Starting phenix.real_space_refine on Tue Mar 19 19:15:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/03_2024/6qx7_4662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/03_2024/6qx7_4662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/03_2024/6qx7_4662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/03_2024/6qx7_4662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/03_2024/6qx7_4662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/03_2024/6qx7_4662.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.083 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 16164 2.51 5 N 4152 2.21 5 O 4764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0a PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0a TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0a TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0b TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0b TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0c PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0c TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0c TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0d PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0d TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0d TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0e PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0e TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0e TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0f PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0f TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0f TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0g PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0g TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0g TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0h PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0h TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0h TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0i PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0i TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0i TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0j PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0j TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0j TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0k PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0k TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0k TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0l PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0l TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0l TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25164 Number of models: 1 Model: "" Number of chains: 12 Chain: "0a" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0b" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0c" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0d" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0e" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0f" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0g" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0h" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0i" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0j" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0k" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0l" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Time building chain proxies: 12.57, per 1000 atoms: 0.50 Number of scatterers: 25164 At special positions: 0 Unit cell: (159.728, 159.728, 91.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 4764 8.00 N 4152 7.00 C 16164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.29 Conformation dependent library (CDL) restraints added in 4.1 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5928 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 48 sheets defined 41.4% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain '0a' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0a 28 " --> pdb=" O PHE0a 24 " (cutoff:3.500A) Processing helix chain '0a' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0a 54 " --> pdb=" O PRO0a 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0a 56 " --> pdb=" O PHE0a 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0a 57 " --> pdb=" O LEU0a 53 " (cutoff:3.500A) Processing helix chain '0a' and resid 130 through 154 Processing helix chain '0a' and resid 155 through 157 No H-bonds generated for 'chain '0a' and resid 155 through 157' Processing helix chain '0a' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0a 173 " --> pdb=" O LEU0a 169 " (cutoff:3.500A) Processing helix chain '0a' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0a 212 " --> pdb=" O ASP0a 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0a 220 " --> pdb=" O ALA0a 216 " (cutoff:3.500A) Processing helix chain '0a' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0a 256 " --> pdb=" O SER0a 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0a 257 " --> pdb=" O SER0a 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0a 260 " --> pdb=" O VAL0a 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0a 261 " --> pdb=" O PHE0a 257 " (cutoff:3.500A) Processing helix chain '0a' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0a 270 " --> pdb=" O GLU0a 266 " (cutoff:3.500A) Processing helix chain '0b' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0b 28 " --> pdb=" O PHE0b 24 " (cutoff:3.500A) Processing helix chain '0b' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0b 54 " --> pdb=" O PRO0b 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0b 56 " --> pdb=" O PHE0b 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0b 57 " --> pdb=" O LEU0b 53 " (cutoff:3.500A) Processing helix chain '0b' and resid 130 through 154 Processing helix chain '0b' and resid 155 through 157 No H-bonds generated for 'chain '0b' and resid 155 through 157' Processing helix chain '0b' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0b 173 " --> pdb=" O LEU0b 169 " (cutoff:3.500A) Processing helix chain '0b' and resid 206 through 225 removed outlier: 3.709A pdb=" N ALA0b 212 " --> pdb=" O ASP0b 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0b 220 " --> pdb=" O ALA0b 216 " (cutoff:3.500A) Processing helix chain '0b' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0b 256 " --> pdb=" O SER0b 252 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE0b 257 " --> pdb=" O SER0b 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0b 260 " --> pdb=" O VAL0b 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0b 261 " --> pdb=" O PHE0b 257 " (cutoff:3.500A) Processing helix chain '0b' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0b 270 " --> pdb=" O GLU0b 266 " (cutoff:3.500A) Processing helix chain '0c' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0c 28 " --> pdb=" O PHE0c 24 " (cutoff:3.500A) Processing helix chain '0c' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0c 54 " --> pdb=" O PRO0c 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0c 56 " --> pdb=" O PHE0c 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0c 57 " --> pdb=" O LEU0c 53 " (cutoff:3.500A) Processing helix chain '0c' and resid 130 through 154 Processing helix chain '0c' and resid 155 through 157 No H-bonds generated for 'chain '0c' and resid 155 through 157' Processing helix chain '0c' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0c 173 " --> pdb=" O LEU0c 169 " (cutoff:3.500A) Processing helix chain '0c' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0c 212 " --> pdb=" O ASP0c 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0c 220 " --> pdb=" O ALA0c 216 " (cutoff:3.500A) Processing helix chain '0c' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0c 256 " --> pdb=" O SER0c 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0c 257 " --> pdb=" O SER0c 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0c 260 " --> pdb=" O VAL0c 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0c 261 " --> pdb=" O PHE0c 257 " (cutoff:3.500A) Processing helix chain '0c' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0c 270 " --> pdb=" O GLU0c 266 " (cutoff:3.500A) Processing helix chain '0d' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0d 28 " --> pdb=" O PHE0d 24 " (cutoff:3.500A) Processing helix chain '0d' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0d 54 " --> pdb=" O PRO0d 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0d 56 " --> pdb=" O PHE0d 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0d 57 " --> pdb=" O LEU0d 53 " (cutoff:3.500A) Processing helix chain '0d' and resid 130 through 154 Processing helix chain '0d' and resid 155 through 157 No H-bonds generated for 'chain '0d' and resid 155 through 157' Processing helix chain '0d' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0d 173 " --> pdb=" O LEU0d 169 " (cutoff:3.500A) Processing helix chain '0d' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0d 212 " --> pdb=" O ASP0d 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0d 220 " --> pdb=" O ALA0d 216 " (cutoff:3.500A) Processing helix chain '0d' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0d 256 " --> pdb=" O SER0d 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0d 257 " --> pdb=" O SER0d 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0d 260 " --> pdb=" O VAL0d 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0d 261 " --> pdb=" O PHE0d 257 " (cutoff:3.500A) Processing helix chain '0d' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0d 270 " --> pdb=" O GLU0d 266 " (cutoff:3.500A) Processing helix chain '0e' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0e 28 " --> pdb=" O PHE0e 24 " (cutoff:3.500A) Processing helix chain '0e' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0e 54 " --> pdb=" O PRO0e 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0e 56 " --> pdb=" O PHE0e 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0e 57 " --> pdb=" O LEU0e 53 " (cutoff:3.500A) Processing helix chain '0e' and resid 130 through 154 Processing helix chain '0e' and resid 155 through 157 No H-bonds generated for 'chain '0e' and resid 155 through 157' Processing helix chain '0e' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0e 173 " --> pdb=" O LEU0e 169 " (cutoff:3.500A) Processing helix chain '0e' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0e 212 " --> pdb=" O ASP0e 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0e 220 " --> pdb=" O ALA0e 216 " (cutoff:3.500A) Processing helix chain '0e' and resid 250 through 263 removed outlier: 3.839A pdb=" N VAL0e 256 " --> pdb=" O SER0e 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0e 257 " --> pdb=" O SER0e 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0e 260 " --> pdb=" O VAL0e 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0e 261 " --> pdb=" O PHE0e 257 " (cutoff:3.500A) Processing helix chain '0e' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0e 270 " --> pdb=" O GLU0e 266 " (cutoff:3.500A) Processing helix chain '0f' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0f 28 " --> pdb=" O PHE0f 24 " (cutoff:3.500A) Processing helix chain '0f' and resid 49 through 59 removed outlier: 3.598A pdb=" N GLU0f 54 " --> pdb=" O PRO0f 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0f 56 " --> pdb=" O PHE0f 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0f 57 " --> pdb=" O LEU0f 53 " (cutoff:3.500A) Processing helix chain '0f' and resid 130 through 154 Processing helix chain '0f' and resid 155 through 157 No H-bonds generated for 'chain '0f' and resid 155 through 157' Processing helix chain '0f' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0f 173 " --> pdb=" O LEU0f 169 " (cutoff:3.500A) Processing helix chain '0f' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0f 212 " --> pdb=" O ASP0f 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0f 220 " --> pdb=" O ALA0f 216 " (cutoff:3.500A) Processing helix chain '0f' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0f 256 " --> pdb=" O SER0f 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0f 257 " --> pdb=" O SER0f 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0f 260 " --> pdb=" O VAL0f 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0f 261 " --> pdb=" O PHE0f 257 " (cutoff:3.500A) Processing helix chain '0f' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0f 270 " --> pdb=" O GLU0f 266 " (cutoff:3.500A) Processing helix chain '0g' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0g 28 " --> pdb=" O PHE0g 24 " (cutoff:3.500A) Processing helix chain '0g' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0g 54 " --> pdb=" O PRO0g 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0g 56 " --> pdb=" O PHE0g 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0g 57 " --> pdb=" O LEU0g 53 " (cutoff:3.500A) Processing helix chain '0g' and resid 130 through 154 Processing helix chain '0g' and resid 155 through 157 No H-bonds generated for 'chain '0g' and resid 155 through 157' Processing helix chain '0g' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0g 173 " --> pdb=" O LEU0g 169 " (cutoff:3.500A) Processing helix chain '0g' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0g 212 " --> pdb=" O ASP0g 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0g 220 " --> pdb=" O ALA0g 216 " (cutoff:3.500A) Processing helix chain '0g' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0g 256 " --> pdb=" O SER0g 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0g 257 " --> pdb=" O SER0g 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0g 260 " --> pdb=" O VAL0g 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0g 261 " --> pdb=" O PHE0g 257 " (cutoff:3.500A) Processing helix chain '0g' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0g 270 " --> pdb=" O GLU0g 266 " (cutoff:3.500A) Processing helix chain '0h' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0h 28 " --> pdb=" O PHE0h 24 " (cutoff:3.500A) Processing helix chain '0h' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0h 54 " --> pdb=" O PRO0h 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0h 56 " --> pdb=" O PHE0h 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0h 57 " --> pdb=" O LEU0h 53 " (cutoff:3.500A) Processing helix chain '0h' and resid 130 through 154 Processing helix chain '0h' and resid 155 through 157 No H-bonds generated for 'chain '0h' and resid 155 through 157' Processing helix chain '0h' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0h 173 " --> pdb=" O LEU0h 169 " (cutoff:3.500A) Processing helix chain '0h' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0h 212 " --> pdb=" O ASP0h 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0h 220 " --> pdb=" O ALA0h 216 " (cutoff:3.500A) Processing helix chain '0h' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0h 256 " --> pdb=" O SER0h 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0h 257 " --> pdb=" O SER0h 253 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER0h 260 " --> pdb=" O VAL0h 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0h 261 " --> pdb=" O PHE0h 257 " (cutoff:3.500A) Processing helix chain '0h' and resid 264 through 272 removed outlier: 4.956A pdb=" N GLU0h 270 " --> pdb=" O GLU0h 266 " (cutoff:3.500A) Processing helix chain '0i' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0i 28 " --> pdb=" O PHE0i 24 " (cutoff:3.500A) Processing helix chain '0i' and resid 49 through 59 removed outlier: 3.596A pdb=" N GLU0i 54 " --> pdb=" O PRO0i 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0i 56 " --> pdb=" O PHE0i 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0i 57 " --> pdb=" O LEU0i 53 " (cutoff:3.500A) Processing helix chain '0i' and resid 130 through 154 Processing helix chain '0i' and resid 155 through 157 No H-bonds generated for 'chain '0i' and resid 155 through 157' Processing helix chain '0i' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0i 173 " --> pdb=" O LEU0i 169 " (cutoff:3.500A) Processing helix chain '0i' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0i 212 " --> pdb=" O ASP0i 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0i 220 " --> pdb=" O ALA0i 216 " (cutoff:3.500A) Processing helix chain '0i' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0i 256 " --> pdb=" O SER0i 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0i 257 " --> pdb=" O SER0i 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0i 260 " --> pdb=" O VAL0i 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0i 261 " --> pdb=" O PHE0i 257 " (cutoff:3.500A) Processing helix chain '0i' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0i 270 " --> pdb=" O GLU0i 266 " (cutoff:3.500A) Processing helix chain '0j' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0j 28 " --> pdb=" O PHE0j 24 " (cutoff:3.500A) Processing helix chain '0j' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0j 54 " --> pdb=" O PRO0j 50 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER0j 56 " --> pdb=" O PHE0j 52 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE0j 57 " --> pdb=" O LEU0j 53 " (cutoff:3.500A) Processing helix chain '0j' and resid 130 through 154 Processing helix chain '0j' and resid 155 through 157 No H-bonds generated for 'chain '0j' and resid 155 through 157' Processing helix chain '0j' and resid 167 through 178 removed outlier: 4.147A pdb=" N GLN0j 173 " --> pdb=" O LEU0j 169 " (cutoff:3.500A) Processing helix chain '0j' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0j 212 " --> pdb=" O ASP0j 208 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU0j 220 " --> pdb=" O ALA0j 216 " (cutoff:3.500A) Processing helix chain '0j' and resid 250 through 263 removed outlier: 3.837A pdb=" N VAL0j 256 " --> pdb=" O SER0j 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0j 257 " --> pdb=" O SER0j 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0j 260 " --> pdb=" O VAL0j 256 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG0j 261 " --> pdb=" O PHE0j 257 " (cutoff:3.500A) Processing helix chain '0j' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0j 270 " --> pdb=" O GLU0j 266 " (cutoff:3.500A) Processing helix chain '0k' and resid 22 through 33 removed outlier: 3.853A pdb=" N LEU0k 28 " --> pdb=" O PHE0k 24 " (cutoff:3.500A) Processing helix chain '0k' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0k 54 " --> pdb=" O PRO0k 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0k 56 " --> pdb=" O PHE0k 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0k 57 " --> pdb=" O LEU0k 53 " (cutoff:3.500A) Processing helix chain '0k' and resid 130 through 154 Processing helix chain '0k' and resid 155 through 157 No H-bonds generated for 'chain '0k' and resid 155 through 157' Processing helix chain '0k' and resid 167 through 178 removed outlier: 4.149A pdb=" N GLN0k 173 " --> pdb=" O LEU0k 169 " (cutoff:3.500A) Processing helix chain '0k' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0k 212 " --> pdb=" O ASP0k 208 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU0k 220 " --> pdb=" O ALA0k 216 " (cutoff:3.500A) Processing helix chain '0k' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0k 256 " --> pdb=" O SER0k 252 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE0k 257 " --> pdb=" O SER0k 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0k 260 " --> pdb=" O VAL0k 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0k 261 " --> pdb=" O PHE0k 257 " (cutoff:3.500A) Processing helix chain '0k' and resid 264 through 272 removed outlier: 4.957A pdb=" N GLU0k 270 " --> pdb=" O GLU0k 266 " (cutoff:3.500A) Processing helix chain '0l' and resid 22 through 33 removed outlier: 3.854A pdb=" N LEU0l 28 " --> pdb=" O PHE0l 24 " (cutoff:3.500A) Processing helix chain '0l' and resid 49 through 59 removed outlier: 3.597A pdb=" N GLU0l 54 " --> pdb=" O PRO0l 50 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER0l 56 " --> pdb=" O PHE0l 52 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE0l 57 " --> pdb=" O LEU0l 53 " (cutoff:3.500A) Processing helix chain '0l' and resid 130 through 154 Processing helix chain '0l' and resid 155 through 157 No H-bonds generated for 'chain '0l' and resid 155 through 157' Processing helix chain '0l' and resid 167 through 178 removed outlier: 4.148A pdb=" N GLN0l 173 " --> pdb=" O LEU0l 169 " (cutoff:3.500A) Processing helix chain '0l' and resid 206 through 225 removed outlier: 3.708A pdb=" N ALA0l 212 " --> pdb=" O ASP0l 208 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU0l 220 " --> pdb=" O ALA0l 216 " (cutoff:3.500A) Processing helix chain '0l' and resid 250 through 263 removed outlier: 3.838A pdb=" N VAL0l 256 " --> pdb=" O SER0l 252 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE0l 257 " --> pdb=" O SER0l 253 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER0l 260 " --> pdb=" O VAL0l 256 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG0l 261 " --> pdb=" O PHE0l 257 " (cutoff:3.500A) Processing helix chain '0l' and resid 264 through 272 removed outlier: 4.958A pdb=" N GLU0l 270 " --> pdb=" O GLU0l 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0a' and resid 40 through 42 Processing sheet with id=AA2, first strand: chain '0a' and resid 62 through 63 Processing sheet with id=AA3, first strand: chain '0a' and resid 78 through 80 Processing sheet with id=AA4, first strand: chain '0a' and resid 160 through 161 Processing sheet with id=AA5, first strand: chain '0a' and resid 184 through 185 removed outlier: 7.111A pdb=" N VAL0a 184 " --> pdb=" O ILE0l 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '0b' and resid 40 through 42 Processing sheet with id=AA7, first strand: chain '0b' and resid 62 through 63 Processing sheet with id=AA8, first strand: chain '0b' and resid 78 through 80 Processing sheet with id=AA9, first strand: chain '0b' and resid 160 through 161 Processing sheet with id=AB1, first strand: chain '0c' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain '0c' and resid 62 through 63 Processing sheet with id=AB3, first strand: chain '0c' and resid 78 through 80 Processing sheet with id=AB4, first strand: chain '0c' and resid 160 through 161 Processing sheet with id=AB5, first strand: chain '0d' and resid 40 through 42 Processing sheet with id=AB6, first strand: chain '0d' and resid 62 through 63 Processing sheet with id=AB7, first strand: chain '0d' and resid 78 through 80 Processing sheet with id=AB8, first strand: chain '0d' and resid 160 through 161 Processing sheet with id=AB9, first strand: chain '0e' and resid 40 through 42 Processing sheet with id=AC1, first strand: chain '0e' and resid 62 through 63 Processing sheet with id=AC2, first strand: chain '0e' and resid 78 through 80 Processing sheet with id=AC3, first strand: chain '0e' and resid 160 through 161 Processing sheet with id=AC4, first strand: chain '0f' and resid 40 through 42 Processing sheet with id=AC5, first strand: chain '0f' and resid 62 through 63 Processing sheet with id=AC6, first strand: chain '0f' and resid 78 through 80 Processing sheet with id=AC7, first strand: chain '0f' and resid 160 through 161 Processing sheet with id=AC8, first strand: chain '0g' and resid 40 through 42 Processing sheet with id=AC9, first strand: chain '0g' and resid 62 through 63 Processing sheet with id=AD1, first strand: chain '0g' and resid 78 through 80 Processing sheet with id=AD2, first strand: chain '0g' and resid 160 through 161 Processing sheet with id=AD3, first strand: chain '0h' and resid 40 through 42 Processing sheet with id=AD4, first strand: chain '0h' and resid 62 through 63 Processing sheet with id=AD5, first strand: chain '0h' and resid 78 through 80 Processing sheet with id=AD6, first strand: chain '0h' and resid 160 through 161 Processing sheet with id=AD7, first strand: chain '0i' and resid 40 through 42 Processing sheet with id=AD8, first strand: chain '0i' and resid 62 through 63 Processing sheet with id=AD9, first strand: chain '0i' and resid 78 through 80 Processing sheet with id=AE1, first strand: chain '0i' and resid 160 through 161 Processing sheet with id=AE2, first strand: chain '0j' and resid 40 through 42 Processing sheet with id=AE3, first strand: chain '0j' and resid 62 through 63 Processing sheet with id=AE4, first strand: chain '0j' and resid 78 through 80 Processing sheet with id=AE5, first strand: chain '0j' and resid 160 through 161 Processing sheet with id=AE6, first strand: chain '0k' and resid 40 through 42 Processing sheet with id=AE7, first strand: chain '0k' and resid 62 through 63 Processing sheet with id=AE8, first strand: chain '0k' and resid 78 through 80 Processing sheet with id=AE9, first strand: chain '0k' and resid 160 through 161 Processing sheet with id=AF1, first strand: chain '0l' and resid 40 through 42 Processing sheet with id=AF2, first strand: chain '0l' and resid 62 through 63 Processing sheet with id=AF3, first strand: chain '0l' and resid 78 through 80 863 hydrogen bonds defined for protein. 2481 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: 6.77 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6951 1.33 - 1.45: 4657 1.45 - 1.57: 13976 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 25728 Sorted by residual: bond pdb=" N ILE0c 227 " pdb=" CA ILE0c 227 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.50e+01 bond pdb=" N ILE0k 227 " pdb=" CA ILE0k 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.48e+01 bond pdb=" N ILE0f 227 " pdb=" CA ILE0f 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 bond pdb=" N ILE0b 227 " pdb=" CA ILE0b 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 bond pdb=" N ILE0i 227 " pdb=" CA ILE0i 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 ... (remaining 25723 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 934 107.44 - 114.08: 13755 114.08 - 120.71: 11509 120.71 - 127.35: 8405 127.35 - 133.98: 257 Bond angle restraints: 34860 Sorted by residual: angle pdb=" N ALA0j 187 " pdb=" CA ALA0j 187 " pdb=" C ALA0j 187 " ideal model delta sigma weight residual 108.07 116.19 -8.12 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0f 187 " pdb=" CA ALA0f 187 " pdb=" C ALA0f 187 " ideal model delta sigma weight residual 108.07 116.19 -8.12 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0h 187 " pdb=" CA ALA0h 187 " pdb=" C ALA0h 187 " ideal model delta sigma weight residual 108.07 116.18 -8.11 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0i 187 " pdb=" CA ALA0i 187 " pdb=" C ALA0i 187 " ideal model delta sigma weight residual 108.07 116.18 -8.11 1.38e+00 5.25e-01 3.45e+01 angle pdb=" N ALA0a 187 " pdb=" CA ALA0a 187 " pdb=" C ALA0a 187 " ideal model delta sigma weight residual 108.07 116.15 -8.08 1.38e+00 5.25e-01 3.43e+01 ... (remaining 34855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.44: 12962 10.44 - 20.88: 1811 20.88 - 31.33: 407 31.33 - 41.77: 204 41.77 - 52.21: 84 Dihedral angle restraints: 15468 sinusoidal: 6300 harmonic: 9168 Sorted by residual: dihedral pdb=" CA THR0b 91 " pdb=" C THR0b 91 " pdb=" N VAL0b 92 " pdb=" CA VAL0b 92 " ideal model delta harmonic sigma weight residual 180.00 -137.44 -42.56 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CA THR0k 91 " pdb=" C THR0k 91 " pdb=" N VAL0k 92 " pdb=" CA VAL0k 92 " ideal model delta harmonic sigma weight residual 180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 dihedral pdb=" CA THR0j 91 " pdb=" C THR0j 91 " pdb=" N VAL0j 92 " pdb=" CA VAL0j 92 " ideal model delta harmonic sigma weight residual 180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 ... (remaining 15465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2347 0.048 - 0.096: 918 0.096 - 0.144: 313 0.144 - 0.192: 154 0.192 - 0.240: 24 Chirality restraints: 3756 Sorted by residual: chirality pdb=" CB VAL0d 70 " pdb=" CA VAL0d 70 " pdb=" CG1 VAL0d 70 " pdb=" CG2 VAL0d 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL0c 70 " pdb=" CA VAL0c 70 " pdb=" CG1 VAL0c 70 " pdb=" CG2 VAL0c 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL0g 70 " pdb=" CA VAL0g 70 " pdb=" CG1 VAL0g 70 " pdb=" CG2 VAL0g 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3753 not shown) Planarity restraints: 4548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN0e 59 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C GLN0e 59 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN0e 59 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE0e 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN0b 59 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C GLN0b 59 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN0b 59 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE0b 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN0l 59 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C GLN0l 59 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN0l 59 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE0l 60 " -0.017 2.00e-02 2.50e+03 ... (remaining 4545 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 36 1.56 - 2.40: 172 2.40 - 3.23: 25127 3.23 - 4.07: 62972 4.07 - 4.90: 114396 Warning: very small nonbonded interaction distances. Nonbonded interactions: 202703 Sorted by model distance: nonbonded pdb=" CD GLU0f 248 " pdb=" O LYS0g 228 " model vdw 0.726 3.270 nonbonded pdb=" CD GLU0j 248 " pdb=" O LYS0k 228 " model vdw 0.734 3.270 nonbonded pdb=" CD GLU0i 248 " pdb=" O LYS0j 228 " model vdw 0.739 3.270 nonbonded pdb=" CD GLU0e 248 " pdb=" O LYS0f 228 " model vdw 0.740 3.270 nonbonded pdb=" CD GLU0k 248 " pdb=" O LYS0l 228 " model vdw 0.742 3.270 ... (remaining 202698 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 '0a' selection = chain '0b' selection = chain '0c' selection = chain '0d' selection = chain '0e' selection = chain '0f' selection = chain '0g' selection = chain '0h' selection = chain '0i' selection = chain '0j' selection = chain '0k' selection = chain '0l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.880 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 62.530 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 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 : 0.006 0.047 25728 Z= 0.402 Angle : 1.156 10.241 34860 Z= 0.697 Chirality : 0.064 0.240 3756 Planarity : 0.006 0.047 4548 Dihedral : 11.549 52.212 9540 Min Nonbonded Distance : 0.726 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 1.59 % Allowed : 14.29 % Favored : 84.13 % Rotamer: Outliers : 1.75 % Allowed : 0.88 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.12), residues: 3024 helix: -3.25 (0.10), residues: 1056 sheet: -3.14 (0.26), residues: 372 loop : -3.39 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP0e 41 HIS 0.006 0.003 HIS0g 188 PHE 0.027 0.004 PHE0k 24 TYR 0.023 0.004 TYR0h 175 ARG 0.003 0.001 ARG0d 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1108 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 40 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5849 (mt-10) REVERT: 0a 68 ASP cc_start: 0.5120 (m-30) cc_final: 0.4773 (m-30) REVERT: 0a 141 LEU cc_start: 0.8707 (tp) cc_final: 0.8370 (mt) REVERT: 0a 152 GLN cc_start: 0.8414 (mt0) cc_final: 0.8069 (mt0) REVERT: 0a 213 GLN cc_start: 0.8022 (tp40) cc_final: 0.7814 (tp40) REVERT: 0a 217 VAL cc_start: 0.8103 (t) cc_final: 0.7622 (t) REVERT: 0a 281 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7654 (mmm-85) REVERT: 0b 30 TYR cc_start: 0.6539 (t80) cc_final: 0.6282 (t80) REVERT: 0b 40 GLU cc_start: 0.6436 (mm-30) cc_final: 0.6115 (mt-10) REVERT: 0b 44 LEU cc_start: 0.7667 (mt) cc_final: 0.7410 (mt) REVERT: 0b 68 ASP cc_start: 0.4736 (m-30) cc_final: 0.4256 (m-30) REVERT: 0b 141 LEU cc_start: 0.8723 (tp) cc_final: 0.8495 (mt) REVERT: 0b 152 GLN cc_start: 0.8435 (mt0) cc_final: 0.8186 (mt0) REVERT: 0b 213 GLN cc_start: 0.7909 (tp40) cc_final: 0.7685 (tp40) REVERT: 0b 217 VAL cc_start: 0.8196 (t) cc_final: 0.7705 (t) REVERT: 0b 249 GLN cc_start: 0.5696 (tt0) cc_final: 0.5094 (tt0) REVERT: 0b 281 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7826 (mmm160) REVERT: 0c 40 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6296 (mt-10) REVERT: 0c 44 LEU cc_start: 0.7948 (mt) cc_final: 0.7690 (mt) REVERT: 0c 68 ASP cc_start: 0.4894 (m-30) cc_final: 0.4672 (m-30) REVERT: 0c 141 LEU cc_start: 0.8851 (tp) cc_final: 0.8583 (mt) REVERT: 0c 145 LYS cc_start: 0.7365 (tttp) cc_final: 0.7152 (tptp) REVERT: 0c 262 GLU cc_start: 0.7416 (tp30) cc_final: 0.7163 (tp30) REVERT: 0c 270 GLU cc_start: 0.5124 (mt-10) cc_final: 0.4789 (mt-10) REVERT: 0d 40 GLU cc_start: 0.6456 (mm-30) cc_final: 0.6061 (mt-10) REVERT: 0d 50 PRO cc_start: 0.5941 (Cg_endo) cc_final: 0.5643 (Cg_exo) REVERT: 0d 68 ASP cc_start: 0.5136 (m-30) cc_final: 0.4681 (m-30) REVERT: 0d 141 LEU cc_start: 0.8783 (tp) cc_final: 0.8472 (mt) REVERT: 0d 152 GLN cc_start: 0.8343 (mt0) cc_final: 0.8083 (mt0) REVERT: 0d 213 GLN cc_start: 0.8033 (tp40) cc_final: 0.7695 (tp40) REVERT: 0d 217 VAL cc_start: 0.8156 (t) cc_final: 0.7833 (t) REVERT: 0d 281 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7750 (mmm-85) REVERT: 0e 30 TYR cc_start: 0.6692 (t80) cc_final: 0.6435 (t80) REVERT: 0e 68 ASP cc_start: 0.4659 (m-30) cc_final: 0.4138 (m-30) REVERT: 0e 108 ASN cc_start: 0.3251 (t0) cc_final: 0.2902 (p0) REVERT: 0e 141 LEU cc_start: 0.8827 (tp) cc_final: 0.8549 (mt) REVERT: 0e 152 GLN cc_start: 0.8393 (mt0) cc_final: 0.8134 (mt0) REVERT: 0e 213 GLN cc_start: 0.7808 (tp40) cc_final: 0.7494 (tp40) REVERT: 0e 217 VAL cc_start: 0.8180 (t) cc_final: 0.7778 (t) REVERT: 0e 249 GLN cc_start: 0.6037 (tt0) cc_final: 0.5434 (tt0) REVERT: 0e 281 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7361 (mmm160) REVERT: 0f 40 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6152 (mt-10) REVERT: 0f 44 LEU cc_start: 0.7853 (mt) cc_final: 0.7599 (mt) REVERT: 0f 50 PRO cc_start: 0.5907 (Cg_endo) cc_final: 0.5613 (Cg_exo) REVERT: 0f 141 LEU cc_start: 0.8894 (tp) cc_final: 0.8644 (mt) REVERT: 0f 249 GLN cc_start: 0.5547 (tt0) cc_final: 0.5233 (tt0) REVERT: 0f 270 GLU cc_start: 0.5172 (mt-10) cc_final: 0.4818 (mt-10) REVERT: 0g 32 GLN cc_start: 0.7676 (mt0) cc_final: 0.7237 (mt0) REVERT: 0g 36 TYR cc_start: 0.7103 (p90) cc_final: 0.6724 (p90) REVERT: 0g 40 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6094 (mt-10) REVERT: 0g 50 PRO cc_start: 0.5893 (Cg_endo) cc_final: 0.5597 (Cg_exo) REVERT: 0g 68 ASP cc_start: 0.5328 (m-30) cc_final: 0.4855 (m-30) REVERT: 0g 141 LEU cc_start: 0.8747 (tp) cc_final: 0.8429 (mt) REVERT: 0g 152 GLN cc_start: 0.8442 (mt0) cc_final: 0.8200 (mt0) REVERT: 0g 213 GLN cc_start: 0.8059 (tp40) cc_final: 0.7789 (tp40) REVERT: 0g 217 VAL cc_start: 0.8156 (t) cc_final: 0.7872 (t) REVERT: 0g 281 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7778 (mmm-85) REVERT: 0h 30 TYR cc_start: 0.6542 (t80) cc_final: 0.6259 (t80) REVERT: 0h 40 GLU cc_start: 0.6493 (mm-30) cc_final: 0.6165 (mt-10) REVERT: 0h 44 LEU cc_start: 0.7614 (mt) cc_final: 0.7374 (mt) REVERT: 0h 68 ASP cc_start: 0.4539 (m-30) cc_final: 0.4205 (m-30) REVERT: 0h 106 LEU cc_start: 0.4200 (tp) cc_final: 0.3921 (tp) REVERT: 0h 141 LEU cc_start: 0.8766 (tp) cc_final: 0.8498 (mt) REVERT: 0h 213 GLN cc_start: 0.7922 (tp40) cc_final: 0.7649 (tp40) REVERT: 0h 217 VAL cc_start: 0.8193 (t) cc_final: 0.7694 (t) REVERT: 0h 249 GLN cc_start: 0.5725 (tt0) cc_final: 0.5163 (tt0) REVERT: 0h 281 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7860 (mmm160) REVERT: 0i 19 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8948 (mmtt) REVERT: 0i 40 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6174 (mt-10) REVERT: 0i 68 ASP cc_start: 0.5032 (m-30) cc_final: 0.4737 (m-30) REVERT: 0i 141 LEU cc_start: 0.8874 (tp) cc_final: 0.8442 (mt) REVERT: 0i 249 GLN cc_start: 0.5506 (tt0) cc_final: 0.5282 (tt0) REVERT: 0i 270 GLU cc_start: 0.5103 (mt-10) cc_final: 0.4838 (mt-10) REVERT: 0j 40 GLU cc_start: 0.6431 (mm-30) cc_final: 0.5878 (mt-10) REVERT: 0j 68 ASP cc_start: 0.5173 (m-30) cc_final: 0.4851 (m-30) REVERT: 0j 141 LEU cc_start: 0.8783 (tp) cc_final: 0.8438 (mt) REVERT: 0j 152 GLN cc_start: 0.8413 (mt0) cc_final: 0.8129 (mt0) REVERT: 0j 213 GLN cc_start: 0.8014 (tp40) cc_final: 0.7792 (tp40) REVERT: 0j 217 VAL cc_start: 0.8166 (t) cc_final: 0.7927 (t) REVERT: 0j 281 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7761 (mmm-85) REVERT: 0k 30 TYR cc_start: 0.6668 (t80) cc_final: 0.6367 (t80) REVERT: 0k 40 GLU cc_start: 0.6427 (mm-30) cc_final: 0.6200 (mt-10) REVERT: 0k 44 LEU cc_start: 0.7692 (mt) cc_final: 0.7327 (mt) REVERT: 0k 68 ASP cc_start: 0.4747 (m-30) cc_final: 0.4258 (m-30) REVERT: 0k 141 LEU cc_start: 0.8792 (tp) cc_final: 0.8558 (mt) REVERT: 0k 152 GLN cc_start: 0.8427 (mt0) cc_final: 0.8135 (mt0) REVERT: 0k 213 GLN cc_start: 0.7935 (tp40) cc_final: 0.7675 (tp40) REVERT: 0k 217 VAL cc_start: 0.8195 (t) cc_final: 0.7718 (t) REVERT: 0k 228 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5651 (mmtm) REVERT: 0k 281 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7724 (mmm160) REVERT: 0l 40 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6366 (mt-10) REVERT: 0l 44 LEU cc_start: 0.7871 (mt) cc_final: 0.7580 (mt) REVERT: 0l 68 ASP cc_start: 0.4925 (m-30) cc_final: 0.4695 (m-30) REVERT: 0l 106 LEU cc_start: 0.4175 (tp) cc_final: 0.3629 (tt) REVERT: 0l 141 LEU cc_start: 0.8820 (tp) cc_final: 0.8301 (mt) REVERT: 0l 205 TYR cc_start: 0.8462 (t80) cc_final: 0.8165 (t80) REVERT: 0l 217 VAL cc_start: 0.7937 (t) cc_final: 0.7419 (t) REVERT: 0l 250 ILE cc_start: 0.6933 (pt) cc_final: 0.6630 (pt) REVERT: 0l 262 GLU cc_start: 0.7436 (tp30) cc_final: 0.7121 (tp30) outliers start: 48 outliers final: 20 residues processed: 1144 average time/residue: 0.3830 time to fit residues: 659.7728 Evaluate side-chains 754 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 733 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 12 ILE Chi-restraints excluded: chain 0a residue 225 LEU Chi-restraints excluded: chain 0b residue 12 ILE Chi-restraints excluded: chain 0b residue 225 LEU Chi-restraints excluded: chain 0c residue 12 ILE Chi-restraints excluded: chain 0d residue 12 ILE Chi-restraints excluded: chain 0d residue 225 LEU Chi-restraints excluded: chain 0e residue 12 ILE Chi-restraints excluded: chain 0e residue 225 LEU Chi-restraints excluded: chain 0f residue 12 ILE Chi-restraints excluded: chain 0g residue 12 ILE Chi-restraints excluded: chain 0g residue 225 LEU Chi-restraints excluded: chain 0h residue 12 ILE Chi-restraints excluded: chain 0h residue 225 LEU Chi-restraints excluded: chain 0i residue 12 ILE Chi-restraints excluded: chain 0j residue 12 ILE Chi-restraints excluded: chain 0j residue 225 LEU Chi-restraints excluded: chain 0k residue 12 ILE Chi-restraints excluded: chain 0k residue 225 LEU Chi-restraints excluded: chain 0k residue 228 LYS Chi-restraints excluded: chain 0l residue 12 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 272 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 168 GLN 0a 173 GLN 0a 188 HIS ** 0b 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN ** 0b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 168 GLN 0b 173 GLN 0b 188 HIS ** 0c 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 168 GLN 0c 173 GLN 0c 188 HIS 0d 26 HIS ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 153 ASN ** 0d 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 168 GLN 0d 173 GLN 0d 188 HIS ** 0e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 26 HIS ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 167 ASN 0e 168 GLN 0e 188 HIS ** 0f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 167 ASN 0f 168 GLN 0f 173 GLN 0f 188 HIS 0g 26 HIS ** 0g 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 153 ASN ** 0g 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 168 GLN 0g 173 GLN 0g 188 HIS ** 0h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 26 HIS ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 153 ASN ** 0h 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 168 GLN 0h 173 GLN 0h 188 HIS 0i 29 ASN 0i 32 GLN ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 168 GLN 0i 188 HIS 0j 26 HIS ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 153 ASN 0j 167 ASN 0j 168 GLN 0j 173 GLN 0j 188 HIS ** 0k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 153 ASN 0k 167 ASN 0k 168 GLN 0k 188 HIS ** 0l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 168 GLN 0l 173 GLN 0l 188 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25728 Z= 0.272 Angle : 0.843 7.230 34860 Z= 0.464 Chirality : 0.050 0.201 3756 Planarity : 0.005 0.047 4548 Dihedral : 9.209 59.954 3392 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 1.59 % Allowed : 16.34 % Favored : 82.08 % Rotamer: Outliers : 5.01 % Allowed : 12.54 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.14), residues: 3024 helix: -1.68 (0.13), residues: 1056 sheet: -3.28 (0.24), residues: 372 loop : -2.67 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP0g 41 HIS 0.009 0.002 HIS0e 26 PHE 0.030 0.002 PHE0g 24 TYR 0.028 0.002 TYR0f 205 ARG 0.003 0.001 ARG0e 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 798 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 18 GLN cc_start: 0.8162 (mm110) cc_final: 0.7533 (tp40) REVERT: 0a 36 TYR cc_start: 0.6888 (p90) cc_final: 0.6477 (p90) REVERT: 0a 40 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6182 (mt-10) REVERT: 0a 100 TYR cc_start: 0.5207 (OUTLIER) cc_final: 0.4357 (t80) REVERT: 0a 126 MET cc_start: 0.8415 (mtt) cc_final: 0.7725 (mtt) REVERT: 0a 153 ASN cc_start: 0.7409 (t0) cc_final: 0.7161 (t0) REVERT: 0b 18 GLN cc_start: 0.8003 (mm110) cc_final: 0.7167 (tt0) REVERT: 0b 30 TYR cc_start: 0.7034 (t80) cc_final: 0.6790 (t80) REVERT: 0b 44 LEU cc_start: 0.7516 (mt) cc_final: 0.7235 (mt) REVERT: 0b 126 MET cc_start: 0.8523 (mtt) cc_final: 0.7692 (mtt) REVERT: 0b 153 ASN cc_start: 0.7364 (t0) cc_final: 0.7131 (t0) REVERT: 0b 194 ASP cc_start: 0.7603 (t0) cc_final: 0.6719 (t0) REVERT: 0b 214 LYS cc_start: 0.8027 (tttm) cc_final: 0.7793 (tttm) REVERT: 0b 225 LEU cc_start: 0.8006 (mt) cc_final: 0.7264 (mt) REVERT: 0b 281 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7820 (mmp80) REVERT: 0c 30 TYR cc_start: 0.6486 (t80) cc_final: 0.5882 (t80) REVERT: 0c 40 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6291 (mt-10) REVERT: 0c 100 TYR cc_start: 0.5386 (OUTLIER) cc_final: 0.4661 (t80) REVERT: 0c 126 MET cc_start: 0.8394 (mtt) cc_final: 0.7850 (mtt) REVERT: 0c 194 ASP cc_start: 0.7086 (t0) cc_final: 0.5933 (t0) REVERT: 0c 281 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7719 (mmm-85) REVERT: 0d 18 GLN cc_start: 0.8161 (mm110) cc_final: 0.7853 (tp40) REVERT: 0d 100 TYR cc_start: 0.5023 (OUTLIER) cc_final: 0.4154 (t80) REVERT: 0d 126 MET cc_start: 0.8367 (mtt) cc_final: 0.7532 (mtt) REVERT: 0d 213 GLN cc_start: 0.7815 (tp40) cc_final: 0.7605 (tm-30) REVERT: 0d 221 MET cc_start: 0.7469 (tpp) cc_final: 0.7198 (tpp) REVERT: 0e 18 GLN cc_start: 0.8251 (mm110) cc_final: 0.6829 (tp40) REVERT: 0e 30 TYR cc_start: 0.6418 (t80) cc_final: 0.5824 (t80) REVERT: 0e 112 MET cc_start: 0.5828 (tpt) cc_final: 0.5428 (ptm) REVERT: 0e 126 MET cc_start: 0.8523 (mtt) cc_final: 0.7767 (mtt) REVERT: 0e 152 GLN cc_start: 0.8585 (mt0) cc_final: 0.8382 (mt0) REVERT: 0e 153 ASN cc_start: 0.7589 (t0) cc_final: 0.7351 (t0) REVERT: 0e 217 VAL cc_start: 0.8101 (t) cc_final: 0.7765 (t) REVERT: 0f 18 GLN cc_start: 0.7193 (mt0) cc_final: 0.6902 (mt0) REVERT: 0f 30 TYR cc_start: 0.6473 (t80) cc_final: 0.5436 (t80) REVERT: 0f 40 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6309 (mt-10) REVERT: 0f 140 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8586 (tm-30) REVERT: 0f 194 ASP cc_start: 0.6680 (t0) cc_final: 0.5970 (t0) REVERT: 0f 205 TYR cc_start: 0.8684 (t80) cc_final: 0.8114 (t80) REVERT: 0f 281 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7777 (mmm-85) REVERT: 0g 18 GLN cc_start: 0.8185 (mm110) cc_final: 0.7738 (tp40) REVERT: 0g 100 TYR cc_start: 0.4949 (OUTLIER) cc_final: 0.4083 (t80) REVERT: 0g 140 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8396 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8660 (tp) cc_final: 0.8280 (mt) REVERT: 0g 221 MET cc_start: 0.7660 (tpp) cc_final: 0.7410 (tpp) REVERT: 0g 281 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7343 (mmm-85) REVERT: 0h 30 TYR cc_start: 0.6951 (t80) cc_final: 0.6626 (t80) REVERT: 0h 44 LEU cc_start: 0.7536 (mt) cc_final: 0.7275 (mt) REVERT: 0h 112 MET cc_start: 0.5949 (tpt) cc_final: 0.5502 (ttp) REVERT: 0h 126 MET cc_start: 0.8589 (mtt) cc_final: 0.8129 (mtp) REVERT: 0h 145 LYS cc_start: 0.7971 (tmtt) cc_final: 0.7747 (tptp) REVERT: 0h 152 GLN cc_start: 0.8137 (mt0) cc_final: 0.7821 (mt0) REVERT: 0h 194 ASP cc_start: 0.7595 (t0) cc_final: 0.6668 (t0) REVERT: 0h 209 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8401 (mmtp) REVERT: 0h 225 LEU cc_start: 0.8011 (mt) cc_final: 0.7289 (mt) REVERT: 0h 281 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7813 (mmp80) REVERT: 0i 18 GLN cc_start: 0.7283 (mt0) cc_final: 0.6927 (tt0) REVERT: 0i 126 MET cc_start: 0.8604 (mtt) cc_final: 0.8293 (mtt) REVERT: 0i 140 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8571 (tm-30) REVERT: 0i 141 LEU cc_start: 0.8830 (tp) cc_final: 0.8494 (mt) REVERT: 0i 194 ASP cc_start: 0.7173 (t0) cc_final: 0.6908 (t0) REVERT: 0i 205 TYR cc_start: 0.8771 (t80) cc_final: 0.8538 (t80) REVERT: 0i 213 GLN cc_start: 0.8037 (tp40) cc_final: 0.7831 (tp40) REVERT: 0j 18 GLN cc_start: 0.8215 (mm110) cc_final: 0.7791 (tp40) REVERT: 0j 100 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.4140 (t80) REVERT: 0j 126 MET cc_start: 0.8091 (mtt) cc_final: 0.7745 (mtt) REVERT: 0j 217 VAL cc_start: 0.8025 (t) cc_final: 0.7815 (t) REVERT: 0j 221 MET cc_start: 0.7523 (tpp) cc_final: 0.7207 (tpp) REVERT: 0j 281 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7302 (mmm-85) REVERT: 0k 30 TYR cc_start: 0.6445 (t80) cc_final: 0.5991 (t80) REVERT: 0k 44 LEU cc_start: 0.7579 (mt) cc_final: 0.7260 (mt) REVERT: 0k 112 MET cc_start: 0.5995 (tpt) cc_final: 0.5439 (ttp) REVERT: 0k 152 GLN cc_start: 0.8534 (mt0) cc_final: 0.8328 (mt0) REVERT: 0k 153 ASN cc_start: 0.7342 (t0) cc_final: 0.7117 (t0) REVERT: 0k 186 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: 0k 194 ASP cc_start: 0.7840 (t0) cc_final: 0.7009 (t0) REVERT: 0k 213 GLN cc_start: 0.7700 (tp40) cc_final: 0.7466 (tm-30) REVERT: 0k 225 LEU cc_start: 0.8000 (mt) cc_final: 0.7273 (mt) REVERT: 0k 281 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7767 (mmp80) REVERT: 0l 30 TYR cc_start: 0.6002 (t80) cc_final: 0.5259 (t80) REVERT: 0l 137 PHE cc_start: 0.7601 (m-10) cc_final: 0.7399 (m-80) REVERT: 0l 194 ASP cc_start: 0.6997 (t0) cc_final: 0.6746 (t0) REVERT: 0l 205 TYR cc_start: 0.8781 (t80) cc_final: 0.8469 (t80) outliers start: 137 outliers final: 83 residues processed: 881 average time/residue: 0.4225 time to fit residues: 549.5753 Evaluate side-chains 767 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 678 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 25 ILE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 25 ILE Chi-restraints excluded: chain 0b residue 33 SER Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 165 ASP Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 12 ILE Chi-restraints excluded: chain 0c residue 25 ILE Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 165 ASP Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 278 VAL Chi-restraints excluded: chain 0d residue 25 ILE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 165 ASP Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0d residue 278 VAL Chi-restraints excluded: chain 0e residue 25 ILE Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 165 ASP Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 12 ILE Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 133 THR Chi-restraints excluded: chain 0f residue 165 ASP Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 207 VAL Chi-restraints excluded: chain 0f residue 278 VAL Chi-restraints excluded: chain 0g residue 12 ILE Chi-restraints excluded: chain 0g residue 25 ILE Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 165 ASP Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 278 VAL Chi-restraints excluded: chain 0h residue 25 ILE Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 165 ASP Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 12 ILE Chi-restraints excluded: chain 0i residue 25 ILE Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 133 THR Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 278 VAL Chi-restraints excluded: chain 0j residue 25 ILE Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 165 ASP Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 278 VAL Chi-restraints excluded: chain 0k residue 25 ILE Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 124 ASN Chi-restraints excluded: chain 0k residue 165 ASP Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 12 ILE Chi-restraints excluded: chain 0l residue 25 ILE Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 165 ASP Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 226 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 272 optimal weight: 0.7980 chunk 294 optimal weight: 4.9990 chunk 243 optimal weight: 0.5980 chunk 270 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 218 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 167 ASN ** 0a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 21 ASN ** 0b 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 167 ASN 0b 249 GLN 0c 29 ASN 0c 32 GLN ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 167 ASN 0c 173 GLN 0c 211 ASN ** 0d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 167 ASN ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 173 GLN 0e 249 GLN 0f 29 ASN 0f 32 GLN ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 152 GLN 0f 211 ASN ** 0g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 167 ASN ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN 0h 167 ASN 0h 213 GLN ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN 0i 211 ASN ** 0j 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 88 ASN 0j 89 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 88 ASN 0k 89 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 29 ASN 0l 32 GLN ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 167 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25728 Z= 0.196 Angle : 0.758 7.046 34860 Z= 0.416 Chirality : 0.046 0.153 3756 Planarity : 0.005 0.048 4548 Dihedral : 8.129 54.734 3358 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.58 % Favored : 83.99 % Rotamer: Outliers : 4.79 % Allowed : 14.25 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.15), residues: 3024 helix: -0.80 (0.14), residues: 1128 sheet: -3.87 (0.24), residues: 300 loop : -2.42 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP0a 41 HIS 0.004 0.000 HIS0h 58 PHE 0.031 0.002 PHE0a 24 TYR 0.023 0.002 TYR0f 36 ARG 0.007 0.000 ARG0c 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 754 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 36 TYR cc_start: 0.6900 (p90) cc_final: 0.6655 (p90) REVERT: 0a 40 GLU cc_start: 0.6685 (mm-30) cc_final: 0.5651 (mt-10) REVERT: 0a 100 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.4732 (t80) REVERT: 0a 151 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7888 (t0) REVERT: 0a 186 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: 0b 30 TYR cc_start: 0.7065 (t80) cc_final: 0.6584 (t80) REVERT: 0b 32 GLN cc_start: 0.7568 (mt0) cc_final: 0.7245 (mt0) REVERT: 0b 36 TYR cc_start: 0.6900 (p90) cc_final: 0.6593 (p90) REVERT: 0b 112 MET cc_start: 0.5780 (tpt) cc_final: 0.5520 (ttp) REVERT: 0b 145 LYS cc_start: 0.7514 (tptp) cc_final: 0.7273 (tptp) REVERT: 0b 186 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: 0b 194 ASP cc_start: 0.7682 (t0) cc_final: 0.6677 (t0) REVERT: 0b 220 GLU cc_start: 0.7654 (tp30) cc_final: 0.6896 (mt-10) REVERT: 0c 30 TYR cc_start: 0.6624 (t80) cc_final: 0.6187 (t80) REVERT: 0c 32 GLN cc_start: 0.8220 (mt0) cc_final: 0.7785 (mt0) REVERT: 0c 100 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.4839 (t80) REVERT: 0c 140 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8564 (tm-30) REVERT: 0c 145 LYS cc_start: 0.7631 (tptp) cc_final: 0.7396 (tptp) REVERT: 0c 281 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7419 (mmm-85) REVERT: 0d 100 TYR cc_start: 0.5352 (OUTLIER) cc_final: 0.4702 (t80) REVERT: 0d 186 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: 0e 18 GLN cc_start: 0.7644 (mm110) cc_final: 0.7442 (tt0) REVERT: 0e 30 TYR cc_start: 0.6416 (t80) cc_final: 0.5627 (t80) REVERT: 0e 36 TYR cc_start: 0.7007 (p90) cc_final: 0.6680 (p90) REVERT: 0e 145 LYS cc_start: 0.7510 (tptp) cc_final: 0.7246 (tptp) REVERT: 0e 186 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: 0e 193 SER cc_start: 0.6801 (p) cc_final: 0.6571 (t) REVERT: 0e 213 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7467 (tm-30) REVERT: 0e 217 VAL cc_start: 0.7835 (t) cc_final: 0.7514 (t) REVERT: 0e 220 GLU cc_start: 0.7709 (tp30) cc_final: 0.7072 (mt-10) REVERT: 0e 221 MET cc_start: 0.7525 (tpp) cc_final: 0.7063 (tpp) REVERT: 0f 30 TYR cc_start: 0.6571 (t80) cc_final: 0.5772 (t80) REVERT: 0f 54 GLU cc_start: 0.7254 (pt0) cc_final: 0.7017 (pm20) REVERT: 0f 140 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8620 (tm-30) REVERT: 0f 186 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: 0f 194 ASP cc_start: 0.7783 (t0) cc_final: 0.6968 (t0) REVERT: 0g 30 TYR cc_start: 0.5850 (t80) cc_final: 0.4354 (t80) REVERT: 0g 40 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6472 (mm-30) REVERT: 0g 100 TYR cc_start: 0.5358 (OUTLIER) cc_final: 0.4681 (t80) REVERT: 0g 126 MET cc_start: 0.8449 (mtm) cc_final: 0.8081 (mtt) REVERT: 0g 140 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8610 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8744 (tp) cc_final: 0.8543 (mt) REVERT: 0g 186 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: 0g 194 ASP cc_start: 0.7904 (t0) cc_final: 0.7516 (t0) REVERT: 0h 30 TYR cc_start: 0.7022 (t80) cc_final: 0.6621 (t80) REVERT: 0h 112 MET cc_start: 0.5700 (tpt) cc_final: 0.5481 (ttp) REVERT: 0h 140 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8469 (tm-30) REVERT: 0h 145 LYS cc_start: 0.7854 (tmtt) cc_final: 0.7647 (tptp) REVERT: 0h 153 ASN cc_start: 0.7544 (t0) cc_final: 0.7169 (t0) REVERT: 0h 186 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: 0h 194 ASP cc_start: 0.7973 (t0) cc_final: 0.7089 (t0) REVERT: 0h 213 GLN cc_start: 0.7888 (tm130) cc_final: 0.7663 (tm-30) REVERT: 0h 228 LYS cc_start: 0.6403 (tppt) cc_final: 0.6197 (mppt) REVERT: 0i 26 HIS cc_start: 0.8465 (t-90) cc_final: 0.8240 (t-170) REVERT: 0i 40 GLU cc_start: 0.6579 (mm-30) cc_final: 0.5992 (mt-10) REVERT: 0i 151 ASN cc_start: 0.8214 (t0) cc_final: 0.7821 (t0) REVERT: 0i 194 ASP cc_start: 0.8007 (t0) cc_final: 0.7238 (t0) REVERT: 0j 40 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6514 (mm-30) REVERT: 0j 100 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.4680 (t80) REVERT: 0j 112 MET cc_start: 0.5696 (tpt) cc_final: 0.5423 (ttp) REVERT: 0j 186 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: 0k 30 TYR cc_start: 0.6874 (t80) cc_final: 0.6434 (t80) REVERT: 0k 44 LEU cc_start: 0.7563 (mt) cc_final: 0.7204 (mt) REVERT: 0k 112 MET cc_start: 0.5849 (tpt) cc_final: 0.5584 (ttp) REVERT: 0k 141 LEU cc_start: 0.8895 (mt) cc_final: 0.8687 (mt) REVERT: 0k 186 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: 0k 194 ASP cc_start: 0.8166 (t0) cc_final: 0.7499 (t0) REVERT: 0l 40 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6101 (mt-10) REVERT: 0l 194 ASP cc_start: 0.7973 (t0) cc_final: 0.6899 (t0) REVERT: 0l 213 GLN cc_start: 0.8080 (tp40) cc_final: 0.7312 (tm-30) REVERT: 0l 214 LYS cc_start: 0.8005 (tttm) cc_final: 0.7584 (ttpp) REVERT: 0l 225 LEU cc_start: 0.7726 (mt) cc_final: 0.7144 (mp) outliers start: 131 outliers final: 65 residues processed: 835 average time/residue: 0.4267 time to fit residues: 540.0014 Evaluate side-chains 753 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 673 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 151 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 22 ARG Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 150 VAL Chi-restraints excluded: chain 0b residue 165 ASP Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 63 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 150 VAL Chi-restraints excluded: chain 0c residue 165 ASP Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 207 VAL Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 165 ASP Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 37 GLN Chi-restraints excluded: chain 0f residue 63 VAL Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 165 ASP Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 165 ASP Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 165 ASP Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 207 VAL Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 63 VAL Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 165 ASP Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 278 VAL Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 165 ASP Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 88 ASN Chi-restraints excluded: chain 0k residue 124 ASN Chi-restraints excluded: chain 0k residue 165 ASP Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 165 ASP Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 278 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 141 optimal weight: 0.2980 chunk 30 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 21 ASN 0a 59 GLN ** 0a 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 21 ASN ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 211 ASN 0d 59 GLN ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN 0d 173 GLN 0d 213 GLN 0e 26 HIS ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 211 ASN 0f 21 ASN 0f 58 HIS ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN 0f 153 ASN ** 0g 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN 0h 26 HIS ** 0h 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 211 ASN ** 0h 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 21 ASN ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 58 HIS ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 167 ASN 0j 59 GLN ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 151 ASN ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 153 ASN 0k 21 ASN 0k 26 HIS ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 21 ASN ** 0l 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 181 ASN 0l 211 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25728 Z= 0.226 Angle : 0.756 8.387 34860 Z= 0.412 Chirality : 0.046 0.141 3756 Planarity : 0.005 0.054 4548 Dihedral : 7.615 36.564 3348 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.40 % Allowed : 16.40 % Favored : 83.20 % Rotamer: Outliers : 4.93 % Allowed : 16.59 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.16), residues: 3024 helix: -0.38 (0.15), residues: 1116 sheet: -3.72 (0.25), residues: 300 loop : -2.17 (0.17), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP0g 41 HIS 0.006 0.001 HIS0k 26 PHE 0.031 0.002 PHE0l 199 TYR 0.020 0.002 TYR0f 205 ARG 0.006 0.001 ARG0f 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 720 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 22 ARG cc_start: 0.7452 (mmt-90) cc_final: 0.7063 (mmt180) REVERT: 0a 24 PHE cc_start: 0.5354 (p90) cc_final: 0.5150 (p90) REVERT: 0a 40 GLU cc_start: 0.6786 (mm-30) cc_final: 0.5770 (mt-10) REVERT: 0a 100 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5132 (t80) REVERT: 0a 151 ASN cc_start: 0.8347 (m-40) cc_final: 0.7964 (t0) REVERT: 0a 152 GLN cc_start: 0.8107 (mt0) cc_final: 0.7819 (pt0) REVERT: 0a 186 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: 0a 213 GLN cc_start: 0.8207 (tp40) cc_final: 0.7867 (tm-30) REVERT: 0a 220 GLU cc_start: 0.7666 (tp30) cc_final: 0.6917 (mt-10) REVERT: 0b 30 TYR cc_start: 0.7096 (t80) cc_final: 0.6531 (t80) REVERT: 0b 44 LEU cc_start: 0.7557 (mt) cc_final: 0.7232 (mt) REVERT: 0b 145 LYS cc_start: 0.7478 (tptp) cc_final: 0.7205 (tptp) REVERT: 0b 186 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: 0b 194 ASP cc_start: 0.7896 (t0) cc_final: 0.7034 (t0) REVERT: 0b 197 GLU cc_start: 0.8012 (pt0) cc_final: 0.7731 (pt0) REVERT: 0b 218 TRP cc_start: 0.7173 (t-100) cc_final: 0.6957 (t60) REVERT: 0b 220 GLU cc_start: 0.7511 (tp30) cc_final: 0.6901 (mt-10) REVERT: 0b 228 LYS cc_start: 0.6596 (tppt) cc_final: 0.6308 (mmtm) REVERT: 0b 281 ARG cc_start: 0.7969 (mmp80) cc_final: 0.7663 (mmp80) REVERT: 0c 100 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.5151 (t80) REVERT: 0c 140 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8657 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6891 (mt-10) REVERT: 0d 100 TYR cc_start: 0.5820 (OUTLIER) cc_final: 0.5030 (t80) REVERT: 0d 186 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: 0d 213 GLN cc_start: 0.8020 (tm130) cc_final: 0.7701 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6853 (mt-10) REVERT: 0e 22 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7666 (ttm-80) REVERT: 0e 30 TYR cc_start: 0.6491 (t80) cc_final: 0.5764 (t80) REVERT: 0e 37 GLN cc_start: 0.8165 (pp30) cc_final: 0.7680 (tt0) REVERT: 0e 40 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6937 (mm-30) REVERT: 0e 152 GLN cc_start: 0.8339 (mt0) cc_final: 0.8021 (mt0) REVERT: 0e 153 ASN cc_start: 0.7554 (t0) cc_final: 0.7269 (t0) REVERT: 0e 186 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6652 (m-10) REVERT: 0e 213 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7472 (tm-30) REVERT: 0e 214 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7990 (ttpp) REVERT: 0e 220 GLU cc_start: 0.7647 (tp30) cc_final: 0.7046 (mt-10) REVERT: 0e 221 MET cc_start: 0.7558 (tpp) cc_final: 0.7340 (tpp) REVERT: 0f 30 TYR cc_start: 0.6777 (t80) cc_final: 0.6127 (t80) REVERT: 0f 32 GLN cc_start: 0.8162 (mt0) cc_final: 0.7519 (mt0) REVERT: 0f 100 TYR cc_start: 0.6016 (OUTLIER) cc_final: 0.5474 (t80) REVERT: 0f 140 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8675 (tm-30) REVERT: 0f 194 ASP cc_start: 0.8100 (t0) cc_final: 0.7282 (t0) REVERT: 0f 213 GLN cc_start: 0.7825 (tp40) cc_final: 0.7494 (tm-30) REVERT: 0f 214 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7857 (ttpp) REVERT: 0g 30 TYR cc_start: 0.5994 (t80) cc_final: 0.4357 (t80) REVERT: 0g 100 TYR cc_start: 0.5935 (OUTLIER) cc_final: 0.5133 (t80) REVERT: 0g 140 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8621 (tm-30) REVERT: 0g 186 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: 0g 194 ASP cc_start: 0.8146 (t0) cc_final: 0.7694 (t0) REVERT: 0g 220 GLU cc_start: 0.7679 (tp30) cc_final: 0.6758 (mt-10) REVERT: 0h 30 TYR cc_start: 0.7124 (t80) cc_final: 0.6593 (t80) REVERT: 0h 44 LEU cc_start: 0.7560 (mt) cc_final: 0.7179 (mt) REVERT: 0h 140 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8465 (tm-30) REVERT: 0h 186 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: 0h 194 ASP cc_start: 0.8155 (t0) cc_final: 0.7521 (t0) REVERT: 0h 218 TRP cc_start: 0.7196 (t-100) cc_final: 0.6945 (t60) REVERT: 0h 220 GLU cc_start: 0.7598 (tp30) cc_final: 0.6916 (mt-10) REVERT: 0h 270 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5356 (mt-10) REVERT: 0h 281 ARG cc_start: 0.7960 (mmp80) cc_final: 0.7610 (mmp80) REVERT: 0i 22 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7897 (ttm110) REVERT: 0i 30 TYR cc_start: 0.6648 (t80) cc_final: 0.5722 (t80) REVERT: 0i 40 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6121 (mt-10) REVERT: 0i 151 ASN cc_start: 0.8282 (t0) cc_final: 0.7860 (t0) REVERT: 0i 152 GLN cc_start: 0.8042 (mt0) cc_final: 0.7803 (pt0) REVERT: 0i 194 ASP cc_start: 0.8242 (t0) cc_final: 0.7787 (t0) REVERT: 0i 250 ILE cc_start: 0.7507 (mm) cc_final: 0.7105 (mm) REVERT: 0j 18 GLN cc_start: 0.7875 (tp40) cc_final: 0.6650 (tp-100) REVERT: 0j 40 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6818 (mm-30) REVERT: 0j 100 TYR cc_start: 0.5916 (OUTLIER) cc_final: 0.5063 (t80) REVERT: 0j 112 MET cc_start: 0.5712 (tpt) cc_final: 0.5457 (ttp) REVERT: 0j 153 ASN cc_start: 0.6910 (t160) cc_final: 0.6643 (t0) REVERT: 0j 186 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: 0j 213 GLN cc_start: 0.8234 (tp40) cc_final: 0.7614 (tm-30) REVERT: 0j 214 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8100 (ttpp) REVERT: 0j 220 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7111 (mt-10) REVERT: 0k 18 GLN cc_start: 0.7887 (tp40) cc_final: 0.6904 (tp-100) REVERT: 0k 30 TYR cc_start: 0.6689 (t80) cc_final: 0.5926 (t80) REVERT: 0k 44 LEU cc_start: 0.7581 (mt) cc_final: 0.7258 (mt) REVERT: 0k 145 LYS cc_start: 0.7404 (tptp) cc_final: 0.7141 (tptp) REVERT: 0k 152 GLN cc_start: 0.8352 (mt0) cc_final: 0.8032 (mt0) REVERT: 0k 153 ASN cc_start: 0.7476 (t0) cc_final: 0.7169 (t0) REVERT: 0k 186 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: 0k 194 ASP cc_start: 0.8205 (t0) cc_final: 0.7489 (t0) REVERT: 0k 213 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7487 (tm-30) REVERT: 0k 220 GLU cc_start: 0.7670 (tp30) cc_final: 0.6940 (mt-10) REVERT: 0k 281 ARG cc_start: 0.7965 (mmp80) cc_final: 0.7549 (mmp80) REVERT: 0l 30 TYR cc_start: 0.6023 (t80) cc_final: 0.5306 (t80) REVERT: 0l 40 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6171 (mt-10) REVERT: 0l 100 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.5549 (t80) REVERT: 0l 151 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8210 (t0) REVERT: 0l 194 ASP cc_start: 0.8140 (t0) cc_final: 0.7388 (t0) REVERT: 0l 213 GLN cc_start: 0.7986 (tp40) cc_final: 0.7384 (tm-30) REVERT: 0l 214 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7728 (ttpp) outliers start: 135 outliers final: 73 residues processed: 811 average time/residue: 0.3819 time to fit residues: 468.0862 Evaluate side-chains 768 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 677 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 37 GLN Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 165 ASP Chi-restraints excluded: chain 0b residue 170 SER Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 165 ASP Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 207 VAL Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 151 ASN Chi-restraints excluded: chain 0d residue 165 ASP Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 22 ARG Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 165 ASP Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 207 VAL Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 165 ASP Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0h residue 54 GLU Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 170 SER Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 277 LYS Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 25 ILE Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 165 ASP Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 278 VAL Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 165 ASP Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 124 ASN Chi-restraints excluded: chain 0k residue 165 ASP Chi-restraints excluded: chain 0k residue 170 SER Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 207 VAL Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 151 ASN Chi-restraints excluded: chain 0l residue 165 ASP Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Chi-restraints excluded: chain 0l residue 214 LYS Chi-restraints excluded: chain 0l residue 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 215 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 200 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 59 GLN ** 0a 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 173 GLN 0b 88 ASN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 21 ASN ** 0c 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN 0d 153 ASN 0d 173 GLN 0d 181 ASN 0e 59 GLN ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 173 GLN 0f 21 ASN ** 0f 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN 0f 173 GLN 0f 181 ASN 0g 88 ASN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 153 ASN 0g 173 GLN ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 153 ASN 0i 21 ASN ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 181 ASN 0j 59 GLN ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 173 GLN 0k 21 ASN ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 21 ASN 0l 29 ASN 0l 59 GLN 0l 88 ASN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 173 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25728 Z= 0.198 Angle : 0.734 9.226 34860 Z= 0.399 Chirality : 0.046 0.201 3756 Planarity : 0.005 0.055 4548 Dihedral : 7.329 36.017 3348 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.81 % Favored : 84.79 % Rotamer: Outliers : 5.12 % Allowed : 18.35 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 3024 helix: 0.08 (0.16), residues: 1080 sheet: -3.72 (0.26), residues: 300 loop : -2.05 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP0g 41 HIS 0.006 0.001 HIS0h 58 PHE 0.027 0.002 PHE0l 199 TYR 0.018 0.001 TYR0f 205 ARG 0.006 0.001 ARG0l 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 718 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 24 PHE cc_start: 0.5380 (p90) cc_final: 0.5138 (p90) REVERT: 0a 40 GLU cc_start: 0.6804 (mm-30) cc_final: 0.5775 (mt-10) REVERT: 0a 100 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5624 (t80) REVERT: 0a 186 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: 0a 197 GLU cc_start: 0.7931 (pt0) cc_final: 0.7574 (pt0) REVERT: 0a 213 GLN cc_start: 0.8045 (tp40) cc_final: 0.7728 (tm-30) REVERT: 0a 220 GLU cc_start: 0.7605 (tp30) cc_final: 0.7146 (mt-10) REVERT: 0b 30 TYR cc_start: 0.7146 (t80) cc_final: 0.6577 (t80) REVERT: 0b 44 LEU cc_start: 0.7570 (mt) cc_final: 0.7118 (mt) REVERT: 0b 88 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6137 (m-40) REVERT: 0b 145 LYS cc_start: 0.7611 (tptp) cc_final: 0.7309 (tptp) REVERT: 0b 186 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: 0b 194 ASP cc_start: 0.8034 (t0) cc_final: 0.7183 (t0) REVERT: 0b 220 GLU cc_start: 0.7513 (tp30) cc_final: 0.6919 (mt-10) REVERT: 0c 30 TYR cc_start: 0.6574 (t80) cc_final: 0.6099 (t80) REVERT: 0c 100 TYR cc_start: 0.6163 (OUTLIER) cc_final: 0.5399 (t80) REVERT: 0c 140 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8631 (tm-30) REVERT: 0c 141 LEU cc_start: 0.9011 (mt) cc_final: 0.8624 (mt) REVERT: 0c 173 GLN cc_start: 0.6402 (tp-100) cc_final: 0.6186 (tp40) REVERT: 0c 213 GLN cc_start: 0.7958 (tp40) cc_final: 0.7357 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6853 (mt-10) REVERT: 0d 100 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5434 (t80) REVERT: 0d 153 ASN cc_start: 0.7038 (t0) cc_final: 0.6632 (t0) REVERT: 0d 186 PHE cc_start: 0.7551 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: 0d 220 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7129 (mt-10) REVERT: 0e 22 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7615 (ttm-80) REVERT: 0e 30 TYR cc_start: 0.6563 (t80) cc_final: 0.5762 (t80) REVERT: 0e 112 MET cc_start: 0.5500 (tpt) cc_final: 0.4981 (ttt) REVERT: 0e 145 LYS cc_start: 0.7533 (tptp) cc_final: 0.7268 (tptp) REVERT: 0e 152 GLN cc_start: 0.8283 (mt0) cc_final: 0.7995 (mt0) REVERT: 0e 153 ASN cc_start: 0.7587 (t0) cc_final: 0.7300 (t0) REVERT: 0e 186 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: 0e 213 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7675 (tm-30) REVERT: 0e 218 TRP cc_start: 0.7090 (t-100) cc_final: 0.6712 (t60) REVERT: 0e 220 GLU cc_start: 0.7734 (tp30) cc_final: 0.7079 (mt-10) REVERT: 0e 221 MET cc_start: 0.7554 (tpp) cc_final: 0.7351 (tpp) REVERT: 0f 100 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5500 (t80) REVERT: 0f 140 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8685 (tm-30) REVERT: 0f 194 ASP cc_start: 0.8177 (t0) cc_final: 0.7538 (t0) REVERT: 0f 213 GLN cc_start: 0.7875 (tp40) cc_final: 0.7498 (tm-30) REVERT: 0f 214 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7865 (ttpp) REVERT: 0f 220 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6828 (mt-10) REVERT: 0f 269 ASN cc_start: 0.8142 (t0) cc_final: 0.7927 (t0) REVERT: 0g 18 GLN cc_start: 0.8059 (tp40) cc_final: 0.7580 (tp-100) REVERT: 0g 32 GLN cc_start: 0.7866 (mt0) cc_final: 0.7064 (mt0) REVERT: 0g 88 ASN cc_start: 0.6676 (OUTLIER) cc_final: 0.5929 (m-40) REVERT: 0g 100 TYR cc_start: 0.6123 (OUTLIER) cc_final: 0.5486 (t80) REVERT: 0g 112 MET cc_start: 0.6682 (ptm) cc_final: 0.6196 (ppp) REVERT: 0g 137 PHE cc_start: 0.7936 (m-80) cc_final: 0.7734 (m-80) REVERT: 0g 140 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8662 (tm-30) REVERT: 0g 153 ASN cc_start: 0.7154 (t160) cc_final: 0.6731 (t0) REVERT: 0g 186 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: 0g 194 ASP cc_start: 0.8307 (t0) cc_final: 0.7798 (t0) REVERT: 0g 220 GLU cc_start: 0.7647 (tp30) cc_final: 0.6878 (mt-10) REVERT: 0h 18 GLN cc_start: 0.7770 (tp40) cc_final: 0.7273 (tp-100) REVERT: 0h 30 TYR cc_start: 0.7142 (t80) cc_final: 0.6571 (t80) REVERT: 0h 44 LEU cc_start: 0.7629 (mt) cc_final: 0.7242 (mt) REVERT: 0h 112 MET cc_start: 0.5655 (tpt) cc_final: 0.4951 (ttp) REVERT: 0h 140 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8541 (tm-30) REVERT: 0h 186 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: 0h 194 ASP cc_start: 0.8255 (t0) cc_final: 0.7646 (t0) REVERT: 0h 218 TRP cc_start: 0.7104 (t-100) cc_final: 0.6835 (t60) REVERT: 0h 220 GLU cc_start: 0.7436 (tp30) cc_final: 0.6914 (mt-10) REVERT: 0h 281 ARG cc_start: 0.7877 (mmp80) cc_final: 0.7479 (mmp80) REVERT: 0i 30 TYR cc_start: 0.6640 (t80) cc_final: 0.5912 (t80) REVERT: 0i 40 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6145 (mt-10) REVERT: 0i 100 TYR cc_start: 0.6223 (OUTLIER) cc_final: 0.5468 (t80) REVERT: 0i 151 ASN cc_start: 0.8241 (t0) cc_final: 0.7825 (t0) REVERT: 0i 194 ASP cc_start: 0.8436 (t0) cc_final: 0.7977 (t0) REVERT: 0i 220 GLU cc_start: 0.7644 (tp30) cc_final: 0.7059 (mt-10) REVERT: 0i 250 ILE cc_start: 0.7687 (mm) cc_final: 0.7297 (mm) REVERT: 0j 40 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6738 (mm-30) REVERT: 0j 54 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: 0j 100 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.5312 (t80) REVERT: 0j 151 ASN cc_start: 0.7986 (t0) cc_final: 0.7250 (t0) REVERT: 0j 153 ASN cc_start: 0.7048 (t160) cc_final: 0.6617 (t0) REVERT: 0j 186 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: 0j 213 GLN cc_start: 0.8152 (tp40) cc_final: 0.7608 (tm-30) REVERT: 0j 214 LYS cc_start: 0.8243 (ttpp) cc_final: 0.8012 (ttpp) REVERT: 0j 220 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7203 (mt-10) REVERT: 0j 249 GLN cc_start: 0.7892 (mm-40) cc_final: 0.6830 (mm-40) REVERT: 0k 18 GLN cc_start: 0.7692 (tp40) cc_final: 0.7201 (tp-100) REVERT: 0k 22 ARG cc_start: 0.7906 (tpp-160) cc_final: 0.7557 (ttp-170) REVERT: 0k 30 TYR cc_start: 0.6717 (t80) cc_final: 0.6127 (t80) REVERT: 0k 44 LEU cc_start: 0.7734 (mt) cc_final: 0.7312 (mt) REVERT: 0k 145 LYS cc_start: 0.7520 (tptp) cc_final: 0.7242 (tptp) REVERT: 0k 152 GLN cc_start: 0.8212 (mt0) cc_final: 0.7921 (mt0) REVERT: 0k 153 ASN cc_start: 0.7542 (t0) cc_final: 0.7282 (t0) REVERT: 0k 186 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: 0k 194 ASP cc_start: 0.8324 (t0) cc_final: 0.7801 (t0) REVERT: 0k 205 TYR cc_start: 0.8873 (t80) cc_final: 0.8605 (t80) REVERT: 0k 213 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7276 (tm-30) REVERT: 0k 220 GLU cc_start: 0.7612 (tp30) cc_final: 0.6992 (mt-10) REVERT: 0k 249 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7932 (mm-40) REVERT: 0k 281 ARG cc_start: 0.7920 (mmp80) cc_final: 0.7491 (mmp80) REVERT: 0l 30 TYR cc_start: 0.6285 (t80) cc_final: 0.5324 (t80) REVERT: 0l 40 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6087 (mt-10) REVERT: 0l 88 ASN cc_start: 0.6638 (OUTLIER) cc_final: 0.5923 (m-40) REVERT: 0l 100 TYR cc_start: 0.6352 (OUTLIER) cc_final: 0.5626 (t80) REVERT: 0l 144 LEU cc_start: 0.7860 (tp) cc_final: 0.7320 (mt) REVERT: 0l 213 GLN cc_start: 0.8009 (tp40) cc_final: 0.7506 (tm-30) REVERT: 0l 220 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6948 (mt-10) outliers start: 140 outliers final: 84 residues processed: 811 average time/residue: 0.3804 time to fit residues: 467.2899 Evaluate side-chains 763 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 658 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 37 GLN Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 88 ASN Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 63 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 207 VAL Chi-restraints excluded: chain 0c residue 281 ARG Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 150 VAL Chi-restraints excluded: chain 0d residue 151 ASN Chi-restraints excluded: chain 0d residue 165 ASP Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 22 ARG Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 136 LEU Chi-restraints excluded: chain 0e residue 170 SER Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 63 VAL Chi-restraints excluded: chain 0f residue 77 ASN Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 165 ASP Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 207 VAL Chi-restraints excluded: chain 0f residue 255 THR Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 88 ASN Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 136 LEU Chi-restraints excluded: chain 0g residue 165 ASP Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 54 GLU Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 141 LEU Chi-restraints excluded: chain 0h residue 165 ASP Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 207 VAL Chi-restraints excluded: chain 0h residue 277 LYS Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 63 VAL Chi-restraints excluded: chain 0i residue 77 ASN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 223 THR Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 136 LEU Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0j residue 255 THR Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 124 ASN Chi-restraints excluded: chain 0k residue 170 SER Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 207 VAL Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 88 ASN Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 165 ASP Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 290 optimal weight: 8.9990 chunk 240 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 88 ASN 0b 89 GLN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 88 ASN 0c 89 GLN ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN 0e 29 ASN 0e 32 GLN ** 0e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 88 ASN 0g 89 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 173 GLN ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 21 ASN ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 173 GLN ** 0j 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0l 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.6648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25728 Z= 0.204 Angle : 0.732 9.670 34860 Z= 0.396 Chirality : 0.046 0.208 3756 Planarity : 0.005 0.058 4548 Dihedral : 7.192 36.276 3348 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.58 % Favored : 83.99 % Rotamer: Outliers : 4.82 % Allowed : 20.87 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 3024 helix: 0.35 (0.16), residues: 1080 sheet: -3.68 (0.26), residues: 300 loop : -2.07 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP0b 218 HIS 0.005 0.001 HIS0e 58 PHE 0.025 0.002 PHE0l 199 TYR 0.023 0.001 TYR0f 30 ARG 0.007 0.001 ARG0b 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 682 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 18 GLN cc_start: 0.7727 (tp40) cc_final: 0.6967 (tp-100) REVERT: 0a 20 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6764 (mmm160) REVERT: 0a 40 GLU cc_start: 0.6965 (mm-30) cc_final: 0.5912 (mt-10) REVERT: 0a 100 TYR cc_start: 0.6462 (OUTLIER) cc_final: 0.5716 (t80) REVERT: 0a 186 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: 0a 220 GLU cc_start: 0.7629 (tp30) cc_final: 0.6989 (mt-10) REVERT: 0b 30 TYR cc_start: 0.7097 (t80) cc_final: 0.6645 (t80) REVERT: 0b 44 LEU cc_start: 0.7482 (mt) cc_final: 0.7090 (mt) REVERT: 0b 88 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6425 (m-40) REVERT: 0b 145 LYS cc_start: 0.7508 (tptp) cc_final: 0.7238 (tptp) REVERT: 0b 186 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: 0b 194 ASP cc_start: 0.8173 (t0) cc_final: 0.7392 (t0) REVERT: 0b 220 GLU cc_start: 0.7528 (tp30) cc_final: 0.6989 (mt-10) REVERT: 0b 281 ARG cc_start: 0.7755 (mmp80) cc_final: 0.7153 (mmm-85) REVERT: 0c 30 TYR cc_start: 0.6296 (t80) cc_final: 0.5701 (t80) REVERT: 0c 37 GLN cc_start: 0.8216 (pp30) cc_final: 0.7921 (tt0) REVERT: 0c 88 ASN cc_start: 0.6684 (OUTLIER) cc_final: 0.6033 (m-40) REVERT: 0c 100 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5667 (t80) REVERT: 0c 112 MET cc_start: 0.5837 (ppp) cc_final: 0.5600 (ppp) REVERT: 0c 140 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8643 (tm-30) REVERT: 0c 141 LEU cc_start: 0.9055 (mt) cc_final: 0.8644 (mt) REVERT: 0c 213 GLN cc_start: 0.8085 (tp40) cc_final: 0.7464 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6920 (mt-10) REVERT: 0d 100 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.5744 (t80) REVERT: 0d 153 ASN cc_start: 0.7055 (t0) cc_final: 0.6623 (t0) REVERT: 0d 186 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: 0d 220 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7103 (mt-10) REVERT: 0d 263 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: 0e 30 TYR cc_start: 0.6515 (t80) cc_final: 0.5709 (t80) REVERT: 0e 112 MET cc_start: 0.5585 (tpt) cc_final: 0.5196 (ttt) REVERT: 0e 145 LYS cc_start: 0.7599 (tptp) cc_final: 0.7317 (tptp) REVERT: 0e 152 GLN cc_start: 0.8172 (mt0) cc_final: 0.7915 (mt0) REVERT: 0e 153 ASN cc_start: 0.7554 (t0) cc_final: 0.7261 (t0) REVERT: 0e 213 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7696 (tm-30) REVERT: 0e 218 TRP cc_start: 0.7048 (t-100) cc_final: 0.6657 (t60) REVERT: 0e 220 GLU cc_start: 0.7703 (tp30) cc_final: 0.7227 (mt-10) REVERT: 0f 22 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7691 (ttm110) REVERT: 0f 30 TYR cc_start: 0.6092 (t80) cc_final: 0.5237 (t80) REVERT: 0f 100 TYR cc_start: 0.6266 (OUTLIER) cc_final: 0.5631 (t80) REVERT: 0f 112 MET cc_start: 0.5924 (ppp) cc_final: 0.5680 (ppp) REVERT: 0f 140 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8732 (tm-30) REVERT: 0f 194 ASP cc_start: 0.8236 (t0) cc_final: 0.7625 (t0) REVERT: 0f 213 GLN cc_start: 0.7937 (tp40) cc_final: 0.7499 (tm-30) REVERT: 0f 214 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7653 (ttpp) REVERT: 0f 220 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6874 (mt-10) REVERT: 0f 269 ASN cc_start: 0.8226 (t0) cc_final: 0.7990 (t0) REVERT: 0g 88 ASN cc_start: 0.6643 (OUTLIER) cc_final: 0.6142 (m-40) REVERT: 0g 100 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5713 (t80) REVERT: 0g 137 PHE cc_start: 0.7943 (m-80) cc_final: 0.7666 (m-80) REVERT: 0g 140 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8651 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8832 (tp) cc_final: 0.8545 (mt) REVERT: 0g 194 ASP cc_start: 0.8388 (t0) cc_final: 0.7867 (t0) REVERT: 0g 220 GLU cc_start: 0.7650 (tp30) cc_final: 0.6940 (mt-10) REVERT: 0h 30 TYR cc_start: 0.7216 (t80) cc_final: 0.6662 (t80) REVERT: 0h 44 LEU cc_start: 0.7592 (mt) cc_final: 0.7163 (mt) REVERT: 0h 140 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8584 (tm-30) REVERT: 0h 186 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6570 (m-80) REVERT: 0h 194 ASP cc_start: 0.8212 (t0) cc_final: 0.7702 (t0) REVERT: 0h 218 TRP cc_start: 0.7131 (t-100) cc_final: 0.6814 (t60) REVERT: 0h 220 GLU cc_start: 0.7554 (tp30) cc_final: 0.6939 (mt-10) REVERT: 0i 30 TYR cc_start: 0.6302 (t80) cc_final: 0.5565 (t80) REVERT: 0i 100 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5656 (t80) REVERT: 0i 112 MET cc_start: 0.5972 (ppp) cc_final: 0.4191 (mmp) REVERT: 0i 151 ASN cc_start: 0.8231 (t0) cc_final: 0.7818 (t0) REVERT: 0i 194 ASP cc_start: 0.8498 (t0) cc_final: 0.7887 (t0) REVERT: 0i 220 GLU cc_start: 0.7626 (tp30) cc_final: 0.7067 (mt-10) REVERT: 0i 225 LEU cc_start: 0.7408 (mt) cc_final: 0.6750 (mp) REVERT: 0i 250 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7411 (mm) REVERT: 0j 22 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7511 (ttm110) REVERT: 0j 32 GLN cc_start: 0.7687 (mt0) cc_final: 0.6653 (mt0) REVERT: 0j 36 TYR cc_start: 0.6515 (p90) cc_final: 0.6276 (p90) REVERT: 0j 40 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6919 (mm-30) REVERT: 0j 54 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: 0j 100 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.5703 (t80) REVERT: 0j 151 ASN cc_start: 0.7891 (t0) cc_final: 0.7128 (t0) REVERT: 0j 153 ASN cc_start: 0.7115 (t0) cc_final: 0.6678 (t0) REVERT: 0j 186 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: 0j 213 GLN cc_start: 0.7996 (tp40) cc_final: 0.7710 (tm-30) REVERT: 0j 214 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7971 (ttpp) REVERT: 0j 220 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7040 (mt-10) REVERT: 0k 18 GLN cc_start: 0.7741 (tp40) cc_final: 0.7396 (tp-100) REVERT: 0k 22 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7526 (tpp-160) REVERT: 0k 30 TYR cc_start: 0.6852 (t80) cc_final: 0.6167 (t80) REVERT: 0k 44 LEU cc_start: 0.7747 (mt) cc_final: 0.7346 (mt) REVERT: 0k 145 LYS cc_start: 0.7476 (tptp) cc_final: 0.7173 (tptp) REVERT: 0k 152 GLN cc_start: 0.8134 (mt0) cc_final: 0.7891 (mt0) REVERT: 0k 153 ASN cc_start: 0.7484 (t0) cc_final: 0.7206 (t0) REVERT: 0k 186 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: 0k 194 ASP cc_start: 0.8375 (t0) cc_final: 0.7836 (t0) REVERT: 0k 213 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7384 (tm-30) REVERT: 0k 218 TRP cc_start: 0.7091 (t-100) cc_final: 0.6722 (t60) REVERT: 0k 220 GLU cc_start: 0.7537 (tp30) cc_final: 0.6911 (mt-10) REVERT: 0k 225 LEU cc_start: 0.7953 (mt) cc_final: 0.7697 (mp) REVERT: 0k 249 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7913 (mm-40) REVERT: 0k 281 ARG cc_start: 0.7782 (mmp80) cc_final: 0.7536 (mmp80) REVERT: 0l 30 TYR cc_start: 0.6412 (t80) cc_final: 0.5505 (t80) REVERT: 0l 40 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6104 (mt-10) REVERT: 0l 100 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.5726 (t80) REVERT: 0l 112 MET cc_start: 0.6403 (ptm) cc_final: 0.5872 (ppp) REVERT: 0l 144 LEU cc_start: 0.7901 (tp) cc_final: 0.7391 (mt) REVERT: 0l 213 GLN cc_start: 0.7964 (tp40) cc_final: 0.7481 (tm-30) REVERT: 0l 220 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6861 (mt-10) outliers start: 132 outliers final: 90 residues processed: 772 average time/residue: 0.3811 time to fit residues: 447.1488 Evaluate side-chains 754 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 643 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 37 GLN Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 88 ASN Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 63 VAL Chi-restraints excluded: chain 0c residue 88 ASN Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 207 VAL Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 165 ASP Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 263 GLU Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 32 GLN Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 136 LEU Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 22 ARG Chi-restraints excluded: chain 0f residue 33 SER Chi-restraints excluded: chain 0f residue 63 VAL Chi-restraints excluded: chain 0f residue 77 ASN Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 136 LEU Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 255 THR Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 81 SER Chi-restraints excluded: chain 0g residue 88 ASN Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 165 ASP Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 54 GLU Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 165 ASP Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 207 VAL Chi-restraints excluded: chain 0h residue 277 LYS Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 25 ILE Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 63 VAL Chi-restraints excluded: chain 0i residue 77 ASN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 250 ILE Chi-restraints excluded: chain 0i residue 255 THR Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 141 LEU Chi-restraints excluded: chain 0j residue 165 ASP Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 124 ASN Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 207 VAL Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 165 ASP Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Chi-restraints excluded: chain 0l residue 221 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 180 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 43 ASN 0a 58 HIS 0a 59 GLN ** 0a 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 21 ASN ** 0b 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN ** 0b 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 58 HIS 0c 59 GLN ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 58 HIS ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 29 ASN 0e 32 GLN ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 173 GLN ** 0g 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 21 ASN ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 58 HIS ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 153 ASN 0j 173 GLN ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 173 GLN 0l 58 HIS ** 0l 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN 0l 181 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25728 Z= 0.279 Angle : 0.805 10.376 34860 Z= 0.435 Chirality : 0.049 0.213 3756 Planarity : 0.005 0.057 4548 Dihedral : 7.474 37.321 3348 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.43 % Allowed : 16.30 % Favored : 83.27 % Rotamer: Outliers : 5.04 % Allowed : 22.15 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.68 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 3024 helix: 0.24 (0.16), residues: 1044 sheet: -3.47 (0.27), residues: 300 loop : -2.11 (0.17), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP0g 41 HIS 0.005 0.001 HIS0e 58 PHE 0.022 0.002 PHE0l 199 TYR 0.017 0.002 TYR0f 205 ARG 0.009 0.001 ARG0j 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 671 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 100 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.5518 (t80) REVERT: 0a 112 MET cc_start: 0.5680 (tpt) cc_final: 0.5472 (ttp) REVERT: 0a 145 LYS cc_start: 0.7618 (tptp) cc_final: 0.7314 (tptp) REVERT: 0a 186 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: 0a 220 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6949 (mt-10) REVERT: 0b 22 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7329 (ttm110) REVERT: 0b 30 TYR cc_start: 0.7137 (t80) cc_final: 0.6603 (t80) REVERT: 0b 44 LEU cc_start: 0.7669 (mt) cc_final: 0.7298 (mt) REVERT: 0b 112 MET cc_start: 0.5242 (tpt) cc_final: 0.4990 (ttp) REVERT: 0b 145 LYS cc_start: 0.7634 (tptp) cc_final: 0.7333 (tptp) REVERT: 0b 194 ASP cc_start: 0.8482 (t0) cc_final: 0.7776 (t0) REVERT: 0b 220 GLU cc_start: 0.7442 (tp30) cc_final: 0.6939 (mt-10) REVERT: 0b 222 MET cc_start: 0.7262 (mmm) cc_final: 0.6841 (mmm) REVERT: 0b 262 GLU cc_start: 0.6960 (tp30) cc_final: 0.6635 (tp30) REVERT: 0c 18 GLN cc_start: 0.7431 (tt0) cc_final: 0.7180 (tt0) REVERT: 0c 30 TYR cc_start: 0.6417 (t80) cc_final: 0.5698 (t80) REVERT: 0c 100 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.5646 (t80) REVERT: 0c 141 LEU cc_start: 0.9100 (mt) cc_final: 0.8878 (mt) REVERT: 0c 146 GLU cc_start: 0.7446 (tt0) cc_final: 0.7128 (tt0) REVERT: 0c 213 GLN cc_start: 0.8224 (tp40) cc_final: 0.7596 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7613 (mm-30) cc_final: 0.6936 (mt-10) REVERT: 0d 22 ARG cc_start: 0.7842 (tpp-160) cc_final: 0.7396 (ttm-80) REVERT: 0d 100 TYR cc_start: 0.6726 (OUTLIER) cc_final: 0.5691 (t80) REVERT: 0d 153 ASN cc_start: 0.7039 (t0) cc_final: 0.6655 (t0) REVERT: 0d 186 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: 0d 220 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7041 (mt-10) REVERT: 0d 263 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: 0e 22 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: 0e 30 TYR cc_start: 0.6703 (t80) cc_final: 0.6109 (t80) REVERT: 0e 140 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8685 (tm-30) REVERT: 0e 145 LYS cc_start: 0.7602 (tptp) cc_final: 0.7328 (tptp) REVERT: 0e 152 GLN cc_start: 0.8313 (mt0) cc_final: 0.8037 (mt0) REVERT: 0e 153 ASN cc_start: 0.7599 (t0) cc_final: 0.7327 (t0) REVERT: 0e 213 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7788 (tm-30) REVERT: 0e 218 TRP cc_start: 0.7180 (t-100) cc_final: 0.6848 (t60) REVERT: 0e 220 GLU cc_start: 0.7809 (tp30) cc_final: 0.7268 (mt-10) REVERT: 0e 249 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7951 (mm-40) REVERT: 0f 22 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7702 (ttm110) REVERT: 0f 100 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5559 (t80) REVERT: 0f 140 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8647 (tm-30) REVERT: 0f 146 GLU cc_start: 0.7453 (tt0) cc_final: 0.7122 (tt0) REVERT: 0f 220 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6914 (mt-10) REVERT: 0f 225 LEU cc_start: 0.7673 (mt) cc_final: 0.7206 (mp) REVERT: 0f 269 ASN cc_start: 0.8270 (t0) cc_final: 0.8068 (t0) REVERT: 0g 32 GLN cc_start: 0.7805 (mt0) cc_final: 0.7368 (mt0) REVERT: 0g 100 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.5636 (t80) REVERT: 0g 140 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8639 (tm-30) REVERT: 0g 141 LEU cc_start: 0.9024 (tp) cc_final: 0.8702 (mt) REVERT: 0g 153 ASN cc_start: 0.7166 (t0) cc_final: 0.6724 (t0) REVERT: 0g 173 GLN cc_start: 0.6281 (tp40) cc_final: 0.6067 (tp40) REVERT: 0g 194 ASP cc_start: 0.8501 (t0) cc_final: 0.7972 (t0) REVERT: 0g 220 GLU cc_start: 0.7640 (tp30) cc_final: 0.6860 (mt-10) REVERT: 0h 30 TYR cc_start: 0.7278 (t80) cc_final: 0.6657 (t80) REVERT: 0h 44 LEU cc_start: 0.7727 (mt) cc_final: 0.7331 (mt) REVERT: 0h 140 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8594 (tm-30) REVERT: 0h 194 ASP cc_start: 0.8465 (t0) cc_final: 0.7974 (t0) REVERT: 0h 218 TRP cc_start: 0.7163 (t-100) cc_final: 0.6918 (t60) REVERT: 0i 30 TYR cc_start: 0.6300 (t80) cc_final: 0.5387 (t80) REVERT: 0i 40 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6400 (mt-10) REVERT: 0i 146 GLU cc_start: 0.7497 (tt0) cc_final: 0.7289 (tt0) REVERT: 0i 186 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7112 (m-80) REVERT: 0i 194 ASP cc_start: 0.8609 (t0) cc_final: 0.7973 (t0) REVERT: 0i 213 GLN cc_start: 0.8556 (tp40) cc_final: 0.8150 (tp40) REVERT: 0i 225 LEU cc_start: 0.7403 (mt) cc_final: 0.7077 (mp) REVERT: 0i 250 ILE cc_start: 0.7713 (mm) cc_final: 0.7357 (mm) REVERT: 0j 32 GLN cc_start: 0.7843 (mt0) cc_final: 0.7309 (mt0) REVERT: 0j 36 TYR cc_start: 0.6781 (p90) cc_final: 0.6568 (p90) REVERT: 0j 40 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6993 (mm-30) REVERT: 0j 54 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: 0j 100 TYR cc_start: 0.6649 (OUTLIER) cc_final: 0.5572 (t80) REVERT: 0j 153 ASN cc_start: 0.7567 (t0) cc_final: 0.7271 (t0) REVERT: 0j 213 GLN cc_start: 0.8073 (tp40) cc_final: 0.7845 (tm-30) REVERT: 0j 214 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8068 (ttpp) REVERT: 0j 220 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7052 (mt-10) REVERT: 0k 18 GLN cc_start: 0.7785 (tp40) cc_final: 0.7411 (mm-40) REVERT: 0k 22 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7330 (tpp-160) REVERT: 0k 30 TYR cc_start: 0.6914 (t80) cc_final: 0.6339 (t80) REVERT: 0k 44 LEU cc_start: 0.7871 (mt) cc_final: 0.7535 (mt) REVERT: 0k 145 LYS cc_start: 0.7596 (tptp) cc_final: 0.7288 (tptp) REVERT: 0k 152 GLN cc_start: 0.8153 (mt0) cc_final: 0.7907 (mt0) REVERT: 0k 194 ASP cc_start: 0.8476 (t0) cc_final: 0.8012 (t0) REVERT: 0k 213 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7662 (tm-30) REVERT: 0k 218 TRP cc_start: 0.7225 (t-100) cc_final: 0.6927 (t60) REVERT: 0k 220 GLU cc_start: 0.7543 (tp30) cc_final: 0.6882 (mt-10) REVERT: 0k 262 GLU cc_start: 0.7044 (tp30) cc_final: 0.6787 (tp30) REVERT: 0l 30 TYR cc_start: 0.6616 (t80) cc_final: 0.5846 (t80) REVERT: 0l 100 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.5607 (t80) REVERT: 0l 220 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7003 (mt-10) outliers start: 138 outliers final: 97 residues processed: 778 average time/residue: 0.3920 time to fit residues: 463.1040 Evaluate side-chains 757 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 646 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 37 GLN Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 198 VAL Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0a residue 220 GLU Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 136 LEU Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 255 THR Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 165 ASP Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 263 GLU Chi-restraints excluded: chain 0d residue 276 VAL Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 136 LEU Chi-restraints excluded: chain 0e residue 170 SER Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 22 ARG Chi-restraints excluded: chain 0f residue 33 SER Chi-restraints excluded: chain 0f residue 77 ASN Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 136 LEU Chi-restraints excluded: chain 0f residue 165 ASP Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0g residue 52 PHE Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 81 SER Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 165 ASP Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 54 GLU Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 141 LEU Chi-restraints excluded: chain 0h residue 170 SER Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 277 LYS Chi-restraints excluded: chain 0h residue 278 VAL Chi-restraints excluded: chain 0i residue 25 ILE Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 77 ASN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 255 THR Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 141 LEU Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 124 ASN Chi-restraints excluded: chain 0k residue 136 LEU Chi-restraints excluded: chain 0k residue 170 SER Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 206 VAL Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 170 SER Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 221 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.1980 chunk 115 optimal weight: 5.9990 chunk 172 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 21 ASN ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 43 ASN 0a 59 GLN 0a 88 ASN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 21 ASN 0b 88 ASN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 211 ASN ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 29 ASN 0c 59 GLN ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 88 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 181 ASN ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 29 ASN ** 0g 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 88 ASN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 153 ASN ** 0j 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 59 GLN ** 0l 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 181 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25728 Z= 0.199 Angle : 0.763 10.199 34860 Z= 0.408 Chirality : 0.047 0.218 3756 Planarity : 0.004 0.056 4548 Dihedral : 7.028 36.590 3348 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.88 % Favored : 84.72 % Rotamer: Outliers : 4.42 % Allowed : 24.23 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.16), residues: 3024 helix: 0.51 (0.16), residues: 1080 sheet: -3.55 (0.27), residues: 300 loop : -2.05 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP0g 41 HIS 0.006 0.001 HIS0e 58 PHE 0.024 0.002 PHE0g 65 TYR 0.020 0.001 TYR0e 36 ARG 0.011 0.000 ARG0j 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 658 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 22 ARG cc_start: 0.7846 (tpp-160) cc_final: 0.7516 (tpp-160) REVERT: 0a 88 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6349 (m-40) REVERT: 0a 145 LYS cc_start: 0.7618 (tptp) cc_final: 0.7348 (tptp) REVERT: 0a 222 MET cc_start: 0.7395 (mmm) cc_final: 0.6878 (tpp) REVERT: 0a 225 LEU cc_start: 0.7522 (mt) cc_final: 0.7120 (mp) REVERT: 0b 22 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7177 (ttm110) REVERT: 0b 30 TYR cc_start: 0.7011 (t80) cc_final: 0.6530 (t80) REVERT: 0b 44 LEU cc_start: 0.7480 (mt) cc_final: 0.7125 (mt) REVERT: 0b 88 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6354 (m-40) REVERT: 0b 145 LYS cc_start: 0.7640 (tptp) cc_final: 0.7347 (tptp) REVERT: 0b 194 ASP cc_start: 0.8394 (t0) cc_final: 0.7753 (t0) REVERT: 0b 220 GLU cc_start: 0.7415 (tp30) cc_final: 0.6957 (mt-10) REVERT: 0b 225 LEU cc_start: 0.7361 (mt) cc_final: 0.7118 (mp) REVERT: 0b 262 GLU cc_start: 0.7067 (tp30) cc_final: 0.6829 (tp30) REVERT: 0b 281 ARG cc_start: 0.7804 (mmp80) cc_final: 0.7527 (mmp80) REVERT: 0c 30 TYR cc_start: 0.6383 (t80) cc_final: 0.5453 (t80) REVERT: 0c 88 ASN cc_start: 0.6645 (p0) cc_final: 0.6288 (m-40) REVERT: 0c 100 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.5849 (t80) REVERT: 0c 112 MET cc_start: 0.5602 (ppp) cc_final: 0.5327 (ppp) REVERT: 0c 140 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8508 (tm-30) REVERT: 0c 141 LEU cc_start: 0.9017 (mt) cc_final: 0.8807 (mt) REVERT: 0c 146 GLU cc_start: 0.7352 (tt0) cc_final: 0.7055 (tt0) REVERT: 0c 213 GLN cc_start: 0.8147 (tp40) cc_final: 0.7473 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7025 (mt-10) REVERT: 0d 22 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7394 (tpp-160) REVERT: 0d 54 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6590 (pm20) REVERT: 0d 88 ASN cc_start: 0.6528 (OUTLIER) cc_final: 0.6243 (m-40) REVERT: 0d 100 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.5859 (t80) REVERT: 0d 112 MET cc_start: 0.6003 (ptm) cc_final: 0.5774 (ppp) REVERT: 0d 145 LYS cc_start: 0.7592 (tptp) cc_final: 0.7294 (tptp) REVERT: 0d 186 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: 0d 213 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7976 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7096 (mt-10) REVERT: 0d 263 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: 0d 281 ARG cc_start: 0.7531 (mmp80) cc_final: 0.7249 (mmm-85) REVERT: 0e 22 ARG cc_start: 0.7505 (ttm-80) cc_final: 0.7109 (ttm-80) REVERT: 0e 30 TYR cc_start: 0.6502 (t80) cc_final: 0.5723 (t80) REVERT: 0e 145 LYS cc_start: 0.7634 (tptp) cc_final: 0.7332 (tptp) REVERT: 0e 152 GLN cc_start: 0.8100 (mt0) cc_final: 0.7898 (mt0) REVERT: 0e 153 ASN cc_start: 0.7621 (t0) cc_final: 0.7350 (t0) REVERT: 0e 213 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7685 (tm-30) REVERT: 0e 218 TRP cc_start: 0.7073 (t-100) cc_final: 0.6717 (t60) REVERT: 0e 220 GLU cc_start: 0.7552 (tp30) cc_final: 0.7158 (mt-10) REVERT: 0f 100 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.5799 (t80) REVERT: 0f 140 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8772 (tm-30) REVERT: 0f 146 GLU cc_start: 0.7372 (tt0) cc_final: 0.7063 (tt0) REVERT: 0f 153 ASN cc_start: 0.7534 (t0) cc_final: 0.7224 (t0) REVERT: 0f 220 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7046 (mt-10) REVERT: 0g 100 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5766 (t80) REVERT: 0g 113 LYS cc_start: 0.4691 (mmtt) cc_final: 0.2848 (ttmm) REVERT: 0g 140 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8667 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8904 (tp) cc_final: 0.8632 (mt) REVERT: 0g 153 ASN cc_start: 0.7037 (t0) cc_final: 0.6596 (t0) REVERT: 0g 186 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: 0g 194 ASP cc_start: 0.8506 (t0) cc_final: 0.7996 (t0) REVERT: 0g 220 GLU cc_start: 0.7509 (tp30) cc_final: 0.6883 (mt-10) REVERT: 0g 225 LEU cc_start: 0.7534 (mt) cc_final: 0.7291 (mp) REVERT: 0h 30 TYR cc_start: 0.7194 (t80) cc_final: 0.6585 (t80) REVERT: 0h 37 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: 0h 44 LEU cc_start: 0.7529 (mt) cc_final: 0.7209 (mt) REVERT: 0h 112 MET cc_start: 0.5782 (tpt) cc_final: 0.5339 (ttt) REVERT: 0h 140 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8623 (tm-30) REVERT: 0h 194 ASP cc_start: 0.8387 (t0) cc_final: 0.7992 (t0) REVERT: 0h 218 TRP cc_start: 0.7052 (t-100) cc_final: 0.6816 (t60) REVERT: 0h 220 GLU cc_start: 0.7598 (tp30) cc_final: 0.7054 (mt-10) REVERT: 0h 262 GLU cc_start: 0.6921 (tp30) cc_final: 0.6629 (tp30) REVERT: 0h 281 ARG cc_start: 0.7796 (mmp80) cc_final: 0.7585 (mmp80) REVERT: 0i 30 TYR cc_start: 0.6234 (t80) cc_final: 0.5302 (t80) REVERT: 0i 40 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6041 (mt-10) REVERT: 0i 100 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.5839 (t80) REVERT: 0i 112 MET cc_start: 0.5563 (ppp) cc_final: 0.5337 (ppp) REVERT: 0i 151 ASN cc_start: 0.8422 (t0) cc_final: 0.7990 (t0) REVERT: 0i 186 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6951 (m-80) REVERT: 0i 194 ASP cc_start: 0.8523 (t0) cc_final: 0.7828 (t0) REVERT: 0i 213 GLN cc_start: 0.8397 (tp40) cc_final: 0.8050 (tp40) REVERT: 0i 220 GLU cc_start: 0.7645 (tp30) cc_final: 0.7247 (mt-10) REVERT: 0i 250 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7347 (mm) REVERT: 0j 36 TYR cc_start: 0.6470 (p90) cc_final: 0.6142 (p90) REVERT: 0j 40 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6927 (mm-30) REVERT: 0j 54 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6734 (pm20) REVERT: 0j 140 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8678 (tm-30) REVERT: 0j 151 ASN cc_start: 0.7949 (t0) cc_final: 0.7217 (t0) REVERT: 0j 214 LYS cc_start: 0.8355 (ttpp) cc_final: 0.8011 (ttpp) REVERT: 0j 220 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6933 (mt-10) REVERT: 0k 30 TYR cc_start: 0.6862 (t80) cc_final: 0.6085 (t80) REVERT: 0k 44 LEU cc_start: 0.7677 (mt) cc_final: 0.7308 (mt) REVERT: 0k 112 MET cc_start: 0.5821 (tpt) cc_final: 0.5381 (ttt) REVERT: 0k 140 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8619 (tm-30) REVERT: 0k 145 LYS cc_start: 0.7557 (tptp) cc_final: 0.7299 (tptp) REVERT: 0k 194 ASP cc_start: 0.8522 (t0) cc_final: 0.8170 (t0) REVERT: 0k 218 TRP cc_start: 0.7046 (t-100) cc_final: 0.6796 (t60) REVERT: 0k 220 GLU cc_start: 0.7554 (tp30) cc_final: 0.7030 (mt-10) REVERT: 0k 225 LEU cc_start: 0.7712 (mt) cc_final: 0.7312 (mp) REVERT: 0k 262 GLU cc_start: 0.7039 (tp30) cc_final: 0.6815 (tp30) REVERT: 0l 30 TYR cc_start: 0.6469 (t80) cc_final: 0.5404 (t80) REVERT: 0l 100 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.5784 (t80) REVERT: 0l 140 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8754 (tm-30) REVERT: 0l 220 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7066 (mt-10) outliers start: 121 outliers final: 80 residues processed: 741 average time/residue: 0.3798 time to fit residues: 425.9893 Evaluate side-chains 712 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 615 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 88 ASN Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 198 VAL Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0a residue 277 LYS Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 88 ASN Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 54 GLU Chi-restraints excluded: chain 0d residue 88 ASN Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 165 ASP Chi-restraints excluded: chain 0d residue 185 ILE Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 263 GLU Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 136 LEU Chi-restraints excluded: chain 0e residue 170 SER Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 24 PHE Chi-restraints excluded: chain 0f residue 33 SER Chi-restraints excluded: chain 0f residue 77 ASN Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 255 THR Chi-restraints excluded: chain 0g residue 52 PHE Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 112 MET Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 165 ASP Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0g residue 267 LYS Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 54 GLU Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 277 LYS Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 77 ASN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 250 ILE Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 141 LEU Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 206 VAL Chi-restraints excluded: chain 0k residue 223 THR Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0l residue 33 SER Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Chi-restraints excluded: chain 0l residue 221 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.3980 chunk 211 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 268 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 88 ASN 0a 89 GLN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 21 ASN 0b 88 ASN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 59 GLN ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 88 ASN 0d 89 GLN ** 0d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 249 GLN 0k 88 ASN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 153 ASN 0k 211 ASN ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 59 GLN ** 0l 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 181 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25728 Z= 0.209 Angle : 0.779 10.858 34860 Z= 0.412 Chirality : 0.047 0.267 3756 Planarity : 0.005 0.058 4548 Dihedral : 6.912 36.468 3348 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.88 % Favored : 84.72 % Rotamer: Outliers : 3.91 % Allowed : 25.22 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.16), residues: 3024 helix: 0.55 (0.16), residues: 1080 sheet: -3.59 (0.27), residues: 300 loop : -2.01 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP0g 41 HIS 0.006 0.001 HIS0e 58 PHE 0.023 0.002 PHE0k 199 TYR 0.018 0.001 TYR0b 36 ARG 0.011 0.001 ARG0j 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 647 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 22 ARG cc_start: 0.7946 (tpp-160) cc_final: 0.7640 (tpp-160) REVERT: 0a 140 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8693 (tm-30) REVERT: 0a 145 LYS cc_start: 0.7607 (tptp) cc_final: 0.7340 (tptp) REVERT: 0a 186 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: 0a 222 MET cc_start: 0.7417 (mmm) cc_final: 0.7174 (tpp) REVERT: 0b 22 ARG cc_start: 0.7615 (ttm110) cc_final: 0.6986 (ttm110) REVERT: 0b 30 TYR cc_start: 0.7037 (t80) cc_final: 0.6557 (t80) REVERT: 0b 44 LEU cc_start: 0.7509 (mt) cc_final: 0.7163 (mt) REVERT: 0b 88 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6402 (m-40) REVERT: 0b 145 LYS cc_start: 0.7686 (tptp) cc_final: 0.7375 (tptp) REVERT: 0b 194 ASP cc_start: 0.8399 (t0) cc_final: 0.7797 (t0) REVERT: 0b 220 GLU cc_start: 0.7406 (tp30) cc_final: 0.6954 (mt-10) REVERT: 0b 281 ARG cc_start: 0.7706 (mmp80) cc_final: 0.7426 (mmp80) REVERT: 0c 30 TYR cc_start: 0.6366 (t80) cc_final: 0.5485 (t80) REVERT: 0c 100 TYR cc_start: 0.6557 (OUTLIER) cc_final: 0.5921 (t80) REVERT: 0c 140 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8540 (tm-30) REVERT: 0c 141 LEU cc_start: 0.9011 (mt) cc_final: 0.8757 (mt) REVERT: 0c 145 LYS cc_start: 0.7681 (tptp) cc_final: 0.7363 (tptp) REVERT: 0c 146 GLU cc_start: 0.7430 (tt0) cc_final: 0.7138 (tt0) REVERT: 0c 213 GLN cc_start: 0.8147 (tp40) cc_final: 0.7494 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7093 (mt-10) REVERT: 0d 18 GLN cc_start: 0.7663 (tp40) cc_final: 0.7411 (tp-100) REVERT: 0d 22 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7503 (tpp-160) REVERT: 0d 54 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6587 (pm20) REVERT: 0d 88 ASN cc_start: 0.6349 (OUTLIER) cc_final: 0.6067 (m-40) REVERT: 0d 100 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.5826 (t80) REVERT: 0d 145 LYS cc_start: 0.7595 (tptp) cc_final: 0.7273 (tptp) REVERT: 0d 153 ASN cc_start: 0.7200 (t0) cc_final: 0.6903 (t0) REVERT: 0d 186 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: 0d 213 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7979 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7020 (mt-10) REVERT: 0d 281 ARG cc_start: 0.7497 (mmp80) cc_final: 0.7214 (mmm-85) REVERT: 0e 30 TYR cc_start: 0.6644 (t80) cc_final: 0.5875 (t80) REVERT: 0e 140 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8691 (tm-30) REVERT: 0e 145 LYS cc_start: 0.7742 (tptp) cc_final: 0.7415 (tptp) REVERT: 0e 153 ASN cc_start: 0.7572 (t0) cc_final: 0.7291 (t0) REVERT: 0e 213 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7668 (tm-30) REVERT: 0e 218 TRP cc_start: 0.7066 (t-100) cc_final: 0.6758 (t60) REVERT: 0e 220 GLU cc_start: 0.7454 (tp30) cc_final: 0.7183 (mt-10) REVERT: 0f 18 GLN cc_start: 0.7386 (tt0) cc_final: 0.6917 (tp-100) REVERT: 0f 22 ARG cc_start: 0.8062 (ttm110) cc_final: 0.6975 (ttm110) REVERT: 0f 30 TYR cc_start: 0.6341 (t80) cc_final: 0.5226 (t80) REVERT: 0f 100 TYR cc_start: 0.6691 (OUTLIER) cc_final: 0.6172 (t80) REVERT: 0f 140 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8736 (tm-30) REVERT: 0f 146 GLU cc_start: 0.7398 (tt0) cc_final: 0.7074 (tt0) REVERT: 0f 153 ASN cc_start: 0.7489 (t0) cc_final: 0.7155 (t0) REVERT: 0f 194 ASP cc_start: 0.8432 (t0) cc_final: 0.7824 (t0) REVERT: 0f 213 GLN cc_start: 0.8230 (tp40) cc_final: 0.7738 (tm-30) REVERT: 0f 220 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7099 (mt-10) REVERT: 0g 113 LYS cc_start: 0.4681 (mmtt) cc_final: 0.2826 (ttmm) REVERT: 0g 141 LEU cc_start: 0.8919 (tp) cc_final: 0.8699 (mt) REVERT: 0g 186 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: 0g 194 ASP cc_start: 0.8499 (t0) cc_final: 0.8049 (t0) REVERT: 0g 220 GLU cc_start: 0.7534 (tp30) cc_final: 0.6904 (mt-10) REVERT: 0g 225 LEU cc_start: 0.7540 (mt) cc_final: 0.7273 (mp) REVERT: 0h 30 TYR cc_start: 0.7188 (t80) cc_final: 0.6587 (t80) REVERT: 0h 37 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: 0h 44 LEU cc_start: 0.7515 (mt) cc_final: 0.7189 (mt) REVERT: 0h 112 MET cc_start: 0.5432 (tpt) cc_final: 0.4999 (ttp) REVERT: 0h 140 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8662 (tm-30) REVERT: 0h 194 ASP cc_start: 0.8465 (t0) cc_final: 0.8120 (t0) REVERT: 0h 209 LYS cc_start: 0.8473 (mmtp) cc_final: 0.8186 (mmtm) REVERT: 0h 218 TRP cc_start: 0.7049 (t-100) cc_final: 0.6809 (t60) REVERT: 0h 220 GLU cc_start: 0.7608 (tp30) cc_final: 0.7045 (mt-10) REVERT: 0h 262 GLU cc_start: 0.6858 (tp30) cc_final: 0.6580 (tp30) REVERT: 0i 30 TYR cc_start: 0.6391 (t80) cc_final: 0.5542 (t80) REVERT: 0i 100 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.5857 (t80) REVERT: 0i 112 MET cc_start: 0.5568 (ppp) cc_final: 0.5305 (ppp) REVERT: 0i 151 ASN cc_start: 0.8336 (t0) cc_final: 0.7949 (t0) REVERT: 0i 186 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: 0i 194 ASP cc_start: 0.8453 (t0) cc_final: 0.7800 (t0) REVERT: 0i 213 GLN cc_start: 0.8322 (tp40) cc_final: 0.7975 (tp40) REVERT: 0i 218 TRP cc_start: 0.7038 (t-100) cc_final: 0.6820 (t-100) REVERT: 0i 220 GLU cc_start: 0.7660 (tp30) cc_final: 0.7329 (mt-10) REVERT: 0i 250 ILE cc_start: 0.7659 (mm) cc_final: 0.7352 (mm) REVERT: 0j 22 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7447 (ttm110) REVERT: 0j 36 TYR cc_start: 0.6422 (p90) cc_final: 0.6097 (p90) REVERT: 0j 40 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6994 (mm-30) REVERT: 0j 54 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: 0j 145 LYS cc_start: 0.7729 (tptp) cc_final: 0.7446 (tptp) REVERT: 0j 151 ASN cc_start: 0.7999 (t0) cc_final: 0.7185 (t0) REVERT: 0j 214 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8067 (ttpp) REVERT: 0j 220 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6927 (mt-10) REVERT: 0k 22 ARG cc_start: 0.7974 (tpp-160) cc_final: 0.7733 (tpp-160) REVERT: 0k 30 TYR cc_start: 0.6870 (t80) cc_final: 0.6097 (t80) REVERT: 0k 44 LEU cc_start: 0.7631 (mt) cc_final: 0.7260 (mt) REVERT: 0k 88 ASN cc_start: 0.6701 (OUTLIER) cc_final: 0.6361 (m-40) REVERT: 0k 112 MET cc_start: 0.5688 (tpt) cc_final: 0.5197 (ttp) REVERT: 0k 140 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8662 (tm-30) REVERT: 0k 145 LYS cc_start: 0.7638 (tptp) cc_final: 0.7332 (tptp) REVERT: 0k 194 ASP cc_start: 0.8511 (t0) cc_final: 0.8174 (t0) REVERT: 0k 218 TRP cc_start: 0.7047 (t-100) cc_final: 0.6809 (t60) REVERT: 0k 220 GLU cc_start: 0.7511 (tp30) cc_final: 0.6998 (mt-10) REVERT: 0k 281 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7616 (mmp80) REVERT: 0l 30 TYR cc_start: 0.6460 (t80) cc_final: 0.5347 (t80) REVERT: 0l 100 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.5934 (t80) REVERT: 0l 140 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8733 (tm-30) REVERT: 0l 186 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: 0l 194 ASP cc_start: 0.8429 (t0) cc_final: 0.7693 (t0) REVERT: 0l 220 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7059 (mt-10) REVERT: 0l 269 ASN cc_start: 0.8186 (t0) cc_final: 0.7933 (t0) outliers start: 107 outliers final: 75 residues processed: 718 average time/residue: 0.3937 time to fit residues: 425.7855 Evaluate side-chains 688 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 597 time to evaluate : 2.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 165 ASP Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 198 VAL Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0a residue 277 LYS Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 88 ASN Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 170 SER Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0c residue 54 GLU Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 54 GLU Chi-restraints excluded: chain 0d residue 88 ASN Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 185 ILE Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 170 SER Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 24 PHE Chi-restraints excluded: chain 0f residue 77 ASN Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 165 ASP Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 223 THR Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 112 MET Chi-restraints excluded: chain 0g residue 124 ASN Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0g residue 267 LYS Chi-restraints excluded: chain 0g residue 277 LYS Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 54 GLU Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 136 LEU Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 277 LYS Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 77 ASN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 124 ASN Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 255 THR Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0j residue 217 VAL Chi-restraints excluded: chain 0j residue 249 GLN Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 88 ASN Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 185 ILE Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 223 THR Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Chi-restraints excluded: chain 0l residue 221 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 135 optimal weight: 0.0060 chunk 198 optimal weight: 0.0370 chunk 298 optimal weight: 0.9990 chunk 275 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 145 optimal weight: 4.9990 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 59 GLN ** 0b 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN ** 0b 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 88 ASN ** 0d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 153 ASN ** 0f 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 26 HIS ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 181 ASN 0i 29 ASN ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 59 GLN ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 59 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.7820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25728 Z= 0.204 Angle : 0.791 10.861 34860 Z= 0.416 Chirality : 0.047 0.275 3756 Planarity : 0.005 0.059 4548 Dihedral : 6.799 36.058 3348 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.99 % Favored : 85.62 % Rotamer: Outliers : 3.14 % Allowed : 27.01 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 3024 helix: 0.67 (0.16), residues: 1080 sheet: -3.61 (0.27), residues: 300 loop : -2.04 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP0g 41 HIS 0.006 0.001 HIS0e 58 PHE 0.037 0.002 PHE0d 137 TYR 0.017 0.001 TYR0e 205 ARG 0.011 0.001 ARG0i 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 623 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0a 22 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7676 (tpp-160) REVERT: 0a 126 MET cc_start: 0.8142 (mtm) cc_final: 0.7579 (mpp) REVERT: 0a 145 LYS cc_start: 0.7553 (tptp) cc_final: 0.7309 (tptp) REVERT: 0a 186 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: 0a 222 MET cc_start: 0.7471 (mmm) cc_final: 0.7031 (tpp) REVERT: 0b 22 ARG cc_start: 0.7524 (ttm110) cc_final: 0.7158 (ttm110) REVERT: 0b 30 TYR cc_start: 0.7171 (t80) cc_final: 0.6706 (t80) REVERT: 0b 44 LEU cc_start: 0.7449 (mt) cc_final: 0.7124 (mt) REVERT: 0b 88 ASN cc_start: 0.6672 (p0) cc_final: 0.6307 (m-40) REVERT: 0b 137 PHE cc_start: 0.7761 (m-80) cc_final: 0.7515 (m-10) REVERT: 0b 145 LYS cc_start: 0.7669 (tptp) cc_final: 0.7356 (tptp) REVERT: 0b 185 ILE cc_start: 0.7677 (pt) cc_final: 0.7115 (pt) REVERT: 0b 194 ASP cc_start: 0.8402 (t0) cc_final: 0.7904 (t0) REVERT: 0b 220 GLU cc_start: 0.7387 (tp30) cc_final: 0.7009 (mt-10) REVERT: 0c 30 TYR cc_start: 0.6326 (t80) cc_final: 0.5444 (t80) REVERT: 0c 100 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.5918 (t80) REVERT: 0c 140 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8633 (tm-30) REVERT: 0c 146 GLU cc_start: 0.7429 (tt0) cc_final: 0.7103 (tt0) REVERT: 0c 153 ASN cc_start: 0.7587 (t0) cc_final: 0.7175 (t0) REVERT: 0c 186 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: 0c 220 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7120 (mt-10) REVERT: 0d 54 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: 0d 88 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6236 (m-40) REVERT: 0d 145 LYS cc_start: 0.7568 (tptp) cc_final: 0.7258 (tptp) REVERT: 0d 153 ASN cc_start: 0.7173 (t0) cc_final: 0.6847 (t0) REVERT: 0d 186 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: 0d 213 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7985 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6816 (mt-10) REVERT: 0d 281 ARG cc_start: 0.7464 (mmp80) cc_final: 0.7202 (mmm-85) REVERT: 0e 22 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7294 (ttm-80) REVERT: 0e 30 TYR cc_start: 0.6668 (t80) cc_final: 0.5953 (t80) REVERT: 0e 37 GLN cc_start: 0.7826 (pp30) cc_final: 0.7367 (tm-30) REVERT: 0e 112 MET cc_start: 0.5736 (tpt) cc_final: 0.5126 (ptm) REVERT: 0e 140 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8691 (tm-30) REVERT: 0e 145 LYS cc_start: 0.7725 (tptp) cc_final: 0.7420 (tptp) REVERT: 0e 153 ASN cc_start: 0.7496 (t0) cc_final: 0.7229 (t0) REVERT: 0e 185 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7632 (pt) REVERT: 0e 218 TRP cc_start: 0.6976 (t-100) cc_final: 0.6640 (t60) REVERT: 0f 18 GLN cc_start: 0.7396 (tt0) cc_final: 0.6996 (tp-100) REVERT: 0f 22 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7247 (ttm170) REVERT: 0f 30 TYR cc_start: 0.6312 (t80) cc_final: 0.5180 (t80) REVERT: 0f 100 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.6185 (t80) REVERT: 0f 140 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8767 (tm-30) REVERT: 0f 146 GLU cc_start: 0.7326 (tt0) cc_final: 0.7018 (tt0) REVERT: 0f 194 ASP cc_start: 0.8390 (t0) cc_final: 0.7805 (t0) REVERT: 0f 209 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8574 (mmtm) REVERT: 0f 220 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7032 (mt-10) REVERT: 0f 225 LEU cc_start: 0.7355 (mt) cc_final: 0.7049 (mp) REVERT: 0g 145 LYS cc_start: 0.7839 (tptp) cc_final: 0.7508 (tptp) REVERT: 0g 186 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6810 (m-80) REVERT: 0g 220 GLU cc_start: 0.7537 (tp30) cc_final: 0.6896 (mt-10) REVERT: 0h 26 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8226 (t-90) REVERT: 0h 30 TYR cc_start: 0.7165 (t80) cc_final: 0.6569 (t80) REVERT: 0h 44 LEU cc_start: 0.7513 (mt) cc_final: 0.7162 (mt) REVERT: 0h 112 MET cc_start: 0.5430 (tpt) cc_final: 0.5066 (ttt) REVERT: 0h 140 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8689 (tm-30) REVERT: 0h 145 LYS cc_start: 0.7878 (tmtt) cc_final: 0.7584 (tptp) REVERT: 0h 194 ASP cc_start: 0.8456 (t0) cc_final: 0.8195 (t0) REVERT: 0h 209 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8155 (mmtm) REVERT: 0h 218 TRP cc_start: 0.6998 (t-100) cc_final: 0.6720 (t60) REVERT: 0h 220 GLU cc_start: 0.7570 (tp30) cc_final: 0.7002 (mt-10) REVERT: 0h 262 GLU cc_start: 0.6801 (tp30) cc_final: 0.6523 (tp30) REVERT: 0i 30 TYR cc_start: 0.6329 (t80) cc_final: 0.5495 (t80) REVERT: 0i 100 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.5958 (t80) REVERT: 0i 112 MET cc_start: 0.5602 (ppp) cc_final: 0.5339 (ppp) REVERT: 0i 186 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: 0i 213 GLN cc_start: 0.8201 (tp40) cc_final: 0.7896 (tp40) REVERT: 0i 250 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7345 (mm) REVERT: 0j 36 TYR cc_start: 0.6168 (p90) cc_final: 0.5810 (p90) REVERT: 0j 54 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: 0j 112 MET cc_start: 0.5306 (ppp) cc_final: 0.4805 (ptt) REVERT: 0j 145 LYS cc_start: 0.7680 (tptp) cc_final: 0.7427 (tptp) REVERT: 0j 151 ASN cc_start: 0.7961 (t0) cc_final: 0.7268 (t0) REVERT: 0j 214 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8184 (ttpp) REVERT: 0j 220 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6832 (tp30) REVERT: 0k 30 TYR cc_start: 0.7162 (t80) cc_final: 0.6467 (t80) REVERT: 0k 44 LEU cc_start: 0.7589 (mt) cc_final: 0.7256 (mt) REVERT: 0k 88 ASN cc_start: 0.6672 (p0) cc_final: 0.6427 (m-40) REVERT: 0k 112 MET cc_start: 0.5668 (tpt) cc_final: 0.5306 (ttt) REVERT: 0k 140 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8688 (tm-30) REVERT: 0k 145 LYS cc_start: 0.7618 (tptp) cc_final: 0.7344 (tptp) REVERT: 0k 194 ASP cc_start: 0.8499 (t0) cc_final: 0.8201 (t0) REVERT: 0k 209 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8157 (mmtm) REVERT: 0k 218 TRP cc_start: 0.7014 (t-100) cc_final: 0.6663 (t60) REVERT: 0l 22 ARG cc_start: 0.7838 (ttm110) cc_final: 0.7513 (ptp-110) REVERT: 0l 30 TYR cc_start: 0.6415 (t80) cc_final: 0.5287 (t80) REVERT: 0l 100 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6278 (t80) REVERT: 0l 140 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8773 (tm-30) REVERT: 0l 186 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: 0l 220 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7029 (mt-10) outliers start: 86 outliers final: 62 residues processed: 678 average time/residue: 0.3892 time to fit residues: 396.7439 Evaluate side-chains 667 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 589 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 124 ASN Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 198 VAL Chi-restraints excluded: chain 0a residue 227 ILE Chi-restraints excluded: chain 0a residue 277 LYS Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 124 ASN Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 277 LYS Chi-restraints excluded: chain 0c residue 54 GLU Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 124 ASN Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 54 GLU Chi-restraints excluded: chain 0d residue 88 ASN Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 124 ASN Chi-restraints excluded: chain 0d residue 185 ILE Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 277 LYS Chi-restraints excluded: chain 0e residue 24 PHE Chi-restraints excluded: chain 0e residue 124 ASN Chi-restraints excluded: chain 0e residue 170 SER Chi-restraints excluded: chain 0e residue 185 ILE Chi-restraints excluded: chain 0e residue 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL Chi-restraints excluded: chain 0f residue 24 PHE Chi-restraints excluded: chain 0f residue 100 TYR Chi-restraints excluded: chain 0f residue 124 ASN Chi-restraints excluded: chain 0f residue 165 ASP Chi-restraints excluded: chain 0f residue 170 SER Chi-restraints excluded: chain 0f residue 186 PHE Chi-restraints excluded: chain 0f residue 198 VAL Chi-restraints excluded: chain 0f residue 223 THR Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 112 MET Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 217 VAL Chi-restraints excluded: chain 0g residue 267 LYS Chi-restraints excluded: chain 0g residue 277 LYS Chi-restraints excluded: chain 0h residue 26 HIS Chi-restraints excluded: chain 0h residue 54 GLU Chi-restraints excluded: chain 0h residue 124 ASN Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0h residue 277 LYS Chi-restraints excluded: chain 0i residue 24 PHE Chi-restraints excluded: chain 0i residue 37 GLN Chi-restraints excluded: chain 0i residue 77 ASN Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 250 ILE Chi-restraints excluded: chain 0i residue 255 THR Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 124 ASN Chi-restraints excluded: chain 0j residue 186 PHE Chi-restraints excluded: chain 0j residue 198 VAL Chi-restraints excluded: chain 0k residue 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 185 ILE Chi-restraints excluded: chain 0k residue 186 PHE Chi-restraints excluded: chain 0k residue 198 VAL Chi-restraints excluded: chain 0k residue 223 THR Chi-restraints excluded: chain 0k residue 277 LYS Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 124 ASN Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 207 VAL Chi-restraints excluded: chain 0l residue 221 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 219 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 99 optimal weight: 0.1980 chunk 244 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 88 ASN ** 0d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 49 ASN ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 211 ASN 0g 37 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 26 HIS ** 0h 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 153 ASN 0l 59 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.239359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.233780 restraints weight = 57227.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.234843 restraints weight = 37635.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.235545 restraints weight = 24882.087| |-----------------------------------------------------------------------------| r_work (final): 0.4623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25728 Z= 0.212 Angle : 0.795 10.495 34860 Z= 0.417 Chirality : 0.047 0.252 3756 Planarity : 0.005 0.089 4548 Dihedral : 6.719 35.822 3348 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.32 % Favored : 85.28 % Rotamer: Outliers : 2.96 % Allowed : 27.74 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 3024 helix: 0.41 (0.16), residues: 1152 sheet: -3.49 (0.42), residues: 132 loop : -2.35 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP0d 41 HIS 0.022 0.001 HIS0h 26 PHE 0.026 0.002 PHE0c 65 TYR 0.021 0.001 TYR0e 205 ARG 0.012 0.001 ARG0g 281 =============================================================================== Job complete usr+sys time: 7431.97 seconds wall clock time: 133 minutes 16.60 seconds (7996.60 seconds total)