Starting phenix.real_space_refine on Fri Apr 12 06:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4t_41894/04_2024/8u4t_41894_updated.pdb" } resolution = 3.38 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8032 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 92 5.16 5 C 11200 2.51 5 N 2716 2.21 5 O 2956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 65": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "R GLU 26": "OE1" <-> "OE2" Residue "R GLU 32": "OE1" <-> "OE2" Residue "R PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 182": "OD1" <-> "OD2" Residue "R PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I GLU 32": "OE1" <-> "OE2" Residue "I PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 182": "OD1" <-> "OD2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 65": "OD1" <-> "OD2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 114": "OD1" <-> "OD2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q GLU 32": "OE1" <-> "OE2" Residue "Q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 182": "OD1" <-> "OD2" Residue "Q PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 65": "OD1" <-> "OD2" Residue "Z TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 114": "OD1" <-> "OD2" Residue "AA GLU 26": "OE1" <-> "OE2" Residue "AA GLU 32": "OE1" <-> "OE2" Residue "AA PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 182": "OD1" <-> "OD2" Residue "AA PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16968 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "R" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2245 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "F" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "I" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2245 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "O" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "P" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "Q" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2245 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "Y" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "Z" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "AA" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2245 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 1 Chain: "R" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'D21': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "I" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'D21': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "Q" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'D21': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "AA" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'D21': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 8.59, per 1000 atoms: 0.51 Number of scatterers: 16968 At special positions: 0 Unit cell: (113.05, 113.05, 110.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 4 15.00 O 2956 8.00 N 2716 7.00 C 11200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 28 " - pdb=" SG CYS I 274 " distance=2.03 Simple disulfide: pdb=" SG CYS I 109 " - pdb=" SG CYS I 186 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 28 " - pdb=" SG CYS Q 274 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 186 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 93 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 28 " - pdb=" SG CYSAA 274 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 109 " - pdb=" SG CYSAA 186 " distance=2.03 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: 6.20 Conformation dependent library (CDL) restraints added in 2.9 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 24 sheets defined 43.4% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'R' and resid 35 through 65 Proline residue: R 42 - end of helix removed outlier: 3.710A pdb=" N VAL R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 99 removed outlier: 3.578A pdb=" N HIS R 79 " --> pdb=" O LYS R 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 91 " --> pdb=" O PHE R 87 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 106 through 139 removed outlier: 3.739A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR R 121 " --> pdb=" O THR R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 153 Processing helix chain 'R' and resid 155 through 174 removed outlier: 4.080A pdb=" N ILE R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Proline residue: R 163 - end of helix removed outlier: 3.890A pdb=" N THR R 168 " --> pdb=" O ALA R 164 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 207 Processing helix chain 'R' and resid 209 through 227 Processing helix chain 'R' and resid 236 through 266 removed outlier: 3.620A pdb=" N LEU R 244 " --> pdb=" O THR R 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE R 245 " --> pdb=" O THR R 241 " (cutoff:3.500A) Proline residue: R 254 - end of helix removed outlier: 3.643A pdb=" N ILE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 258 " --> pdb=" O PRO R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 304 removed outlier: 4.981A pdb=" N PHE R 293 " --> pdb=" O ALA R 289 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN R 298 " --> pdb=" O HIS R 294 " (cutoff:3.500A) Proline residue: R 299 - end of helix removed outlier: 4.143A pdb=" N TYR R 302 " --> pdb=" O ASN R 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA R 303 " --> pdb=" O PRO R 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'I' and resid 35 through 65 Proline residue: I 42 - end of helix removed outlier: 3.710A pdb=" N VAL I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 99 removed outlier: 3.578A pdb=" N HIS I 79 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR I 90 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU I 91 " --> pdb=" O PHE I 87 " (cutoff:3.500A) Proline residue: I 92 - end of helix Processing helix chain 'I' and resid 106 through 139 removed outlier: 3.739A pdb=" N LEU I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR I 121 " --> pdb=" O THR I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 153 Processing helix chain 'I' and resid 155 through 174 removed outlier: 4.080A pdb=" N ILE I 162 " --> pdb=" O VAL I 158 " (cutoff:3.500A) Proline residue: I 163 - end of helix removed outlier: 3.890A pdb=" N THR I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Proline residue: I 170 - end of helix Processing helix chain 'I' and resid 193 through 207 Processing helix chain 'I' and resid 209 through 227 Processing helix chain 'I' and resid 236 through 266 removed outlier: 3.620A pdb=" N LEU I 244 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE I 245 " --> pdb=" O THR I 241 " (cutoff:3.500A) Proline residue: I 254 - end of helix removed outlier: 3.643A pdb=" N ILE I 257 " --> pdb=" O LEU I 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY I 258 " --> pdb=" O PRO I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 304 removed outlier: 4.981A pdb=" N PHE I 293 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS I 294 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS I 295 " --> pdb=" O ALA I 291 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N CYS I 296 " --> pdb=" O PHE I 292 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN I 298 " --> pdb=" O HIS I 294 " (cutoff:3.500A) Proline residue: I 299 - end of helix removed outlier: 4.143A pdb=" N TYR I 302 " --> pdb=" O ASN I 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA I 303 " --> pdb=" O PRO I 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 31 No H-bonds generated for 'chain 'P' and resid 29 through 31' Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing helix chain 'Q' and resid 35 through 65 Proline residue: Q 42 - end of helix removed outlier: 3.710A pdb=" N VAL Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 99 removed outlier: 3.578A pdb=" N HIS Q 79 " --> pdb=" O LYS Q 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR Q 90 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU Q 91 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) Proline residue: Q 92 - end of helix Processing helix chain 'Q' and resid 106 through 139 removed outlier: 3.739A pdb=" N LEU Q 120 " --> pdb=" O TYR Q 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR Q 121 " --> pdb=" O THR Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 153 Processing helix chain 'Q' and resid 155 through 174 removed outlier: 4.080A pdb=" N ILE Q 162 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) Proline residue: Q 163 - end of helix removed outlier: 3.890A pdb=" N THR Q 168 " --> pdb=" O ALA Q 164 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE Q 169 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) Proline residue: Q 170 - end of helix Processing helix chain 'Q' and resid 193 through 207 Processing helix chain 'Q' and resid 209 through 227 Processing helix chain 'Q' and resid 236 through 266 removed outlier: 3.620A pdb=" N LEU Q 244 " --> pdb=" O THR Q 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE Q 245 " --> pdb=" O THR Q 241 " (cutoff:3.500A) Proline residue: Q 254 - end of helix removed outlier: 3.643A pdb=" N ILE Q 257 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY Q 258 " --> pdb=" O PRO Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 304 removed outlier: 4.981A pdb=" N PHE Q 293 " --> pdb=" O ALA Q 289 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS Q 294 " --> pdb=" O LEU Q 290 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS Q 295 " --> pdb=" O ALA Q 291 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N CYS Q 296 " --> pdb=" O PHE Q 292 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN Q 298 " --> pdb=" O HIS Q 294 " (cutoff:3.500A) Proline residue: Q 299 - end of helix removed outlier: 4.143A pdb=" N TYR Q 302 " --> pdb=" O ASN Q 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA Q 303 " --> pdb=" O PRO Q 299 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 31 No H-bonds generated for 'chain 'Z' and resid 29 through 31' Processing helix chain 'Z' and resid 88 through 90 No H-bonds generated for 'chain 'Z' and resid 88 through 90' Processing helix chain 'AA' and resid 35 through 65 Proline residue: AA 42 - end of helix removed outlier: 3.710A pdb=" N VALAA 54 " --> pdb=" O LEUAA 50 " (cutoff:3.500A) Processing helix chain 'AA' and resid 72 through 99 removed outlier: 3.578A pdb=" N HISAA 79 " --> pdb=" O LYSAA 75 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THRAA 90 " --> pdb=" O LEUAA 86 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEUAA 91 " --> pdb=" O PHEAA 87 " (cutoff:3.500A) Proline residue: AA 92 - end of helix Processing helix chain 'AA' and resid 106 through 139 removed outlier: 3.739A pdb=" N LEUAA 120 " --> pdb=" O TYRAA 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYRAA 121 " --> pdb=" O THRAA 117 " (cutoff:3.500A) Processing helix chain 'AA' and resid 145 through 153 Processing helix chain 'AA' and resid 155 through 174 removed outlier: 4.080A pdb=" N ILEAA 162 " --> pdb=" O VALAA 158 " (cutoff:3.500A) Proline residue: AA 163 - end of helix removed outlier: 3.890A pdb=" N THRAA 168 " --> pdb=" O ALAAA 164 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILEAA 169 " --> pdb=" O LEUAA 165 " (cutoff:3.500A) Proline residue: AA 170 - end of helix Processing helix chain 'AA' and resid 193 through 207 Processing helix chain 'AA' and resid 209 through 227 Processing helix chain 'AA' and resid 236 through 266 removed outlier: 3.620A pdb=" N LEUAA 244 " --> pdb=" O THRAA 240 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILEAA 245 " --> pdb=" O THRAA 241 " (cutoff:3.500A) Proline residue: AA 254 - end of helix removed outlier: 3.643A pdb=" N ILEAA 257 " --> pdb=" O LEUAA 253 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLYAA 258 " --> pdb=" O PROAA 254 " (cutoff:3.500A) Processing helix chain 'AA' and resid 275 through 304 removed outlier: 4.981A pdb=" N PHEAA 293 " --> pdb=" O ALAAA 289 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HISAA 294 " --> pdb=" O LEUAA 290 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYSAA 295 " --> pdb=" O ALAAA 291 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N CYSAA 296 " --> pdb=" O PHEAA 292 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASNAA 298 " --> pdb=" O HISAA 294 " (cutoff:3.500A) Proline residue: AA 299 - end of helix removed outlier: 4.143A pdb=" N TYRAA 302 " --> pdb=" O ASNAA 298 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALAAA 303 " --> pdb=" O PROAA 299 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= B, first strand: chain 'L' and resid 107 through 109 removed outlier: 3.630A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE L 53 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN L 42 " --> pdb=" O ARG L 51 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG L 51 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA H 40 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 17 through 19 Processing sheet with id= F, first strand: chain 'R' and resid 175 through 180 Processing sheet with id= G, first strand: chain 'F' and resid 5 through 7 Processing sheet with id= H, first strand: chain 'F' and resid 107 through 109 removed outlier: 3.630A pdb=" N GLY F 89 " --> pdb=" O VAL F 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE F 53 " --> pdb=" O TRP F 40 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN F 42 " --> pdb=" O ARG F 51 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA G 40 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'I' and resid 175 through 180 Processing sheet with id= M, first strand: chain 'O' and resid 5 through 7 Processing sheet with id= N, first strand: chain 'O' and resid 107 through 109 removed outlier: 3.630A pdb=" N GLY O 89 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE O 53 " --> pdb=" O TRP O 40 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN O 42 " --> pdb=" O ARG O 51 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG O 51 " --> pdb=" O GLN O 42 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'P' and resid 3 through 6 Processing sheet with id= P, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA P 40 " --> pdb=" O ILE P 45 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE P 45 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 17 through 19 Processing sheet with id= R, first strand: chain 'Q' and resid 175 through 180 Processing sheet with id= S, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id= T, first strand: chain 'Y' and resid 107 through 109 removed outlier: 3.630A pdb=" N GLY Y 89 " --> pdb=" O VAL Y 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE Y 53 " --> pdb=" O TRP Y 40 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN Y 42 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG Y 51 " --> pdb=" O GLN Y 42 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Z' and resid 3 through 6 Processing sheet with id= V, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.071A pdb=" N ARG Z 38 " --> pdb=" O TRP Z 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TRP Z 47 " --> pdb=" O ARG Z 38 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA Z 40 " --> pdb=" O ILE Z 45 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE Z 45 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'Z' and resid 17 through 19 Processing sheet with id= X, first strand: chain 'AA' and resid 175 through 180 804 hydrogen bonds defined for protein. 2148 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: 4.85 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4952 1.34 - 1.47: 4648 1.47 - 1.60: 7700 1.60 - 1.73: 0 1.73 - 1.86: 136 Bond restraints: 17436 Sorted by residual: bond pdb=" O22 D21AA 704 " pdb=" P23 D21AA 704 " ideal model delta sigma weight residual 1.643 1.855 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O22 D21 R 704 " pdb=" P23 D21 R 704 " ideal model delta sigma weight residual 1.643 1.855 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O22 D21 Q 704 " pdb=" P23 D21 Q 704 " ideal model delta sigma weight residual 1.643 1.855 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" O22 D21 I 704 " pdb=" P23 D21 I 704 " ideal model delta sigma weight residual 1.643 1.855 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C16 D21AA 704 " pdb=" O18 D21AA 704 " ideal model delta sigma weight residual 1.408 1.346 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 17431 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.79: 420 105.79 - 112.84: 9384 112.84 - 119.89: 5972 119.89 - 126.94: 7756 126.94 - 133.99: 236 Bond angle restraints: 23768 Sorted by residual: angle pdb=" N LEUAA 69 " pdb=" CA LEUAA 69 " pdb=" C LEUAA 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N LEU R 69 " pdb=" CA LEU R 69 " pdb=" C LEU R 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N LEU Q 69 " pdb=" CA LEU Q 69 " pdb=" C LEU Q 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N LEU I 69 " pdb=" CA LEU I 69 " pdb=" C LEU I 69 " ideal model delta sigma weight residual 108.41 115.42 -7.01 1.63e+00 3.76e-01 1.85e+01 angle pdb=" N SER R 71 " pdb=" CA SER R 71 " pdb=" C SER R 71 " ideal model delta sigma weight residual 109.72 115.95 -6.23 1.60e+00 3.91e-01 1.52e+01 ... (remaining 23763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9884 17.92 - 35.83: 836 35.83 - 53.75: 168 53.75 - 71.66: 40 71.66 - 89.58: 12 Dihedral angle restraints: 10940 sinusoidal: 4956 harmonic: 5984 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 138.55 -45.55 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 138.55 -45.55 1 1.00e+01 1.00e-02 2.88e+01 dihedral pdb=" CB CYS O 23 " pdb=" SG CYS O 23 " pdb=" SG CYS O 93 " pdb=" CB CYS O 93 " ideal model delta sinusoidal sigma weight residual 93.00 138.55 -45.55 1 1.00e+01 1.00e-02 2.88e+01 ... (remaining 10937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2372 0.078 - 0.155: 264 0.155 - 0.233: 4 0.233 - 0.310: 44 0.310 - 0.388: 24 Chirality restraints: 2708 Sorted by residual: chirality pdb=" C17 CLRAA 703 " pdb=" C13 CLRAA 703 " pdb=" C16 CLRAA 703 " pdb=" C20 CLRAA 703 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C17 CLR Q 703 " pdb=" C13 CLR Q 703 " pdb=" C16 CLR Q 703 " pdb=" C20 CLR Q 703 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C17 CLR R 703 " pdb=" C13 CLR R 703 " pdb=" C16 CLR R 703 " pdb=" C20 CLR R 703 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2705 not shown) Planarity restraints: 2836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG O 44 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO O 45 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO O 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO O 45 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG Y 44 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO Y 45 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO Y 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO Y 45 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 44 " 0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO F 45 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO F 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 45 " 0.046 5.00e-02 4.00e+02 ... (remaining 2833 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1248 2.74 - 3.28: 16676 3.28 - 3.82: 26624 3.82 - 4.36: 30296 4.36 - 4.90: 56633 Nonbonded interactions: 131477 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 74 " pdb=" OH TYR Q 302 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASPAA 74 " pdb=" OH TYRAA 302 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP I 74 " pdb=" OH TYR I 302 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASP R 74 " pdb=" OH TYR R 302 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR R 117 " pdb=" OD2 ASP R 171 " model vdw 2.225 2.440 ... (remaining 131472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'I' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'O' selection = chain 'Y' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'P' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 10.740 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 43.890 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 0.212 17436 Z= 0.417 Angle : 0.960 10.730 23768 Z= 0.451 Chirality : 0.067 0.388 2708 Planarity : 0.006 0.084 2836 Dihedral : 13.846 89.575 7068 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2024 helix: 1.48 (0.18), residues: 872 sheet: 0.29 (0.24), residues: 496 loop : -1.22 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 36 HIS 0.001 0.000 HIS G 99 PHE 0.017 0.001 PHE R 87 TYR 0.020 0.001 TYR P 107 ARG 0.008 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 1.814 Fit side-chains REVERT: L 31 TYR cc_start: 0.8455 (t80) cc_final: 0.8193 (t80) REVERT: L 47 GLN cc_start: 0.7966 (mp10) cc_final: 0.7646 (mp10) REVERT: R 188 ARG cc_start: 0.8325 (mtt90) cc_final: 0.7926 (mtt90) REVERT: R 239 LYS cc_start: 0.5241 (mmmt) cc_final: 0.4913 (mmmt) REVERT: F 31 TYR cc_start: 0.8457 (t80) cc_final: 0.8193 (t80) REVERT: F 47 GLN cc_start: 0.7970 (mp10) cc_final: 0.7651 (mp10) REVERT: I 188 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7929 (mtt90) REVERT: I 239 LYS cc_start: 0.5241 (mmmt) cc_final: 0.4910 (mmmt) REVERT: O 31 TYR cc_start: 0.8459 (t80) cc_final: 0.8197 (t80) REVERT: O 47 GLN cc_start: 0.7965 (mp10) cc_final: 0.7638 (mp10) REVERT: Q 188 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7930 (mtt90) REVERT: Q 239 LYS cc_start: 0.5241 (mmmt) cc_final: 0.4911 (mmmt) REVERT: Y 31 TYR cc_start: 0.8455 (t80) cc_final: 0.8193 (t80) REVERT: Y 47 GLN cc_start: 0.7965 (mp10) cc_final: 0.7640 (mp10) REVERT: AA 188 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7914 (mtt90) REVERT: AA 239 LYS cc_start: 0.5238 (mmmt) cc_final: 0.4913 (mmmt) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.3618 time to fit residues: 205.0049 Evaluate side-chains 312 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.0470 chunk 51 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17436 Z= 0.196 Angle : 0.559 5.909 23768 Z= 0.295 Chirality : 0.041 0.149 2708 Planarity : 0.005 0.034 2836 Dihedral : 8.246 79.328 3392 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.46 % Allowed : 12.22 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.19), residues: 2024 helix: 1.80 (0.18), residues: 872 sheet: 0.48 (0.24), residues: 496 loop : -1.28 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 36 HIS 0.002 0.001 HISAA 79 PHE 0.010 0.001 PHEAA 29 TYR 0.012 0.001 TYR H 107 ARG 0.005 0.000 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 308 time to evaluate : 1.779 Fit side-chains REVERT: L 31 TYR cc_start: 0.8361 (t80) cc_final: 0.8152 (t80) REVERT: R 188 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7857 (mtt90) REVERT: R 239 LYS cc_start: 0.5245 (mmmt) cc_final: 0.4825 (mmmt) REVERT: F 31 TYR cc_start: 0.8364 (t80) cc_final: 0.8154 (t80) REVERT: I 188 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7857 (mtt90) REVERT: I 239 LYS cc_start: 0.5247 (mmmt) cc_final: 0.4825 (mmmt) REVERT: O 31 TYR cc_start: 0.8366 (t80) cc_final: 0.8156 (t80) REVERT: Q 188 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7856 (mtt90) REVERT: Q 239 LYS cc_start: 0.5246 (mmmt) cc_final: 0.4822 (mmmt) REVERT: Y 31 TYR cc_start: 0.8367 (t80) cc_final: 0.8157 (t80) REVERT: AA 188 ARG cc_start: 0.8308 (mtt90) cc_final: 0.7856 (mtt90) REVERT: AA 239 LYS cc_start: 0.5246 (mmmt) cc_final: 0.4826 (mmmt) outliers start: 44 outliers final: 28 residues processed: 324 average time/residue: 0.3484 time to fit residues: 160.2925 Evaluate side-chains 324 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 296 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 222 ILE Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 222 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 123 optimal weight: 0.0070 chunk 50 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 106 ASN G 62 GLN G 106 ASN I 66 GLN P 62 GLN P 106 ASN Z 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17436 Z= 0.225 Angle : 0.545 5.518 23768 Z= 0.287 Chirality : 0.041 0.152 2708 Planarity : 0.004 0.026 2836 Dihedral : 8.125 79.287 3392 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.57 % Allowed : 15.29 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2024 helix: 1.62 (0.18), residues: 876 sheet: 0.46 (0.25), residues: 496 loop : -1.32 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAA 283 HIS 0.002 0.001 HIS I 294 PHE 0.008 0.001 PHEAA 29 TYR 0.017 0.001 TYR Q 135 ARG 0.006 0.000 ARG O 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 321 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 239 LYS cc_start: 0.5180 (mmmt) cc_final: 0.4765 (mmmt) REVERT: I 239 LYS cc_start: 0.5179 (mmmt) cc_final: 0.4763 (mmmt) REVERT: Q 239 LYS cc_start: 0.5182 (mmmt) cc_final: 0.4762 (mmmt) REVERT: AA 239 LYS cc_start: 0.5181 (mmmt) cc_final: 0.4765 (mmmt) outliers start: 64 outliers final: 48 residues processed: 353 average time/residue: 0.3524 time to fit residues: 181.1708 Evaluate side-chains 355 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 307 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 72 SER Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN Q 66 GLN Z 106 ASN AA 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17436 Z= 0.208 Angle : 0.523 5.380 23768 Z= 0.275 Chirality : 0.041 0.148 2708 Planarity : 0.004 0.026 2836 Dihedral : 7.803 76.144 3392 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.35 % Allowed : 17.80 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 2024 helix: 1.57 (0.18), residues: 880 sheet: 0.36 (0.24), residues: 496 loop : -1.33 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPAA 283 HIS 0.002 0.001 HISAA 294 PHE 0.012 0.001 PHE I 87 TYR 0.017 0.001 TYR R 135 ARG 0.007 0.001 ARG O 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 331 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 108 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8149 (ttpp) REVERT: R 84 ASP cc_start: 0.8016 (m-30) cc_final: 0.7792 (m-30) REVERT: R 239 LYS cc_start: 0.5220 (mmmt) cc_final: 0.4824 (mmmt) REVERT: F 108 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8153 (ttpp) REVERT: I 84 ASP cc_start: 0.8014 (m-30) cc_final: 0.7793 (m-30) REVERT: I 239 LYS cc_start: 0.5220 (mmmt) cc_final: 0.4823 (mmmt) REVERT: O 108 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8150 (ttpp) REVERT: Q 84 ASP cc_start: 0.8011 (m-30) cc_final: 0.7791 (m-30) REVERT: Q 239 LYS cc_start: 0.5221 (mmmt) cc_final: 0.4821 (mmmt) REVERT: Y 108 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8148 (ttpp) REVERT: AA 84 ASP cc_start: 0.8009 (m-30) cc_final: 0.7790 (m-30) REVERT: AA 239 LYS cc_start: 0.5219 (mmmt) cc_final: 0.4822 (mmmt) outliers start: 60 outliers final: 52 residues processed: 367 average time/residue: 0.3259 time to fit residues: 172.8793 Evaluate side-chains 356 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 304 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 194 LEU Chi-restraints excluded: chain Q residue 222 ILE Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 194 LEU Chi-restraints excluded: chain AA residue 222 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 173 optimal weight: 0.0060 chunk 48 optimal weight: 3.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17436 Z= 0.216 Angle : 0.533 5.444 23768 Z= 0.280 Chirality : 0.041 0.149 2708 Planarity : 0.004 0.026 2836 Dihedral : 7.254 70.846 3392 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.18 % Allowed : 18.92 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2024 helix: 1.56 (0.18), residues: 880 sheet: 0.35 (0.24), residues: 496 loop : -1.37 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPAA 283 HIS 0.003 0.001 HIS I 79 PHE 0.024 0.001 PHEAA 248 TYR 0.009 0.001 TYR Z 111 ARG 0.006 0.000 ARG O 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 304 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 108 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8143 (ttpp) REVERT: R 84 ASP cc_start: 0.8038 (m-30) cc_final: 0.7814 (m-30) REVERT: R 239 LYS cc_start: 0.5024 (mmmt) cc_final: 0.4662 (mmmt) REVERT: F 108 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8149 (ttpp) REVERT: I 84 ASP cc_start: 0.8038 (m-30) cc_final: 0.7816 (m-30) REVERT: I 239 LYS cc_start: 0.5026 (mmmt) cc_final: 0.4662 (mmmt) REVERT: O 108 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8145 (ttpp) REVERT: Q 84 ASP cc_start: 0.8034 (m-30) cc_final: 0.7813 (m-30) REVERT: Q 239 LYS cc_start: 0.5024 (mmmt) cc_final: 0.4660 (mmmt) REVERT: Y 108 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8144 (ttpp) REVERT: AA 84 ASP cc_start: 0.8033 (m-30) cc_final: 0.7809 (m-30) REVERT: AA 239 LYS cc_start: 0.5025 (mmmt) cc_final: 0.4663 (mmmt) outliers start: 57 outliers final: 53 residues processed: 345 average time/residue: 0.3394 time to fit residues: 168.2909 Evaluate side-chains 345 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 292 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 194 LEU Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 177 VAL Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 194 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 145 GLN Q 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17436 Z= 0.163 Angle : 0.506 5.402 23768 Z= 0.265 Chirality : 0.040 0.144 2708 Planarity : 0.004 0.027 2836 Dihedral : 6.805 60.279 3392 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.41 % Allowed : 18.30 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 2024 helix: 1.72 (0.18), residues: 876 sheet: 0.40 (0.24), residues: 496 loop : -1.44 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPAA 195 HIS 0.002 0.001 HIS R 79 PHE 0.020 0.001 PHEAA 248 TYR 0.018 0.001 TYR I 135 ARG 0.006 0.000 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 327 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 108 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8149 (ttpp) REVERT: H 90 ASP cc_start: 0.8504 (t0) cc_final: 0.8107 (m-30) REVERT: R 188 ARG cc_start: 0.8443 (mtt90) cc_final: 0.7768 (mtt-85) REVERT: R 239 LYS cc_start: 0.4846 (mmmt) cc_final: 0.4434 (mmmt) REVERT: F 108 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8156 (ttpp) REVERT: G 90 ASP cc_start: 0.8503 (t0) cc_final: 0.8107 (m-30) REVERT: I 188 ARG cc_start: 0.8443 (mtt90) cc_final: 0.7767 (mtt-85) REVERT: I 239 LYS cc_start: 0.4845 (mmmt) cc_final: 0.4434 (mmmt) REVERT: O 108 LYS cc_start: 0.8411 (ttpt) cc_final: 0.8152 (ttpp) REVERT: P 90 ASP cc_start: 0.8506 (t0) cc_final: 0.8111 (m-30) REVERT: Q 188 ARG cc_start: 0.8441 (mtt90) cc_final: 0.7765 (mtt-85) REVERT: Q 239 LYS cc_start: 0.4843 (mmmt) cc_final: 0.4432 (mmmt) REVERT: Y 108 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8150 (ttpp) REVERT: AA 239 LYS cc_start: 0.4847 (mmmt) cc_final: 0.4437 (mmmt) outliers start: 79 outliers final: 63 residues processed: 379 average time/residue: 0.3307 time to fit residues: 181.8411 Evaluate side-chains 375 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 312 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 222 ILE Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 222 ILE Chi-restraints excluded: chain AA residue 266 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 0.3980 chunk 108 optimal weight: 0.0980 chunk 192 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 145 GLN Q 145 GLN AA 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17436 Z= 0.206 Angle : 0.538 5.974 23768 Z= 0.279 Chirality : 0.041 0.149 2708 Planarity : 0.004 0.028 2836 Dihedral : 6.586 53.346 3392 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.41 % Allowed : 18.25 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2024 helix: 1.64 (0.18), residues: 884 sheet: 0.38 (0.25), residues: 492 loop : -1.34 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAA 283 HIS 0.002 0.001 HIS Q 294 PHE 0.009 0.001 PHEAA 249 TYR 0.009 0.001 TYR Z 111 ARG 0.007 0.000 ARG Y 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 312 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.8011 (mp10) cc_final: 0.7715 (mp10) REVERT: L 108 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8150 (ttpp) REVERT: H 90 ASP cc_start: 0.8544 (t0) cc_final: 0.8159 (m-30) REVERT: R 188 ARG cc_start: 0.8482 (mtt90) cc_final: 0.7800 (mtt-85) REVERT: R 239 LYS cc_start: 0.4858 (mmmt) cc_final: 0.4474 (mmmt) REVERT: F 47 GLN cc_start: 0.8012 (mp10) cc_final: 0.7719 (mp10) REVERT: F 108 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8154 (ttpp) REVERT: G 90 ASP cc_start: 0.8542 (t0) cc_final: 0.8161 (m-30) REVERT: I 188 ARG cc_start: 0.8483 (mtt90) cc_final: 0.7801 (mtt-85) REVERT: I 239 LYS cc_start: 0.4857 (mmmt) cc_final: 0.4473 (mmmt) REVERT: O 47 GLN cc_start: 0.8011 (mp10) cc_final: 0.7711 (mp10) REVERT: O 108 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8151 (ttpp) REVERT: P 90 ASP cc_start: 0.8546 (t0) cc_final: 0.8166 (m-30) REVERT: Q 188 ARG cc_start: 0.8481 (mtt90) cc_final: 0.7800 (mtt-85) REVERT: Q 239 LYS cc_start: 0.4854 (mmmt) cc_final: 0.4471 (mmmt) REVERT: Y 47 GLN cc_start: 0.8013 (mp10) cc_final: 0.7717 (mp10) REVERT: Y 108 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8149 (ttpp) REVERT: AA 239 LYS cc_start: 0.4855 (mmmt) cc_final: 0.4475 (mmmt) outliers start: 79 outliers final: 71 residues processed: 363 average time/residue: 0.3419 time to fit residues: 177.6259 Evaluate side-chains 371 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 300 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain O residue 1 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 222 ILE Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Y residue 1 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 222 ILE Chi-restraints excluded: chain AA residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN I 66 GLN I 202 GLN Q 202 GLN AA 202 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17436 Z= 0.160 Angle : 0.527 8.792 23768 Z= 0.268 Chirality : 0.040 0.142 2708 Planarity : 0.004 0.030 2836 Dihedral : 6.183 53.404 3392 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.69 % Allowed : 19.14 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2024 helix: 1.69 (0.18), residues: 880 sheet: 0.44 (0.24), residues: 492 loop : -1.41 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPAA 283 HIS 0.002 0.000 HIS Q 294 PHE 0.015 0.001 PHEAA 87 TYR 0.019 0.001 TYRAA 135 ARG 0.008 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 321 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.8029 (mp10) cc_final: 0.7716 (mp10) REVERT: L 108 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8121 (ttpp) REVERT: H 90 ASP cc_start: 0.8498 (t0) cc_final: 0.8123 (m-30) REVERT: R 84 ASP cc_start: 0.7851 (m-30) cc_final: 0.7569 (m-30) REVERT: R 188 ARG cc_start: 0.8469 (mtt90) cc_final: 0.7780 (mtt-85) REVERT: R 239 LYS cc_start: 0.4829 (mmmt) cc_final: 0.4331 (mmmt) REVERT: F 47 GLN cc_start: 0.8031 (mp10) cc_final: 0.7721 (mp10) REVERT: F 108 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8127 (ttpp) REVERT: G 90 ASP cc_start: 0.8494 (t0) cc_final: 0.8124 (m-30) REVERT: I 84 ASP cc_start: 0.7850 (m-30) cc_final: 0.7568 (m-30) REVERT: I 188 ARG cc_start: 0.8468 (mtt90) cc_final: 0.7781 (mtt-85) REVERT: I 239 LYS cc_start: 0.4831 (mmmt) cc_final: 0.4330 (mmmt) REVERT: O 47 GLN cc_start: 0.8027 (mp10) cc_final: 0.7709 (mp10) REVERT: O 108 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8124 (ttpp) REVERT: P 90 ASP cc_start: 0.8500 (t0) cc_final: 0.8128 (m-30) REVERT: Q 84 ASP cc_start: 0.7848 (m-30) cc_final: 0.7570 (m-30) REVERT: Q 188 ARG cc_start: 0.8467 (mtt90) cc_final: 0.7779 (mtt-85) REVERT: Q 239 LYS cc_start: 0.4831 (mmmt) cc_final: 0.4329 (mmmt) REVERT: Y 47 GLN cc_start: 0.8033 (mp10) cc_final: 0.7720 (mp10) REVERT: Y 108 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8122 (ttpp) REVERT: AA 84 ASP cc_start: 0.7847 (m-30) cc_final: 0.7570 (m-30) REVERT: AA 188 ARG cc_start: 0.8431 (mtt90) cc_final: 0.7704 (mtt-85) REVERT: AA 239 LYS cc_start: 0.4832 (mmmt) cc_final: 0.4329 (mmmt) outliers start: 84 outliers final: 72 residues processed: 373 average time/residue: 0.3503 time to fit residues: 187.7565 Evaluate side-chains 383 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 311 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain O residue 1 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 222 ILE Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Y residue 1 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 177 VAL Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 222 ILE Chi-restraints excluded: chain AA residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 chunk 162 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 66 GLN AA 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17436 Z= 0.198 Angle : 0.547 7.904 23768 Z= 0.279 Chirality : 0.040 0.145 2708 Planarity : 0.004 0.032 2836 Dihedral : 6.113 54.193 3392 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.02 % Allowed : 19.64 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2024 helix: 1.63 (0.18), residues: 884 sheet: 0.43 (0.24), residues: 492 loop : -1.41 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 283 HIS 0.002 0.001 HIS I 79 PHE 0.007 0.001 PHEAA 249 TYR 0.008 0.001 TYR H 111 ARG 0.009 0.001 ARG Y 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 312 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.8019 (mp10) cc_final: 0.7700 (mp10) REVERT: L 108 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8120 (ttpp) REVERT: H 90 ASP cc_start: 0.8521 (t0) cc_final: 0.8147 (m-30) REVERT: R 84 ASP cc_start: 0.7814 (m-30) cc_final: 0.7503 (m-30) REVERT: R 188 ARG cc_start: 0.8483 (mtt90) cc_final: 0.7794 (mtt-85) REVERT: R 239 LYS cc_start: 0.4860 (mmmt) cc_final: 0.4544 (mmmt) REVERT: F 47 GLN cc_start: 0.8021 (mp10) cc_final: 0.7704 (mp10) REVERT: F 108 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8127 (ttpp) REVERT: G 90 ASP cc_start: 0.8519 (t0) cc_final: 0.8149 (m-30) REVERT: I 84 ASP cc_start: 0.7809 (m-30) cc_final: 0.7502 (m-30) REVERT: I 188 ARG cc_start: 0.8483 (mtt90) cc_final: 0.7796 (mtt-85) REVERT: I 239 LYS cc_start: 0.4862 (mmmt) cc_final: 0.4546 (mmmt) REVERT: O 47 GLN cc_start: 0.8017 (mp10) cc_final: 0.7693 (mp10) REVERT: O 108 LYS cc_start: 0.8377 (ttpt) cc_final: 0.8125 (ttpp) REVERT: P 90 ASP cc_start: 0.8521 (t0) cc_final: 0.8152 (m-30) REVERT: Q 84 ASP cc_start: 0.7808 (m-30) cc_final: 0.7504 (m-30) REVERT: Q 188 ARG cc_start: 0.8481 (mtt90) cc_final: 0.7796 (mtt-85) REVERT: Q 239 LYS cc_start: 0.4863 (mmmt) cc_final: 0.4543 (mmmt) REVERT: Y 47 GLN cc_start: 0.8020 (mp10) cc_final: 0.7700 (mp10) REVERT: Y 108 LYS cc_start: 0.8375 (ttpt) cc_final: 0.8122 (ttpp) REVERT: AA 84 ASP cc_start: 0.7812 (m-30) cc_final: 0.7505 (m-30) REVERT: AA 188 ARG cc_start: 0.8452 (mtt90) cc_final: 0.7713 (mtt-85) REVERT: AA 239 LYS cc_start: 0.4865 (mmmt) cc_final: 0.4545 (mmmt) outliers start: 72 outliers final: 72 residues processed: 352 average time/residue: 0.3393 time to fit residues: 171.6693 Evaluate side-chains 376 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 304 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 30 ARG Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain O residue 1 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 30 ARG Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 222 ILE Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Y residue 1 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 5 THR Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 30 ARG Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 90 THR Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 177 VAL Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 222 ILE Chi-restraints excluded: chain AA residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 0.0020 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17436 Z= 0.142 Angle : 0.520 7.910 23768 Z= 0.264 Chirality : 0.039 0.141 2708 Planarity : 0.004 0.034 2836 Dihedral : 5.737 55.860 3392 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.68 % Allowed : 19.70 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 2024 helix: 1.82 (0.18), residues: 880 sheet: 0.34 (0.24), residues: 504 loop : -1.50 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAA 195 HIS 0.001 0.000 HIS Q 294 PHE 0.015 0.001 PHEAA 87 TYR 0.007 0.001 TYR Q 302 ARG 0.009 0.001 ARG L 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 326 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 47 GLN cc_start: 0.7991 (mp10) cc_final: 0.7699 (mp10) REVERT: L 108 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8158 (ttpp) REVERT: H 46 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7592 (tt0) REVERT: R 84 ASP cc_start: 0.7703 (m-30) cc_final: 0.7438 (m-30) REVERT: R 188 ARG cc_start: 0.8463 (mtt90) cc_final: 0.7769 (mtt-85) REVERT: R 239 LYS cc_start: 0.4793 (mmmt) cc_final: 0.4517 (mmmt) REVERT: F 47 GLN cc_start: 0.7994 (mp10) cc_final: 0.7701 (mp10) REVERT: F 108 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8165 (ttpp) REVERT: G 46 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7589 (tt0) REVERT: I 84 ASP cc_start: 0.7700 (m-30) cc_final: 0.7435 (m-30) REVERT: I 188 ARG cc_start: 0.8460 (mtt90) cc_final: 0.7769 (mtt-85) REVERT: I 239 LYS cc_start: 0.4796 (mmmt) cc_final: 0.4520 (mmmt) REVERT: O 47 GLN cc_start: 0.7990 (mp10) cc_final: 0.7691 (mp10) REVERT: O 108 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8160 (ttpp) REVERT: P 46 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7593 (tt0) REVERT: Q 84 ASP cc_start: 0.7701 (m-30) cc_final: 0.7434 (m-30) REVERT: Q 188 ARG cc_start: 0.8460 (mtt90) cc_final: 0.7767 (mtt-85) REVERT: Q 239 LYS cc_start: 0.4798 (mmmt) cc_final: 0.4517 (mmmt) REVERT: Y 47 GLN cc_start: 0.7988 (mp10) cc_final: 0.7692 (mp10) REVERT: Y 108 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8161 (ttpp) REVERT: AA 84 ASP cc_start: 0.7702 (m-30) cc_final: 0.7435 (m-30) REVERT: AA 188 ARG cc_start: 0.8433 (mtt90) cc_final: 0.7705 (mtt-85) REVERT: AA 239 LYS cc_start: 0.4799 (mmmt) cc_final: 0.4518 (mmmt) outliers start: 66 outliers final: 53 residues processed: 368 average time/residue: 0.3396 time to fit residues: 179.3490 Evaluate side-chains 367 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 314 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 94 MET Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 39 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 70 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 186 CYS Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain O residue 1 ASP Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 39 ASN Chi-restraints excluded: chain O residue 94 MET Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 70 MET Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 121 THR Chi-restraints excluded: chain Q residue 72 MET Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 186 CYS Chi-restraints excluded: chain Q residue 266 LEU Chi-restraints excluded: chain Y residue 1 ASP Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 94 MET Chi-restraints excluded: chain Z residue 11 VAL Chi-restraints excluded: chain Z residue 70 MET Chi-restraints excluded: chain Z residue 86 LEU Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 121 THR Chi-restraints excluded: chain AA residue 72 MET Chi-restraints excluded: chain AA residue 122 SER Chi-restraints excluded: chain AA residue 177 VAL Chi-restraints excluded: chain AA residue 186 CYS Chi-restraints excluded: chain AA residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103544 restraints weight = 24475.970| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.35 r_work: 0.3100 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17436 Z= 0.235 Angle : 0.575 7.724 23768 Z= 0.294 Chirality : 0.041 0.149 2708 Planarity : 0.004 0.033 2836 Dihedral : 5.951 55.322 3392 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.46 % Allowed : 20.37 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2024 helix: 1.54 (0.18), residues: 888 sheet: 0.28 (0.24), residues: 500 loop : -1.42 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAA 283 HIS 0.003 0.001 HISAA 79 PHE 0.009 0.001 PHE I 249 TYR 0.026 0.001 TYR I 135 ARG 0.009 0.001 ARG O 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3824.20 seconds wall clock time: 70 minutes 39.35 seconds (4239.35 seconds total)