0.247 4344 Planarity : 0.006 0.054 5240 Dihedral : 9.548 78.163 11424 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.13), residues: 3664 helix: -4.80 (0.21), residues: 56 sheet: -1.67 (0.11), residues: 1880 loop : -2.45 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.006 TRP e 67 HIS 0.013 0.002 HIS n 183 PHE 0.024 0.004 PHE k 72 TYR 0.037 0.004 TYR d 68 ARG 0.007 0.001 ARG o 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 852 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 89 MET cc_start: 0.8916 (mmt) cc_final: 0.8715 (mmm) REVERT: b 32 ARG cc_start: 0.8348 (ttt90) cc_final: 0.8142 (mtp85) REVERT: c 89 MET cc_start: 0.8919 (mmt) cc_final: 0.8716 (mmm) REVERT: c 106 THR cc_start: 0.9062 (m) cc_final: 0.8836 (p) REVERT: d 32 ARG cc_start: 0.8349 (ttt90) cc_final: 0.8136 (mtp85) REVERT: e 106 THR cc_start: 0.9020 (m) cc_final: 0.8771 (p) REVERT: g 183 TYR cc_start: 0.9138 (m-80) cc_final: 0.8915 (m-80) REVERT: j 32 ARG cc_start: 0.8350 (ttt90) cc_final: 0.8133 (mtp85) REVERT: k 89 MET cc_start: 0.8925 (mmt) cc_final: 0.8702 (mmm) REVERT: o 183 TYR cc_start: 0.9142 (m-80) cc_final: 0.8923 (m-80) REVERT: p 90 MET cc_start: 0.8604 (mmt) cc_final: 0.8402 (mmt) outliers start: 0 outliers final: 0 residues processed: 852 average time/residue: 0.4923 time to fit residues: 619.2304 Evaluate side-chains 496 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 0.9990 chunk 278 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 ASN b 41 ASN ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 ASN c 186 ASN d 41 ASN ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 ASN e 145 ASN f 41 ASN ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN g 145 ASN ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 24 ASN i 95 GLN i 186 ASN j 41 ASN ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 24 ASN k 95 GLN k 186 ASN l 41 ASN ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN m 95 GLN m 145 ASN m 186 ASN n 41 ASN ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 24 ASN o 145 ASN o 186 ASN ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30096 Z= 0.195 Angle : 0.613 9.293 40488 Z= 0.309 Chirality : 0.048 0.156 4344 Planarity : 0.004 0.034 5240 Dihedral : 4.482 19.848 3992 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.45 % Favored : 95.33 % Rotamer: Outliers : 1.65 % Allowed : 11.16 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.13), residues: 3664 helix: -4.54 (0.17), residues: 152 sheet: -0.78 (0.12), residues: 1832 loop : -1.80 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP g 67 HIS 0.005 0.001 HIS e 82 PHE 0.014 0.001 PHE l 167 TYR 0.015 0.002 TYR b 202 ARG 0.005 0.000 ARG g 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 625 time to evaluate : 3.826 Fit side-chains REVERT: a 81 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6819 (ttp-110) REVERT: b 32 ARG cc_start: 0.8252 (ttt90) cc_final: 0.7972 (mtp85) REVERT: b 44 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7465 (tp) REVERT: d 32 ARG cc_start: 0.8276 (ttt90) cc_final: 0.7978 (mtp85) REVERT: d 44 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7468 (tp) REVERT: g 81 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6804 (ttp-110) REVERT: h 104 ASP cc_start: 0.7270 (m-30) cc_final: 0.6875 (m-30) REVERT: j 32 ARG cc_start: 0.8252 (ttt90) cc_final: 0.7971 (mtp85) REVERT: j 104 ASP cc_start: 0.7244 (m-30) cc_final: 0.6780 (m-30) REVERT: l 44 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7468 (tp) REVERT: l 168 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8599 (mtmm) outliers start: 53 outliers final: 32 residues processed: 647 average time/residue: 0.4111 time to fit residues: 420.0617 Evaluate side-chains 525 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 489 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 44 LEU Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 214 ASN Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 214 ASN Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain j residue 214 ASN Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain l residue 44 LEU Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 168 LYS Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 214 ASN Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 214 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 334 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 178 GLN ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 123 ASN c 178 GLN ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 123 ASN e 40 ASN ** e 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN e 178 GLN ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 123 ASN g 24 ASN ** g 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 ASN g 178 GLN ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 ASN i 178 GLN ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 123 ASN k 178 GLN ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 123 ASN m 24 ASN m 145 ASN m 178 GLN ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 123 ASN o 145 ASN o 178 GLN ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 123 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 30096 Z= 0.488 Angle : 0.748 11.323 40488 Z= 0.374 Chirality : 0.052 0.172 4344 Planarity : 0.005 0.035 5240 Dihedral : 4.806 18.136 3992 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.96 % Favored : 92.85 % Rotamer: Outliers : 3.80 % Allowed : 12.06 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.13), residues: 3664 helix: -4.43 (0.20), residues: 200 sheet: -0.76 (0.12), residues: 1864 loop : -1.44 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP e 67 HIS 0.007 0.002 HIS o 200 PHE 0.020 0.003 PHE d 167 TYR 0.027 0.004 TYR d 68 ARG 0.005 0.001 ARG c 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 470 time to evaluate : 3.886 Fit side-chains REVERT: a 104 ASP cc_start: 0.8820 (t0) cc_final: 0.8607 (t0) REVERT: a 145 ASN cc_start: 0.8379 (m-40) cc_final: 0.8025 (t0) REVERT: a 160 ASN cc_start: 0.8552 (t0) cc_final: 0.8314 (t0) REVERT: b 44 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7904 (tp) REVERT: c 145 ASN cc_start: 0.8409 (m-40) cc_final: 0.8039 (t0) REVERT: c 160 ASN cc_start: 0.8555 (t0) cc_final: 0.8309 (t0) REVERT: d 44 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (tp) REVERT: e 160 ASN cc_start: 0.8580 (t0) cc_final: 0.8342 (t0) REVERT: g 160 ASN cc_start: 0.8563 (t0) cc_final: 0.8306 (t0) REVERT: h 105 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: i 104 ASP cc_start: 0.8832 (t0) cc_final: 0.8622 (t0) REVERT: i 145 ASN cc_start: 0.8401 (m-40) cc_final: 0.8048 (t0) REVERT: i 160 ASN cc_start: 0.8521 (t0) cc_final: 0.8305 (t0) REVERT: j 105 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: k 145 ASN cc_start: 0.8420 (m-40) cc_final: 0.8049 (t0) REVERT: k 160 ASN cc_start: 0.8560 (t0) cc_final: 0.8323 (t0) REVERT: l 44 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7898 (tp) REVERT: m 160 ASN cc_start: 0.8562 (t0) cc_final: 0.8325 (t0) REVERT: o 160 ASN cc_start: 0.8558 (t0) cc_final: 0.8316 (t0) REVERT: p 105 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8119 (m-30) outliers start: 122 outliers final: 92 residues processed: 545 average time/residue: 0.4254 time to fit residues: 363.4852 Evaluate side-chains 548 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 450 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LYS Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 147 ILE Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 90 MET Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain c residue 35 LYS Chi-restraints excluded: chain c residue 40 ASN Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 147 ILE Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain d residue 44 LEU Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain d residue 214 ASN Chi-restraints excluded: chain e residue 35 LYS Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 147 ILE Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 46 LEU Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain f residue 121 LEU Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain f residue 214 ASN Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 147 ILE Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 90 MET Chi-restraints excluded: chain h residue 105 ASP Chi-restraints excluded: chain h residue 121 LEU Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 35 LYS Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 87 SER Chi-restraints excluded: chain i residue 120 LEU Chi-restraints excluded: chain i residue 147 ILE Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain j residue 105 ASP Chi-restraints excluded: chain j residue 121 LEU Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain j residue 214 ASN Chi-restraints excluded: chain k residue 35 LYS Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 120 LEU Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain l residue 44 LEU Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 90 MET Chi-restraints excluded: chain l residue 121 LEU Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 35 LYS Chi-restraints excluded: chain m residue 40 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 120 LEU Chi-restraints excluded: chain m residue 147 ILE Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 90 MET Chi-restraints excluded: chain n residue 121 LEU Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain n residue 214 ASN Chi-restraints excluded: chain o residue 35 LYS Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 120 LEU Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 46 LEU Chi-restraints excluded: chain p residue 105 ASP Chi-restraints excluded: chain p residue 214 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 355 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 318 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 145 ASN ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 145 ASN ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 145 ASN ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30096 Z= 0.218 Angle : 0.597 8.822 40488 Z= 0.296 Chirality : 0.048 0.135 4344 Planarity : 0.004 0.031 5240 Dihedral : 4.276 17.304 3992 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.65 % Allowed : 12.62 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3664 helix: -4.06 (0.21), residues: 208 sheet: -0.41 (0.12), residues: 1832 loop : -1.31 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP e 67 HIS 0.004 0.001 HIS m 182 PHE 0.013 0.001 PHE f 167 TYR 0.017 0.002 TYR m 107 ARG 0.005 0.000 ARG e 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 539 time to evaluate : 3.580 Fit side-chains REVERT: b 68 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.5466 (t80) REVERT: c 104 ASP cc_start: 0.8778 (t0) cc_final: 0.8485 (t0) REVERT: d 68 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.5471 (t80) REVERT: d 84 ASP cc_start: 0.8204 (t0) cc_final: 0.7878 (t70) REVERT: e 104 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8503 (t0) REVERT: f 68 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.5973 (t80) REVERT: f 84 ASP cc_start: 0.8194 (t0) cc_final: 0.7861 (t70) REVERT: g 81 ARG cc_start: 0.7297 (ttp-170) cc_final: 0.6928 (ttp-110) REVERT: h 84 ASP cc_start: 0.8217 (t0) cc_final: 0.7903 (t70) REVERT: h 105 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: j 84 ASP cc_start: 0.8216 (t0) cc_final: 0.7891 (t70) REVERT: k 104 ASP cc_start: 0.8794 (t0) cc_final: 0.8512 (t0) REVERT: l 68 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.5481 (t80) REVERT: l 84 ASP cc_start: 0.8225 (t0) cc_final: 0.7899 (t70) REVERT: m 104 ASP cc_start: 0.8794 (t0) cc_final: 0.8518 (t0) REVERT: n 84 ASP cc_start: 0.8198 (t0) cc_final: 0.7864 (t70) REVERT: p 68 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.5836 (t80) REVERT: p 84 ASP cc_start: 0.8242 (t0) cc_final: 0.7914 (t70) outliers start: 117 outliers final: 58 residues processed: 597 average time/residue: 0.4178 time to fit residues: 391.8892 Evaluate side-chains 537 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 472 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 121 LEU Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain d residue 214 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 214 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 105 ASP Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 214 ASN Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 214 ASN Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 214 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 264 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN g 145 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 145 ASN ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30096 Z= 0.210 Angle : 0.591 8.498 40488 Z= 0.292 Chirality : 0.047 0.167 4344 Planarity : 0.003 0.030 5240 Dihedral : 4.126 16.358 3992 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.71 % Allowed : 13.37 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3664 helix: -3.65 (0.21), residues: 256 sheet: -0.25 (0.12), residues: 1832 loop : -1.13 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 67 HIS 0.004 0.001 HIS e 200 PHE 0.011 0.001 PHE p 167 TYR 0.016 0.002 TYR m 107 ARG 0.006 0.000 ARG k 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 510 time to evaluate : 3.885 Fit side-chains REVERT: a 81 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.7174 (ttp-110) REVERT: b 84 ASP cc_start: 0.8254 (t0) cc_final: 0.7946 (t70) REVERT: c 104 ASP cc_start: 0.8746 (t0) cc_final: 0.8462 (t0) REVERT: d 84 ASP cc_start: 0.8223 (t0) cc_final: 0.7915 (t70) REVERT: e 104 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8483 (t0) REVERT: f 68 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.5932 (t80) REVERT: f 84 ASP cc_start: 0.8210 (t0) cc_final: 0.7895 (t70) REVERT: g 81 ARG cc_start: 0.7207 (ttp-170) cc_final: 0.6895 (ttp-110) REVERT: h 68 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.5826 (t80) REVERT: h 84 ASP cc_start: 0.8231 (t0) cc_final: 0.7943 (t70) REVERT: j 68 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.5825 (t80) REVERT: j 84 ASP cc_start: 0.8233 (t0) cc_final: 0.7941 (t70) REVERT: k 104 ASP cc_start: 0.8764 (t0) cc_final: 0.8486 (t0) REVERT: l 68 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.5805 (t80) REVERT: l 84 ASP cc_start: 0.8244 (t0) cc_final: 0.7939 (t70) REVERT: m 104 ASP cc_start: 0.8774 (t0) cc_final: 0.8498 (t0) REVERT: n 68 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.5772 (t80) REVERT: n 84 ASP cc_start: 0.8211 (t0) cc_final: 0.7900 (t70) REVERT: o 104 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8497 (t0) REVERT: p 68 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.5768 (t80) REVERT: p 84 ASP cc_start: 0.8251 (t0) cc_final: 0.7948 (t70) outliers start: 87 outliers final: 74 residues processed: 551 average time/residue: 0.4140 time to fit residues: 361.4043 Evaluate side-chains 541 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 459 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain d residue 214 ASN Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain f residue 214 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain j residue 214 ASN Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain n residue 214 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 214 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 356 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 171 ASN ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 171 ASN ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 171 ASN ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 171 ASN ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30096 Z= 0.228 Angle : 0.590 8.300 40488 Z= 0.292 Chirality : 0.047 0.166 4344 Planarity : 0.003 0.029 5240 Dihedral : 4.075 15.747 3992 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.96 % Allowed : 14.21 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3664 helix: -3.38 (0.22), residues: 256 sheet: -0.18 (0.12), residues: 1840 loop : -1.07 (0.17), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 67 HIS 0.004 0.001 HIS p 171 PHE 0.012 0.001 PHE f 167 TYR 0.016 0.002 TYR m 107 ARG 0.008 0.000 ARG o 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 478 time to evaluate : 4.283 Fit side-chains REVERT: a 81 ARG cc_start: 0.7378 (ttp-170) cc_final: 0.7086 (ttp-110) REVERT: b 68 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.5533 (t80) REVERT: b 84 ASP cc_start: 0.8251 (t0) cc_final: 0.7963 (t70) REVERT: c 104 ASP cc_start: 0.8737 (t0) cc_final: 0.8455 (t0) REVERT: d 68 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.5657 (t80) REVERT: e 104 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8490 (t0) REVERT: e 145 ASN cc_start: 0.8265 (m-40) cc_final: 0.7918 (t0) REVERT: f 68 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.5839 (t80) REVERT: f 84 ASP cc_start: 0.8217 (t0) cc_final: 0.7918 (t70) REVERT: g 104 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8515 (t0) REVERT: h 68 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.5692 (t80) REVERT: h 84 ASP cc_start: 0.8240 (t0) cc_final: 0.7944 (t70) REVERT: j 68 TYR cc_start: 0.7820 (OUTLIER) cc_final: 0.5687 (t80) REVERT: j 84 ASP cc_start: 0.8230 (t0) cc_final: 0.7939 (t70) REVERT: k 104 ASP cc_start: 0.8759 (t0) cc_final: 0.8491 (t0) REVERT: l 68 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.5712 (t80) REVERT: l 84 ASP cc_start: 0.8246 (t0) cc_final: 0.7951 (t70) REVERT: m 104 ASP cc_start: 0.8771 (t0) cc_final: 0.8502 (t0) REVERT: n 68 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.5676 (t80) REVERT: n 84 ASP cc_start: 0.8220 (t0) cc_final: 0.7921 (t70) REVERT: o 104 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8502 (t0) REVERT: o 145 ASN cc_start: 0.8258 (m-40) cc_final: 0.7915 (t0) REVERT: p 68 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.5759 (t80) REVERT: p 84 ASP cc_start: 0.8244 (t0) cc_final: 0.7946 (t70) outliers start: 95 outliers final: 79 residues processed: 525 average time/residue: 0.4365 time to fit residues: 362.7063 Evaluate side-chains 548 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 458 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 214 ASN Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 187 THR Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain d residue 214 ASN Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain f residue 214 ASN Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 158 ASP Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain i residue 219 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain j residue 214 ASN Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain n residue 214 ASN Chi-restraints excluded: chain o residue 39 THR Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 214 ASN Chi-restraints excluded: chain p residue 217 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 221 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 136 ASN ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 232 HIS ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 136 ASN ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 ASN ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN g 136 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 136 ASN ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 136 ASN ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 136 ASN ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 136 ASN ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30096 Z= 0.422 Angle : 0.691 9.340 40488 Z= 0.345 Chirality : 0.051 0.168 4344 Planarity : 0.004 0.032 5240 Dihedral : 4.470 15.113 3992 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.41 % Rotamer: Outliers : 3.24 % Allowed : 15.15 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3664 helix: -3.28 (0.25), residues: 248 sheet: -0.44 (0.11), residues: 1880 loop : -1.14 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP e 67 HIS 0.006 0.001 HIS e 200 PHE 0.018 0.002 PHE f 167 TYR 0.022 0.003 TYR j 202 ARG 0.007 0.001 ARG e 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 447 time to evaluate : 3.713 Fit side-chains REVERT: b 68 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.5662 (t80) REVERT: c 104 ASP cc_start: 0.8779 (t0) cc_final: 0.8491 (t0) REVERT: d 68 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.5806 (t80) REVERT: e 104 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8526 (t0) REVERT: e 145 ASN cc_start: 0.8394 (m-40) cc_final: 0.8056 (t0) REVERT: f 68 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.5875 (t80) REVERT: g 145 ASN cc_start: 0.8397 (m-40) cc_final: 0.8049 (t0) REVERT: h 68 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.5729 (t80) REVERT: j 68 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.5734 (t80) REVERT: k 104 ASP cc_start: 0.8797 (t0) cc_final: 0.8521 (t0) REVERT: l 68 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.5804 (t80) REVERT: m 104 ASP cc_start: 0.8809 (t0) cc_final: 0.8535 (t0) REVERT: m 145 ASN cc_start: 0.8396 (m-40) cc_final: 0.8060 (t0) REVERT: n 68 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.5615 (t80) REVERT: o 145 ASN cc_start: 0.8401 (m-40) cc_final: 0.8061 (t0) REVERT: p 68 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.5949 (t80) outliers start: 104 outliers final: 79 residues processed: 492 average time/residue: 0.4590 time to fit residues: 353.0321 Evaluate side-chains 521 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 433 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 187 THR Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 187 THR Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain i residue 219 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 40 ASN Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 122 ASN Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain k residue 219 MET Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain n residue 214 ASN Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 214 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 175 optimal weight: 0.0170 chunk 33 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 171 ASN ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 171 ASN ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 171 ASN ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 171 ASN ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30096 Z= 0.205 Angle : 0.587 9.014 40488 Z= 0.292 Chirality : 0.047 0.159 4344 Planarity : 0.003 0.030 5240 Dihedral : 4.096 15.291 3992 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.81 % Allowed : 15.55 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3664 helix: -3.15 (0.24), residues: 248 sheet: -0.26 (0.11), residues: 1904 loop : -0.94 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 67 HIS 0.004 0.001 HIS m 182 PHE 0.012 0.001 PHE l 167 TYR 0.016 0.002 TYR m 107 ARG 0.008 0.000 ARG i 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 474 time to evaluate : 3.744 Fit side-chains REVERT: b 68 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.5416 (t80) REVERT: b 84 ASP cc_start: 0.8246 (t0) cc_final: 0.7964 (t70) REVERT: c 104 ASP cc_start: 0.8752 (t0) cc_final: 0.8466 (t0) REVERT: d 68 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.5489 (t80) REVERT: e 104 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8485 (t0) REVERT: e 145 ASN cc_start: 0.8331 (m-40) cc_final: 0.7971 (t0) REVERT: f 68 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.5707 (t80) REVERT: g 104 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8519 (t0) REVERT: g 145 ASN cc_start: 0.8332 (m-40) cc_final: 0.7976 (t0) REVERT: h 68 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.5568 (t80) REVERT: h 84 ASP cc_start: 0.8233 (t0) cc_final: 0.7957 (t70) REVERT: j 68 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.5565 (t80) REVERT: k 104 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8571 (t0) REVERT: l 68 TYR cc_start: 0.7754 (OUTLIER) cc_final: 0.5639 (t80) REVERT: m 104 ASP cc_start: 0.8757 (t0) cc_final: 0.8491 (t0) REVERT: m 145 ASN cc_start: 0.8328 (m-40) cc_final: 0.7986 (t0) REVERT: n 68 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.5500 (t80) REVERT: o 104 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8556 (t0) REVERT: o 145 ASN cc_start: 0.8338 (m-40) cc_final: 0.7984 (t0) REVERT: p 68 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.5613 (t80) REVERT: p 84 ASP cc_start: 0.8238 (t0) cc_final: 0.7967 (t70) outliers start: 90 outliers final: 76 residues processed: 514 average time/residue: 0.4383 time to fit residues: 350.5807 Evaluate side-chains 538 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 450 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 187 THR Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain a residue 219 MET Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain c residue 219 MET Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain e residue 219 MET Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain i residue 219 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 158 ASP Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 104 ASP Chi-restraints excluded: chain k residue 122 ASN Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain k residue 219 MET Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain m residue 219 MET Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 158 ASP Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain n residue 214 ASN Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 214 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 312 optimal weight: 10.0000 chunk 329 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30096 Z= 0.353 Angle : 0.647 8.175 40488 Z= 0.324 Chirality : 0.049 0.159 4344 Planarity : 0.004 0.037 5240 Dihedral : 4.275 15.182 3992 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.90 % Allowed : 16.08 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3664 helix: -2.94 (0.26), residues: 248 sheet: -0.36 (0.11), residues: 1912 loop : -1.00 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP m 67 HIS 0.005 0.001 HIS e 200 PHE 0.015 0.002 PHE l 167 TYR 0.020 0.003 TYR j 202 ARG 0.008 0.001 ARG o 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 450 time to evaluate : 3.697 Fit side-chains REVERT: b 68 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.5474 (t80) REVERT: b 84 ASP cc_start: 0.8290 (t0) cc_final: 0.8060 (t0) REVERT: b 105 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8235 (m-30) REVERT: c 104 ASP cc_start: 0.8782 (t0) cc_final: 0.8492 (t0) REVERT: d 68 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.5544 (t80) REVERT: e 104 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (t0) REVERT: e 145 ASN cc_start: 0.8363 (m-40) cc_final: 0.8023 (t0) REVERT: f 68 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.5755 (t80) REVERT: g 104 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8607 (t0) REVERT: g 145 ASN cc_start: 0.8393 (m-40) cc_final: 0.8057 (t0) REVERT: h 68 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.5575 (t80) REVERT: h 84 ASP cc_start: 0.8290 (t0) cc_final: 0.8059 (t0) REVERT: j 68 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.5574 (t80) REVERT: k 104 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8525 (t0) REVERT: k 198 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7758 (ttp-110) REVERT: l 68 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.5699 (t80) REVERT: m 104 ASP cc_start: 0.8779 (t0) cc_final: 0.8516 (t0) REVERT: m 145 ASN cc_start: 0.8391 (m-40) cc_final: 0.8068 (t0) REVERT: n 68 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.5506 (t80) REVERT: o 104 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8585 (t0) REVERT: o 145 ASN cc_start: 0.8398 (m-40) cc_final: 0.8065 (t0) REVERT: p 68 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.5755 (t80) REVERT: p 84 ASP cc_start: 0.8296 (t0) cc_final: 0.8062 (t0) outliers start: 93 outliers final: 76 residues processed: 489 average time/residue: 0.4486 time to fit residues: 340.4903 Evaluate side-chains 531 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 442 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 187 THR Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain a residue 219 MET Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 105 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain e residue 219 MET Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 187 THR Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain i residue 219 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 104 ASP Chi-restraints excluded: chain k residue 122 ASN Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain k residue 219 MET Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain m residue 219 MET Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 214 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 366 optimal weight: 9.9990 chunk 337 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30096 Z= 0.284 Angle : 0.622 8.081 40488 Z= 0.312 Chirality : 0.048 0.156 4344 Planarity : 0.004 0.037 5240 Dihedral : 4.215 14.896 3992 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.90 % Allowed : 16.24 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3664 helix: -2.86 (0.26), residues: 248 sheet: -0.32 (0.11), residues: 1912 loop : -0.98 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP e 67 HIS 0.004 0.001 HIS m 200 PHE 0.013 0.002 PHE l 167 TYR 0.018 0.002 TYR b 202 ARG 0.009 0.001 ARG o 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 462 time to evaluate : 3.870 Fit side-chains REVERT: a 198 ARG cc_start: 0.8098 (mtm110) cc_final: 0.7758 (ttp-110) REVERT: b 68 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.5392 (t80) REVERT: b 84 ASP cc_start: 0.8269 (t0) cc_final: 0.8044 (t0) REVERT: b 105 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8191 (m-30) REVERT: c 104 ASP cc_start: 0.8767 (t0) cc_final: 0.8481 (t0) REVERT: d 68 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.5463 (t80) REVERT: e 104 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (t0) REVERT: e 145 ASN cc_start: 0.8360 (m-40) cc_final: 0.8028 (t0) REVERT: e 198 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7795 (ttp-110) REVERT: f 68 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.5620 (t80) REVERT: g 104 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8586 (t0) REVERT: g 145 ASN cc_start: 0.8380 (m-40) cc_final: 0.8049 (t0) REVERT: g 198 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7793 (ttp-110) REVERT: h 68 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.5410 (t80) REVERT: h 84 ASP cc_start: 0.8267 (t0) cc_final: 0.8041 (t0) REVERT: j 68 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.5407 (t80) REVERT: j 84 ASP cc_start: 0.8255 (t0) cc_final: 0.8035 (t0) REVERT: k 104 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8581 (t0) REVERT: k 198 ARG cc_start: 0.8089 (mtm110) cc_final: 0.7749 (ttp-110) REVERT: l 68 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.5557 (t80) REVERT: l 98 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7808 (ttm-80) REVERT: m 104 ASP cc_start: 0.8873 (t0) cc_final: 0.8588 (t0) REVERT: m 145 ASN cc_start: 0.8365 (m-40) cc_final: 0.8043 (t0) REVERT: n 68 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.5450 (t80) REVERT: n 84 ASP cc_start: 0.8249 (t0) cc_final: 0.8027 (t0) REVERT: o 104 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8588 (t0) REVERT: o 145 ASN cc_start: 0.8378 (m-40) cc_final: 0.8049 (t0) REVERT: p 68 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.5728 (t80) REVERT: p 84 ASP cc_start: 0.8265 (t0) cc_final: 0.8045 (t0) outliers start: 93 outliers final: 78 residues processed: 500 average time/residue: 0.4668 time to fit residues: 360.8918 Evaluate side-chains 551 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 459 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 ILE Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 122 ASN Chi-restraints excluded: chain a residue 187 THR Chi-restraints excluded: chain a residue 203 SER Chi-restraints excluded: chain a residue 219 MET Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 68 TYR Chi-restraints excluded: chain b residue 105 ASP Chi-restraints excluded: chain b residue 190 ILE Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain c residue 122 ASN Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain c residue 219 MET Chi-restraints excluded: chain d residue 45 ASP Chi-restraints excluded: chain d residue 68 TYR Chi-restraints excluded: chain d residue 158 ASP Chi-restraints excluded: chain d residue 190 ILE Chi-restraints excluded: chain d residue 210 SER Chi-restraints excluded: chain e residue 40 ASN Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 104 ASP Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 187 THR Chi-restraints excluded: chain e residue 203 SER Chi-restraints excluded: chain e residue 219 MET Chi-restraints excluded: chain f residue 45 ASP Chi-restraints excluded: chain f residue 68 TYR Chi-restraints excluded: chain f residue 158 ASP Chi-restraints excluded: chain f residue 210 SER Chi-restraints excluded: chain g residue 24 ASN Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 63 THR Chi-restraints excluded: chain g residue 104 ASP Chi-restraints excluded: chain g residue 122 ASN Chi-restraints excluded: chain g residue 187 THR Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 203 SER Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 45 ASP Chi-restraints excluded: chain h residue 68 TYR Chi-restraints excluded: chain h residue 210 SER Chi-restraints excluded: chain h residue 214 ASN Chi-restraints excluded: chain i residue 48 ILE Chi-restraints excluded: chain i residue 63 THR Chi-restraints excluded: chain i residue 187 THR Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 203 SER Chi-restraints excluded: chain i residue 219 MET Chi-restraints excluded: chain j residue 45 ASP Chi-restraints excluded: chain j residue 68 TYR Chi-restraints excluded: chain j residue 190 ILE Chi-restraints excluded: chain j residue 210 SER Chi-restraints excluded: chain k residue 48 ILE Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 104 ASP Chi-restraints excluded: chain k residue 122 ASN Chi-restraints excluded: chain k residue 154 THR Chi-restraints excluded: chain k residue 187 THR Chi-restraints excluded: chain k residue 203 SER Chi-restraints excluded: chain k residue 219 MET Chi-restraints excluded: chain l residue 45 ASP Chi-restraints excluded: chain l residue 68 TYR Chi-restraints excluded: chain l residue 98 ARG Chi-restraints excluded: chain l residue 158 ASP Chi-restraints excluded: chain l residue 210 SER Chi-restraints excluded: chain l residue 214 ASN Chi-restraints excluded: chain m residue 24 ASN Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 63 THR Chi-restraints excluded: chain m residue 106 THR Chi-restraints excluded: chain m residue 154 THR Chi-restraints excluded: chain m residue 187 THR Chi-restraints excluded: chain m residue 203 SER Chi-restraints excluded: chain m residue 219 MET Chi-restraints excluded: chain n residue 45 ASP Chi-restraints excluded: chain n residue 68 TYR Chi-restraints excluded: chain n residue 210 SER Chi-restraints excluded: chain o residue 48 ILE Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain o residue 104 ASP Chi-restraints excluded: chain o residue 122 ASN Chi-restraints excluded: chain o residue 203 SER Chi-restraints excluded: chain p residue 45 ASP Chi-restraints excluded: chain p residue 68 TYR Chi-restraints excluded: chain p residue 190 ILE Chi-restraints excluded: chain p residue 210 SER Chi-restraints excluded: chain p residue 214 ASN Chi-restraints excluded: chain p residue 217 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN ** g 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 ASN ** m 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099473 restraints weight = 39198.506| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.42 r_work: 0.2906 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30096 Z= 0.334 Angle : 0.644 8.178 40488 Z= 0.323 Chirality : 0.049 0.157 4344 Planarity : 0.004 0.037 5240 Dihedral : 4.296 14.947 3992 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.05 % Allowed : 16.15 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3664 helix: -2.70 (0.27), residues: 248 sheet: -0.36 (0.11), residues: 1912 loop : -1.03 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP i 67 HIS 0.005 0.001 HIS m 200 PHE 0.015 0.002 PHE l 167 TYR 0.019 0.003 TYR p 202 ARG 0.009 0.001 ARG i 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7257.14 seconds wall clock time: 132 minutes 16.50 seconds (7936.50 seconds total)