Starting phenix.real_space_refine on Mon Sep 30 07:36:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/09_2024/6qx7_4662.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/09_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_4662/09_2024/6qx7_4662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/09_2024/6qx7_4662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/09_2024/6qx7_4662.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/09_2024/6qx7_4662.cif" } 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. Time to flip 36 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25164 Number of models: 1 Model: "" Number of chains: 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 Restraints were copied for chains: 0c, 0a, 0f, 0g, 0d, 0e, 0j, 0k, 0h, 0i, 0l Time building chain proxies: 6.60, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 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: 5.67 Conformation dependent library (CDL) restraints added in 3.1 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: 2.80 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: 7.25 Time building geometry restraints manager: 6.63 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: 0.00 - 2.05: 32337 2.05 - 4.10: 2151 4.10 - 6.14: 264 6.14 - 8.19: 60 8.19 - 10.24: 48 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 Time spend for trying shortcut: 0.00 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: 0.880 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: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 43.680 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.790 ------------------------------------------------------------------------------- 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 : 2.633 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: 0.3860 time to fit residues: 665.9512 Evaluate side-chains 754 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 733 time to evaluate : 3.211 ------------------------------------------------------------------------------- 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: 0.9990 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 272 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 123 ASN 0b 153 ASN ** 0b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 168 GLN 0b 173 GLN 0b 188 HIS ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 89 GLN 0c 123 ASN ** 0c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 168 GLN 0c 173 GLN 0c 188 HIS 0d 26 HIS 0d 89 GLN ** 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 0e 89 GLN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 168 GLN 0e 188 HIS ** 0f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 89 GLN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 167 ASN 0f 168 GLN 0f 173 GLN 0f 188 HIS 0g 26 HIS 0g 89 GLN ** 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 0h 89 GLN ** 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 32 GLN 0i 89 GLN 0i 123 ASN ** 0i 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 168 GLN 0i 188 HIS 0j 26 HIS 0j 123 ASN 0j 153 ASN ** 0j 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 168 GLN 0j 173 GLN 0j 188 HIS ** 0k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS 0k 123 ASN 0k 153 ASN 0k 167 ASN 0k 168 GLN 0k 188 HIS ** 0l 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 123 ASN ** 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: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25728 Z= 0.260 Angle : 0.847 7.378 34860 Z= 0.467 Chirality : 0.050 0.182 3756 Planarity : 0.005 0.049 4548 Dihedral : 9.182 59.775 3392 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 1.59 % Allowed : 15.31 % Favored : 83.10 % Rotamer: Outliers : 4.24 % Allowed : 13.56 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.06 % 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: -3.65 (0.14), residues: 3024 helix: -1.75 (0.13), residues: 1128 sheet: -3.33 (0.25), residues: 372 loop : -2.71 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP0g 41 HIS 0.009 0.001 HIS0k 26 PHE 0.029 0.002 PHE0g 24 TYR 0.028 0.002 TYR0g 36 ARG 0.005 0.001 ARG0j 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 925 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 809 time to evaluate : 2.618 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: 0.8132 (mm110) cc_final: 0.7599 (tp40) REVERT: 0a 36 TYR cc_start: 0.6779 (p90) cc_final: 0.6384 (p90) REVERT: 0a 40 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6061 (mt-10) REVERT: 0a 100 TYR cc_start: 0.5165 (OUTLIER) cc_final: 0.4348 (t80) REVERT: 0a 126 MET cc_start: 0.8423 (mtt) cc_final: 0.8002 (mtt) REVERT: 0a 141 LEU cc_start: 0.8611 (tp) cc_final: 0.8409 (mt) REVERT: 0a 145 LYS cc_start: 0.7926 (tptt) cc_final: 0.7619 (tptp) REVERT: 0a 152 GLN cc_start: 0.8420 (mt0) cc_final: 0.8184 (mt0) REVERT: 0a 153 ASN cc_start: 0.7442 (t0) cc_final: 0.7158 (t0) REVERT: 0a 213 GLN cc_start: 0.7932 (tp40) cc_final: 0.7680 (tm-30) REVERT: 0a 281 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7391 (mmm-85) REVERT: 0b 18 GLN cc_start: 0.8017 (mm110) cc_final: 0.7530 (tt0) REVERT: 0b 30 TYR cc_start: 0.7035 (t80) cc_final: 0.6814 (t80) REVERT: 0b 44 LEU cc_start: 0.7533 (mt) cc_final: 0.7273 (mt) REVERT: 0b 112 MET cc_start: 0.5924 (tpt) cc_final: 0.5464 (ttp) REVERT: 0b 126 MET cc_start: 0.8473 (mtt) cc_final: 0.7665 (mtt) REVERT: 0b 145 LYS cc_start: 0.7871 (tmtt) cc_final: 0.7670 (tptp) REVERT: 0b 152 GLN cc_start: 0.8431 (mt0) cc_final: 0.8221 (mt0) REVERT: 0b 213 GLN cc_start: 0.7892 (tp40) cc_final: 0.7535 (tm-30) REVERT: 0b 225 LEU cc_start: 0.8007 (mt) cc_final: 0.7234 (mt) REVERT: 0b 277 LYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5802 (mmmt) REVERT: 0b 281 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7832 (mmp80) REVERT: 0c 20 ARG cc_start: 0.7283 (mmm160) cc_final: 0.7034 (mmm160) REVERT: 0c 30 TYR cc_start: 0.6574 (t80) cc_final: 0.6146 (t80) REVERT: 0c 40 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6207 (mt-10) REVERT: 0c 100 TYR cc_start: 0.5290 (OUTLIER) cc_final: 0.4584 (t80) REVERT: 0c 126 MET cc_start: 0.8315 (mtt) cc_final: 0.7735 (mtt) REVERT: 0c 194 ASP cc_start: 0.7044 (t0) cc_final: 0.6334 (t0) REVERT: 0c 277 LYS cc_start: 0.6038 (OUTLIER) cc_final: 0.5805 (mmmt) REVERT: 0c 282 TYR cc_start: 0.5928 (t80) cc_final: 0.5476 (t80) REVERT: 0d 18 GLN cc_start: 0.8169 (mm110) cc_final: 0.7879 (tp40) REVERT: 0d 36 TYR cc_start: 0.6850 (p90) cc_final: 0.6612 (p90) REVERT: 0d 100 TYR cc_start: 0.4895 (OUTLIER) cc_final: 0.4049 (t80) REVERT: 0d 112 MET cc_start: 0.5659 (tpt) cc_final: 0.5359 (ttp) REVERT: 0d 126 MET cc_start: 0.8389 (mtt) cc_final: 0.7650 (mtt) REVERT: 0d 213 GLN cc_start: 0.7837 (tp40) cc_final: 0.7551 (tp40) REVERT: 0d 217 VAL cc_start: 0.8001 (t) cc_final: 0.7793 (t) REVERT: 0d 221 MET cc_start: 0.7419 (tpp) cc_final: 0.7156 (tpp) REVERT: 0d 277 LYS cc_start: 0.5825 (OUTLIER) cc_final: 0.5512 (mmmt) REVERT: 0d 281 ARG cc_start: 0.7645 (mmm160) cc_final: 0.7209 (mmm-85) REVERT: 0e 18 GLN cc_start: 0.8196 (mm110) cc_final: 0.7233 (tt0) REVERT: 0e 30 TYR cc_start: 0.6462 (t80) cc_final: 0.5927 (t80) REVERT: 0e 112 MET cc_start: 0.5844 (tpt) cc_final: 0.5587 (ptm) REVERT: 0e 123 ASN cc_start: 0.8368 (t0) cc_final: 0.8005 (t0) REVERT: 0e 153 ASN cc_start: 0.7648 (t0) cc_final: 0.7418 (t0) REVERT: 0e 193 SER cc_start: 0.6275 (p) cc_final: 0.6040 (t) REVERT: 0e 213 GLN cc_start: 0.7842 (tp40) cc_final: 0.7401 (tm-30) REVERT: 0e 217 VAL cc_start: 0.8060 (t) cc_final: 0.7813 (t) REVERT: 0f 20 ARG cc_start: 0.7218 (mmm160) cc_final: 0.6964 (mmm160) REVERT: 0f 30 TYR cc_start: 0.6480 (t80) cc_final: 0.5511 (t80) REVERT: 0f 40 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6249 (mt-10) REVERT: 0f 140 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8568 (tm-30) REVERT: 0f 141 LEU cc_start: 0.8738 (tp) cc_final: 0.8537 (mt) REVERT: 0f 205 TYR cc_start: 0.8643 (t80) cc_final: 0.7940 (t80) REVERT: 0f 281 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7748 (mmm-85) REVERT: 0g 18 GLN cc_start: 0.8180 (mm110) cc_final: 0.7909 (tp40) REVERT: 0g 100 TYR cc_start: 0.4867 (OUTLIER) cc_final: 0.4005 (t80) REVERT: 0g 140 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8441 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8637 (tp) cc_final: 0.8270 (mt) REVERT: 0g 213 GLN cc_start: 0.7881 (tp40) cc_final: 0.7639 (tp40) REVERT: 0g 217 VAL cc_start: 0.8003 (t) cc_final: 0.7632 (t) REVERT: 0g 221 MET cc_start: 0.7564 (tpp) cc_final: 0.7300 (tpp) REVERT: 0g 281 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7311 (mmm-85) REVERT: 0g 282 TYR cc_start: 0.5896 (t80) cc_final: 0.5528 (t80) REVERT: 0h 44 LEU cc_start: 0.7449 (mt) cc_final: 0.7174 (mt) REVERT: 0h 112 MET cc_start: 0.5886 (tpt) cc_final: 0.5479 (ttp) REVERT: 0h 126 MET cc_start: 0.8657 (mtt) cc_final: 0.8033 (mtp) REVERT: 0h 193 SER cc_start: 0.6424 (p) cc_final: 0.6208 (t) REVERT: 0h 194 ASP cc_start: 0.7398 (t0) cc_final: 0.6551 (t0) REVERT: 0h 213 GLN cc_start: 0.7851 (tp40) cc_final: 0.7531 (tm-30) REVERT: 0h 225 LEU cc_start: 0.7991 (mt) cc_final: 0.7223 (mt) REVERT: 0h 281 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7820 (mmp80) REVERT: 0i 18 GLN cc_start: 0.7335 (mt0) cc_final: 0.7099 (tt0) REVERT: 0i 22 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7932 (ttm110) REVERT: 0i 126 MET cc_start: 0.8644 (mtt) cc_final: 0.8312 (mtt) REVERT: 0i 140 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8565 (tm-30) REVERT: 0i 141 LEU cc_start: 0.8812 (tp) cc_final: 0.8504 (mt) REVERT: 0i 194 ASP cc_start: 0.7075 (t0) cc_final: 0.6095 (t0) REVERT: 0i 213 GLN cc_start: 0.8027 (tp40) cc_final: 0.7817 (tp40) REVERT: 0i 282 TYR cc_start: 0.6016 (t80) cc_final: 0.5572 (t80) REVERT: 0j 18 GLN cc_start: 0.8186 (mm110) cc_final: 0.7943 (tp40) REVERT: 0j 36 TYR cc_start: 0.6720 (p90) cc_final: 0.6419 (p90) REVERT: 0j 100 TYR cc_start: 0.4906 (OUTLIER) cc_final: 0.4095 (t80) REVERT: 0j 126 MET cc_start: 0.8123 (mtt) cc_final: 0.7778 (mtt) REVERT: 0j 196 ILE cc_start: 0.7978 (pt) cc_final: 0.7444 (tt) REVERT: 0j 213 GLN cc_start: 0.7856 (tp40) cc_final: 0.7601 (tp40) REVERT: 0j 217 VAL cc_start: 0.8013 (t) cc_final: 0.7812 (t) REVERT: 0j 221 MET cc_start: 0.7561 (tpp) cc_final: 0.7283 (tpp) REVERT: 0j 281 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7463 (mmm-85) REVERT: 0k 18 GLN cc_start: 0.8021 (mm110) cc_final: 0.7152 (tt0) REVERT: 0k 30 TYR cc_start: 0.6533 (t80) cc_final: 0.6101 (t80) REVERT: 0k 44 LEU cc_start: 0.7544 (mt) cc_final: 0.7242 (mt) REVERT: 0k 112 MET cc_start: 0.5837 (tpt) cc_final: 0.5381 (ttp) REVERT: 0k 152 GLN cc_start: 0.8408 (mt0) cc_final: 0.8207 (mt0) REVERT: 0k 186 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: 0k 213 GLN cc_start: 0.7890 (tp40) cc_final: 0.7469 (tm-30) REVERT: 0k 225 LEU cc_start: 0.7976 (mt) cc_final: 0.7188 (mt) REVERT: 0k 277 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5941 (mmmt) REVERT: 0k 281 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7790 (mmp80) REVERT: 0l 18 GLN cc_start: 0.7168 (mt0) cc_final: 0.6890 (mt0) REVERT: 0l 124 ASN cc_start: 0.7714 (p0) cc_final: 0.7470 (p0) REVERT: 0l 194 ASP cc_start: 0.6867 (t0) cc_final: 0.6432 (t0) REVERT: 0l 205 TYR cc_start: 0.8807 (t80) cc_final: 0.8494 (t80) REVERT: 0l 213 GLN cc_start: 0.8154 (tp40) cc_final: 0.7232 (tm-30) REVERT: 0l 214 LYS cc_start: 0.8024 (tttm) cc_final: 0.7766 (tttm) outliers start: 116 outliers final: 59 residues processed: 892 average time/residue: 0.4121 time to fit residues: 543.8618 Evaluate side-chains 759 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 690 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 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 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 170 SER Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 277 LYS 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 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 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 133 THR 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 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 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 278 VAL Chi-restraints excluded: chain 0h residue 12 ILE Chi-restraints excluded: chain 0h residue 25 ILE Chi-restraints excluded: chain 0h residue 33 SER 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 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 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 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 170 SER Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 75 optimal weight: 0.0970 chunk 272 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 243 optimal weight: 0.0870 chunk 270 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 167 ASN ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 151 ASN 0b 167 ASN 0c 32 GLN ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 167 ASN 0c 173 GLN ** 0d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 167 ASN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 167 ASN 0e 173 GLN 0f 32 GLN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 167 ASN ** 0h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN 0h 167 ASN ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 167 ASN 0i 173 GLN 0j 59 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 167 ASN 0k 151 ASN 0l 32 GLN ** 0l 37 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 167 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.5153 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= 0.216 Angle : 0.773 7.467 34860 Z= 0.424 Chirality : 0.047 0.245 3756 Planarity : 0.005 0.053 4548 Dihedral : 8.304 56.143 3360 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.79 % Allowed : 16.01 % Favored : 83.20 % Rotamer: Outliers : 3.44 % Allowed : 13.60 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -0.84 (0.15), residues: 1092 sheet: -3.79 (0.26), residues: 300 loop : -2.37 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP0a 41 HIS 0.003 0.000 HIS0h 58 PHE 0.029 0.002 PHE0a 24 TYR 0.024 0.002 TYR0f 205 ARG 0.006 0.000 ARG0i 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 832 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 738 time to evaluate : 2.781 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: 0a 18 GLN cc_start: 0.8069 (mm110) cc_final: 0.7642 (tp40) REVERT: 0a 42 GLU cc_start: 0.6149 (tm-30) cc_final: 0.5812 (tm-30) REVERT: 0a 100 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.4673 (t80) REVERT: 0a 140 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8524 (tm-30) REVERT: 0a 145 LYS cc_start: 0.7841 (tptt) cc_final: 0.7592 (tptp) REVERT: 0a 151 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7906 (t0) REVERT: 0a 153 ASN cc_start: 0.7390 (t0) cc_final: 0.7019 (t0) REVERT: 0a 186 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: 0a 213 GLN cc_start: 0.7911 (tp40) cc_final: 0.7641 (tp40) REVERT: 0a 249 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7491 (mm-40) REVERT: 0a 281 ARG cc_start: 0.7516 (mmm160) cc_final: 0.6958 (mmm-85) REVERT: 0b 30 TYR cc_start: 0.7237 (t80) cc_final: 0.6842 (t80) REVERT: 0b 44 LEU cc_start: 0.7457 (mt) cc_final: 0.7187 (mt) REVERT: 0b 116 ASP cc_start: 0.4781 (t0) cc_final: 0.4548 (t70) REVERT: 0b 145 LYS cc_start: 0.7887 (tmtt) cc_final: 0.7632 (tptp) REVERT: 0b 153 ASN cc_start: 0.7571 (t0) cc_final: 0.7244 (t0) REVERT: 0b 186 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: 0b 194 ASP cc_start: 0.8041 (t0) cc_final: 0.7283 (t0) REVERT: 0b 213 GLN cc_start: 0.7885 (tp40) cc_final: 0.7561 (tm-30) REVERT: 0b 221 MET cc_start: 0.7561 (tpp) cc_final: 0.7249 (tpp) REVERT: 0b 228 LYS cc_start: 0.6326 (tppt) cc_final: 0.6120 (tppt) REVERT: 0b 277 LYS cc_start: 0.5993 (OUTLIER) cc_final: 0.5592 (mmmt) REVERT: 0c 32 GLN cc_start: 0.8051 (mt0) cc_final: 0.7510 (mt0) REVERT: 0c 36 TYR cc_start: 0.6598 (p90) cc_final: 0.6362 (p90) REVERT: 0c 100 TYR cc_start: 0.5444 (OUTLIER) cc_final: 0.4790 (t80) REVERT: 0c 140 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8552 (tm-30) REVERT: 0c 145 LYS cc_start: 0.7725 (tptp) cc_final: 0.7486 (tptp) REVERT: 0c 277 LYS cc_start: 0.5784 (OUTLIER) cc_final: 0.5339 (mmmt) REVERT: 0d 18 GLN cc_start: 0.7943 (mm110) cc_final: 0.7571 (tp40) REVERT: 0d 22 ARG cc_start: 0.7496 (mmt90) cc_final: 0.7234 (mmt180) REVERT: 0d 40 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6616 (mm-30) REVERT: 0d 100 TYR cc_start: 0.5366 (OUTLIER) cc_final: 0.4694 (t80) REVERT: 0d 151 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7859 (t0) REVERT: 0d 186 PHE cc_start: 0.7504 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: 0d 213 GLN cc_start: 0.7928 (tp40) cc_final: 0.7722 (tp40) REVERT: 0d 217 VAL cc_start: 0.8037 (t) cc_final: 0.7723 (t) REVERT: 0d 249 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7315 (mm-40) REVERT: 0d 277 LYS cc_start: 0.6154 (OUTLIER) cc_final: 0.5805 (mmmt) REVERT: 0e 30 TYR cc_start: 0.6551 (t80) cc_final: 0.6002 (t80) REVERT: 0e 141 LEU cc_start: 0.8787 (mt) cc_final: 0.8570 (mt) REVERT: 0e 186 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: 0e 213 GLN cc_start: 0.7946 (tp40) cc_final: 0.7575 (tm-30) REVERT: 0e 217 VAL cc_start: 0.7998 (t) cc_final: 0.7713 (t) REVERT: 0e 221 MET cc_start: 0.7629 (tpp) cc_final: 0.7111 (tpp) REVERT: 0e 225 LEU cc_start: 0.7936 (mt) cc_final: 0.7380 (mt) REVERT: 0e 249 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7487 (mm-40) REVERT: 0f 30 TYR cc_start: 0.6639 (t80) cc_final: 0.6040 (t80) REVERT: 0f 140 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8667 (tm-30) REVERT: 0f 141 LEU cc_start: 0.8774 (tp) cc_final: 0.8558 (mt) REVERT: 0f 186 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: 0f 193 SER cc_start: 0.6742 (p) cc_final: 0.6395 (t) REVERT: 0f 194 ASP cc_start: 0.7577 (t0) cc_final: 0.6647 (t0) REVERT: 0f 205 TYR cc_start: 0.8727 (t80) cc_final: 0.8209 (t80) REVERT: 0g 18 GLN cc_start: 0.8000 (mm110) cc_final: 0.7583 (tp40) REVERT: 0g 22 ARG cc_start: 0.7555 (mmt90) cc_final: 0.7311 (mmt180) REVERT: 0g 40 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6511 (mm-30) REVERT: 0g 100 TYR cc_start: 0.5352 (OUTLIER) cc_final: 0.4593 (t80) REVERT: 0g 140 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8499 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8660 (tp) cc_final: 0.8279 (mt) REVERT: 0g 186 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: 0g 194 ASP cc_start: 0.8217 (t0) cc_final: 0.7831 (t0) REVERT: 0g 249 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7708 (mm-40) REVERT: 0g 281 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7361 (mmm-85) REVERT: 0h 30 TYR cc_start: 0.6889 (t80) cc_final: 0.6394 (t80) REVERT: 0h 44 LEU cc_start: 0.7503 (mt) cc_final: 0.7209 (mt) REVERT: 0h 116 ASP cc_start: 0.4490 (t0) cc_final: 0.4170 (t70) REVERT: 0h 153 ASN cc_start: 0.7471 (t0) cc_final: 0.7202 (t0) REVERT: 0h 186 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: 0h 194 ASP cc_start: 0.8131 (t0) cc_final: 0.7272 (t0) REVERT: 0h 213 GLN cc_start: 0.7905 (tp40) cc_final: 0.7564 (tm-30) REVERT: 0h 277 LYS cc_start: 0.6190 (mmtm) cc_final: 0.5870 (mmmt) REVERT: 0i 40 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6089 (mt-10) REVERT: 0i 141 LEU cc_start: 0.8803 (tp) cc_final: 0.8505 (mt) REVERT: 0i 151 ASN cc_start: 0.8142 (t0) cc_final: 0.7791 (t0) REVERT: 0i 194 ASP cc_start: 0.8200 (t0) cc_final: 0.7400 (t0) REVERT: 0j 18 GLN cc_start: 0.7975 (mm110) cc_final: 0.7535 (tp40) REVERT: 0j 22 ARG cc_start: 0.7489 (mmt90) cc_final: 0.7219 (mmt180) REVERT: 0j 37 GLN cc_start: 0.6975 (tt0) cc_final: 0.6745 (tt0) REVERT: 0j 40 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6389 (mm-30) REVERT: 0j 100 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4706 (t80) REVERT: 0j 186 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6576 (m-80) REVERT: 0j 193 SER cc_start: 0.6593 (p) cc_final: 0.6312 (t) REVERT: 0j 249 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7388 (mm-40) REVERT: 0k 30 TYR cc_start: 0.6688 (t80) cc_final: 0.6138 (t80) REVERT: 0k 44 LEU cc_start: 0.7525 (mt) cc_final: 0.7196 (mt) REVERT: 0k 145 LYS cc_start: 0.7560 (tptp) cc_final: 0.7282 (tptp) REVERT: 0k 153 ASN cc_start: 0.7584 (t0) cc_final: 0.7238 (t0) REVERT: 0k 186 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: 0k 194 ASP cc_start: 0.7949 (t0) cc_final: 0.7067 (t0) REVERT: 0k 213 GLN cc_start: 0.7892 (tp40) cc_final: 0.7476 (tm-30) REVERT: 0l 32 GLN cc_start: 0.7931 (mt0) cc_final: 0.7666 (mt0) REVERT: 0l 40 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6030 (mt-10) REVERT: 0l 213 GLN cc_start: 0.8107 (tp40) cc_final: 0.7393 (tm-30) REVERT: 0l 262 GLU cc_start: 0.6862 (tp30) cc_final: 0.6616 (tp30) outliers start: 94 outliers final: 39 residues processed: 808 average time/residue: 0.3946 time to fit residues: 478.2906 Evaluate side-chains 710 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 652 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 151 ASN Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 217 VAL Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 100 TYR 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 150 VAL Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 277 LYS Chi-restraints excluded: chain 0c residue 278 VAL Chi-restraints excluded: chain 0d residue 60 PHE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 151 ASN 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 186 PHE Chi-restraints excluded: chain 0e residue 198 VAL 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 54 GLU Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 223 THR Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 150 VAL 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 33 SER Chi-restraints excluded: chain 0i residue 100 TYR 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 278 VAL Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR Chi-restraints excluded: chain 0j residue 170 SER Chi-restraints excluded: chain 0j residue 186 PHE 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 100 TYR 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 223 THR 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: 3.9990 chunk 141 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 21 ASN 0c 58 HIS ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 59 GLN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 26 HIS ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 21 ASN 0f 58 HIS ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 173 GLN 0g 59 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 26 HIS ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 58 HIS ** 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 58 HIS ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 59 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 151 ASN ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 21 ASN ** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.5815 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= 0.217 Angle : 0.752 8.298 34860 Z= 0.410 Chirality : 0.046 0.140 3756 Planarity : 0.005 0.056 4548 Dihedral : 7.625 36.196 3348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.31 % Favored : 84.26 % Rotamer: Outliers : 4.20 % Allowed : 15.79 % Favored : 80.01 % 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: -2.39 (0.16), residues: 3024 helix: -0.21 (0.16), residues: 1080 sheet: -3.70 (0.26), residues: 300 loop : -2.16 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP0d 41 HIS 0.006 0.001 HIS0h 58 PHE 0.032 0.002 PHE0c 199 TYR 0.024 0.002 TYR0i 30 ARG 0.005 0.001 ARG0i 281 *********************** 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 825 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 710 time to evaluate : 2.938 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: 0a 40 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6830 (mm-30) REVERT: 0a 100 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.5307 (t80) REVERT: 0a 140 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8539 (tm-30) REVERT: 0a 151 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8125 (t0) REVERT: 0a 152 GLN cc_start: 0.8310 (mt0) cc_final: 0.8066 (mt0) REVERT: 0a 186 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: 0a 194 ASP cc_start: 0.7866 (t0) cc_final: 0.7635 (t0) REVERT: 0a 213 GLN cc_start: 0.7913 (tp40) cc_final: 0.7647 (tp40) REVERT: 0b 30 TYR cc_start: 0.7251 (t80) cc_final: 0.6876 (t80) REVERT: 0b 44 LEU cc_start: 0.7565 (mt) cc_final: 0.7191 (mt) REVERT: 0b 153 ASN cc_start: 0.7434 (t0) cc_final: 0.7104 (t0) REVERT: 0b 186 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: 0b 194 ASP cc_start: 0.8275 (t0) cc_final: 0.7534 (t0) REVERT: 0c 100 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5155 (t80) REVERT: 0c 128 PHE cc_start: 0.7193 (m-80) cc_final: 0.6969 (m-80) REVERT: 0c 140 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8633 (tm-30) REVERT: 0c 277 LYS cc_start: 0.5866 (OUTLIER) cc_final: 0.5326 (mmmt) REVERT: 0d 100 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.5090 (t80) REVERT: 0d 112 MET cc_start: 0.5534 (tpt) cc_final: 0.5317 (ttp) REVERT: 0d 186 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: 0d 217 VAL cc_start: 0.7920 (t) cc_final: 0.7584 (t) REVERT: 0e 18 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7323 (tp-100) REVERT: 0e 22 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7674 (ttp-170) REVERT: 0e 25 ILE cc_start: 0.7786 (tp) cc_final: 0.7553 (tp) REVERT: 0e 30 TYR cc_start: 0.6682 (t80) cc_final: 0.6166 (t80) REVERT: 0e 32 GLN cc_start: 0.7431 (mt0) cc_final: 0.7145 (mt0) REVERT: 0e 36 TYR cc_start: 0.6756 (p90) cc_final: 0.6442 (p90) REVERT: 0e 153 ASN cc_start: 0.7492 (t0) cc_final: 0.7115 (t0) REVERT: 0e 186 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: 0e 213 GLN cc_start: 0.8120 (tp40) cc_final: 0.7677 (tm-30) REVERT: 0e 217 VAL cc_start: 0.7909 (t) cc_final: 0.7538 (t) REVERT: 0e 220 GLU cc_start: 0.7570 (tp30) cc_final: 0.6896 (mt-10) REVERT: 0e 221 MET cc_start: 0.7449 (tpp) cc_final: 0.7185 (tpp) REVERT: 0e 225 LEU cc_start: 0.7967 (mt) cc_final: 0.7490 (mt) REVERT: 0f 30 TYR cc_start: 0.6844 (t80) cc_final: 0.6134 (t80) REVERT: 0f 194 ASP cc_start: 0.7950 (t0) cc_final: 0.7177 (t0) REVERT: 0g 18 GLN cc_start: 0.7686 (mm110) cc_final: 0.7477 (tp40) REVERT: 0g 32 GLN cc_start: 0.7404 (mt0) cc_final: 0.7185 (mt0) REVERT: 0g 40 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6689 (mm-30) REVERT: 0g 100 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.5124 (t80) REVERT: 0g 140 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8561 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8803 (tp) cc_final: 0.8589 (mt) REVERT: 0g 186 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: 0g 194 ASP cc_start: 0.8459 (t0) cc_final: 0.8049 (t0) REVERT: 0g 213 GLN cc_start: 0.8166 (tp40) cc_final: 0.7908 (tp40) REVERT: 0h 18 GLN cc_start: 0.7891 (tp40) cc_final: 0.6893 (tp-100) REVERT: 0h 30 TYR cc_start: 0.6996 (t80) cc_final: 0.6494 (t80) REVERT: 0h 44 LEU cc_start: 0.7571 (mt) cc_final: 0.7302 (mt) REVERT: 0h 186 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: 0h 194 ASP cc_start: 0.8367 (t0) cc_final: 0.7699 (t0) REVERT: 0h 213 GLN cc_start: 0.8068 (tp40) cc_final: 0.7776 (tm-30) REVERT: 0h 218 TRP cc_start: 0.7272 (t-100) cc_final: 0.6984 (t-100) REVERT: 0h 277 LYS cc_start: 0.6370 (mmtm) cc_final: 0.6084 (mmmt) REVERT: 0i 30 TYR cc_start: 0.6027 (t80) cc_final: 0.5105 (t80) REVERT: 0i 40 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6171 (mt-10) REVERT: 0i 126 MET cc_start: 0.8643 (mtp) cc_final: 0.8433 (mtp) REVERT: 0i 151 ASN cc_start: 0.8143 (t0) cc_final: 0.7747 (t0) REVERT: 0i 194 ASP cc_start: 0.8433 (t0) cc_final: 0.7745 (t0) REVERT: 0i 250 ILE cc_start: 0.7601 (mm) cc_final: 0.7212 (mm) REVERT: 0j 18 GLN cc_start: 0.7855 (mm110) cc_final: 0.7557 (tp40) REVERT: 0j 22 ARG cc_start: 0.7333 (mmt90) cc_final: 0.7020 (mmt180) REVERT: 0j 40 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6656 (mm-30) REVERT: 0j 100 TYR cc_start: 0.5777 (OUTLIER) cc_final: 0.4961 (t80) REVERT: 0j 186 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: 0k 18 GLN cc_start: 0.7635 (tp-100) cc_final: 0.7007 (tp-100) REVERT: 0k 22 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.7506 (ttp-170) REVERT: 0k 30 TYR cc_start: 0.6751 (t80) cc_final: 0.6236 (t80) REVERT: 0k 44 LEU cc_start: 0.7566 (mt) cc_final: 0.7257 (mt) REVERT: 0k 186 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: 0k 197 GLU cc_start: 0.7961 (pt0) cc_final: 0.7557 (pt0) REVERT: 0k 221 MET cc_start: 0.7606 (tpp) cc_final: 0.7397 (tpp) REVERT: 0k 249 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7663 (mm-40) REVERT: 0l 18 GLN cc_start: 0.7110 (mt0) cc_final: 0.6894 (mm-40) REVERT: 0l 40 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6152 (mt-10) REVERT: 0l 213 GLN cc_start: 0.8149 (tp40) cc_final: 0.7443 (tm-30) REVERT: 0l 214 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7753 (ttpp) outliers start: 115 outliers final: 58 residues processed: 812 average time/residue: 0.3905 time to fit residues: 480.8618 Evaluate side-chains 718 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 645 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 151 ASN 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 33 SER Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 54 GLU Chi-restraints excluded: chain 0b residue 100 TYR Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 223 THR 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 170 SER Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 277 LYS Chi-restraints excluded: chain 0d residue 54 GLU Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 170 SER 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 170 SER 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 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 278 VAL Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0h residue 26 HIS Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 100 TYR 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 278 VAL Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 100 TYR 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 278 VAL Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR 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 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 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 100 TYR 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 217 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.0670 chunk 164 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 173 GLN ** 0b 37 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 173 GLN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 173 GLN ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 173 GLN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 173 GLN 0g 18 GLN 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 173 GLN 0h 26 HIS ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 58 HIS ** 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 153 ASN ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 59 GLN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 168 GLN ** 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 21 ASN 0l 59 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 173 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25728 Z= 0.203 Angle : 0.735 8.035 34860 Z= 0.402 Chirality : 0.046 0.137 3756 Planarity : 0.005 0.057 4548 Dihedral : 7.391 36.077 3348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.31 % Favored : 84.29 % Rotamer: Outliers : 3.47 % Allowed : 18.90 % Favored : 77.63 % 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: -2.10 (0.16), residues: 3024 helix: 0.09 (0.16), residues: 1080 sheet: -3.55 (0.27), residues: 300 loop : -2.03 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP0g 41 HIS 0.018 0.001 HIS0h 26 PHE 0.028 0.002 PHE0j 199 TYR 0.028 0.002 TYR0a 205 ARG 0.006 0.000 ARG0i 281 *********************** 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 779 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 684 time to evaluate : 2.918 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: 0a 18 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7307 (tp-100) REVERT: 0a 22 ARG cc_start: 0.7681 (tpp-160) cc_final: 0.7416 (tpp-160) REVERT: 0a 40 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6594 (mm-30) REVERT: 0a 100 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5643 (t80) REVERT: 0a 140 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8552 (tm-30) REVERT: 0a 145 LYS cc_start: 0.7757 (tptt) cc_final: 0.7487 (tptp) REVERT: 0a 152 GLN cc_start: 0.8318 (mt0) cc_final: 0.8064 (mt0) REVERT: 0a 186 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: 0a 194 ASP cc_start: 0.7942 (t0) cc_final: 0.7739 (t0) REVERT: 0a 220 GLU cc_start: 0.7574 (tp30) cc_final: 0.6781 (mt-10) REVERT: 0a 281 ARG cc_start: 0.7564 (mmp80) cc_final: 0.6981 (mmm-85) REVERT: 0b 30 TYR cc_start: 0.7320 (t80) cc_final: 0.6874 (t80) REVERT: 0b 44 LEU cc_start: 0.7532 (mt) cc_final: 0.7184 (mt) REVERT: 0b 145 LYS cc_start: 0.7799 (tmtt) cc_final: 0.7567 (tptp) REVERT: 0b 186 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: 0b 194 ASP cc_start: 0.8535 (t0) cc_final: 0.7778 (t0) REVERT: 0b 220 GLU cc_start: 0.7436 (tp30) cc_final: 0.6788 (mt-10) REVERT: 0c 100 TYR cc_start: 0.6176 (OUTLIER) cc_final: 0.5422 (t80) REVERT: 0c 140 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8579 (tm-30) REVERT: 0c 141 LEU cc_start: 0.9037 (mt) cc_final: 0.8614 (mt) REVERT: 0c 213 GLN cc_start: 0.8269 (tp40) cc_final: 0.7418 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6856 (mt-10) REVERT: 0c 277 LYS cc_start: 0.5901 (OUTLIER) cc_final: 0.5415 (mmmt) REVERT: 0d 100 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.5470 (t80) REVERT: 0d 151 ASN cc_start: 0.7999 (t0) cc_final: 0.7248 (t0) REVERT: 0d 186 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: 0d 213 GLN cc_start: 0.8224 (tp40) cc_final: 0.7695 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7641 (mm-30) cc_final: 0.6974 (mt-10) REVERT: 0e 18 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7498 (tp-100) REVERT: 0e 22 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7759 (tpp-160) REVERT: 0e 30 TYR cc_start: 0.6698 (t80) cc_final: 0.6144 (t80) REVERT: 0e 37 GLN cc_start: 0.8345 (pp30) cc_final: 0.7536 (tt0) REVERT: 0e 186 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: 0e 194 ASP cc_start: 0.8419 (t70) cc_final: 0.7651 (t0) REVERT: 0e 197 GLU cc_start: 0.7881 (pt0) cc_final: 0.7610 (pt0) REVERT: 0e 213 GLN cc_start: 0.8075 (tp40) cc_final: 0.7691 (tm-30) REVERT: 0e 217 VAL cc_start: 0.7900 (t) cc_final: 0.7508 (t) REVERT: 0e 220 GLU cc_start: 0.7520 (tp30) cc_final: 0.6876 (mt-10) REVERT: 0e 221 MET cc_start: 0.7497 (tpp) cc_final: 0.7183 (tpp) REVERT: 0e 225 LEU cc_start: 0.7952 (mt) cc_final: 0.7529 (mt) REVERT: 0f 30 TYR cc_start: 0.6913 (t80) cc_final: 0.6192 (t80) REVERT: 0f 112 MET cc_start: 0.6389 (ptm) cc_final: 0.6157 (ppp) REVERT: 0f 126 MET cc_start: 0.8625 (mtt) cc_final: 0.8300 (mtp) REVERT: 0f 220 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6803 (mt-10) REVERT: 0f 281 ARG cc_start: 0.7719 (mmp80) cc_final: 0.7441 (mmp80) REVERT: 0g 18 GLN cc_start: 0.7511 (mm-40) cc_final: 0.6897 (tp-100) REVERT: 0g 100 TYR cc_start: 0.6150 (OUTLIER) cc_final: 0.5494 (t80) REVERT: 0g 137 PHE cc_start: 0.7996 (m-80) cc_final: 0.7789 (m-80) REVERT: 0g 140 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8572 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8904 (tp) cc_final: 0.8641 (mt) REVERT: 0g 194 ASP cc_start: 0.8544 (t0) cc_final: 0.8068 (t0) REVERT: 0g 197 GLU cc_start: 0.7963 (pt0) cc_final: 0.7758 (pt0) REVERT: 0g 213 GLN cc_start: 0.8184 (tp40) cc_final: 0.7676 (tm-30) REVERT: 0g 220 GLU cc_start: 0.7788 (tp30) cc_final: 0.6747 (mt-10) REVERT: 0h 18 GLN cc_start: 0.7638 (tp40) cc_final: 0.7426 (tp-100) REVERT: 0h 22 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.7715 (tpp-160) REVERT: 0h 30 TYR cc_start: 0.7081 (t80) cc_final: 0.6588 (t80) REVERT: 0h 44 LEU cc_start: 0.7653 (mt) cc_final: 0.7228 (mt) REVERT: 0h 112 MET cc_start: 0.5592 (tpt) cc_final: 0.5039 (ptm) REVERT: 0h 186 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6559 (m-80) REVERT: 0h 194 ASP cc_start: 0.8432 (t0) cc_final: 0.7759 (t0) REVERT: 0h 213 GLN cc_start: 0.8102 (tp40) cc_final: 0.7859 (tm-30) REVERT: 0h 220 GLU cc_start: 0.7467 (tp30) cc_final: 0.6889 (mt-10) REVERT: 0i 22 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7806 (ttm110) REVERT: 0i 40 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6166 (mt-10) REVERT: 0i 151 ASN cc_start: 0.8094 (t0) cc_final: 0.7773 (t0) REVERT: 0i 194 ASP cc_start: 0.8665 (t0) cc_final: 0.7973 (t0) REVERT: 0i 205 TYR cc_start: 0.8749 (t80) cc_final: 0.8528 (t80) REVERT: 0i 213 GLN cc_start: 0.8331 (tp40) cc_final: 0.7987 (tp40) REVERT: 0i 220 GLU cc_start: 0.7625 (mm-30) cc_final: 0.6879 (mt-10) REVERT: 0i 250 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7469 (mm) REVERT: 0j 18 GLN cc_start: 0.7780 (mm110) cc_final: 0.6813 (tp40) REVERT: 0j 40 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6777 (mm-30) REVERT: 0j 100 TYR cc_start: 0.5994 (OUTLIER) cc_final: 0.5268 (t80) REVERT: 0j 112 MET cc_start: 0.6537 (ptm) cc_final: 0.6304 (ppp) REVERT: 0j 140 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8645 (tm-30) REVERT: 0j 145 LYS cc_start: 0.7476 (tptp) cc_final: 0.7250 (tptp) REVERT: 0j 151 ASN cc_start: 0.7999 (t0) cc_final: 0.7383 (t0) REVERT: 0j 186 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: 0j 213 GLN cc_start: 0.7907 (tp40) cc_final: 0.7680 (tp40) REVERT: 0j 220 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7106 (mt-10) REVERT: 0k 18 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7295 (tp-100) REVERT: 0k 22 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7556 (tpp-160) REVERT: 0k 30 TYR cc_start: 0.6786 (t80) cc_final: 0.6189 (t80) REVERT: 0k 44 LEU cc_start: 0.7754 (mt) cc_final: 0.7381 (mt) REVERT: 0k 112 MET cc_start: 0.5664 (tpt) cc_final: 0.5074 (ptm) REVERT: 0k 186 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: 0k 194 ASP cc_start: 0.8437 (t0) cc_final: 0.7799 (t0) REVERT: 0k 220 GLU cc_start: 0.7677 (tp30) cc_final: 0.6908 (mt-10) REVERT: 0l 22 ARG cc_start: 0.7940 (tpp-160) cc_final: 0.7366 (tpp-160) REVERT: 0l 40 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6150 (mt-10) REVERT: 0l 100 TYR cc_start: 0.6208 (OUTLIER) cc_final: 0.5597 (t80) REVERT: 0l 151 ASN cc_start: 0.8156 (t0) cc_final: 0.7953 (t0) REVERT: 0l 213 GLN cc_start: 0.8288 (tp40) cc_final: 0.7595 (tm-30) REVERT: 0l 214 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7755 (ttpp) REVERT: 0l 218 TRP cc_start: 0.7109 (t-100) cc_final: 0.6625 (t60) REVERT: 0l 249 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7788 (mm-40) outliers start: 95 outliers final: 62 residues processed: 766 average time/residue: 0.3783 time to fit residues: 441.2814 Evaluate side-chains 718 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 641 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 100 TYR 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 37 GLN Chi-restraints excluded: chain 0b residue 54 GLU 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 170 SER Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 277 LYS Chi-restraints excluded: chain 0d residue 54 GLU Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 136 LEU 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 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 100 TYR 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 136 LEU 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 0g residue 276 VAL Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 136 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 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 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 0i residue 278 VAL Chi-restraints excluded: chain 0j residue 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR 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 54 GLU Chi-restraints excluded: chain 0k residue 100 TYR Chi-restraints excluded: chain 0k residue 136 LEU 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 37 GLN Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 136 LEU 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 217 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN 0a 173 GLN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN 0c 21 ASN ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 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 32 GLN ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 59 GLN 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 173 GLN ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 59 GLN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 18 GLN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 173 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 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 173 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25728 Z= 0.207 Angle : 0.738 11.321 34860 Z= 0.401 Chirality : 0.046 0.202 3756 Planarity : 0.005 0.058 4548 Dihedral : 7.227 35.887 3348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.05 % Favored : 84.56 % Rotamer: Outliers : 3.87 % Allowed : 21.16 % Favored : 74.96 % 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: -1.96 (0.16), residues: 3024 helix: 0.26 (0.16), residues: 1092 sheet: -3.47 (0.27), residues: 300 loop : -2.02 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP0b 218 HIS 0.006 0.001 HIS0h 58 PHE 0.027 0.002 PHE0j 199 TYR 0.020 0.002 TYR0a 205 ARG 0.012 0.001 ARG0c 281 *********************** 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 801 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 695 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: 0a 18 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7703 (tp-100) REVERT: 0a 40 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6806 (mm-30) REVERT: 0a 54 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: 0a 100 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5732 (t80) REVERT: 0a 145 LYS cc_start: 0.7806 (tptt) cc_final: 0.7539 (tptp) REVERT: 0a 194 ASP cc_start: 0.8205 (t0) cc_final: 0.7940 (t0) REVERT: 0a 213 GLN cc_start: 0.8217 (tp40) cc_final: 0.7685 (tm-30) REVERT: 0a 281 ARG cc_start: 0.7836 (mmp80) cc_final: 0.7622 (mmm-85) REVERT: 0b 18 GLN cc_start: 0.7542 (mm110) cc_final: 0.7018 (tp-100) REVERT: 0b 30 TYR cc_start: 0.7301 (t80) cc_final: 0.6965 (t80) REVERT: 0b 44 LEU cc_start: 0.7500 (mt) cc_final: 0.7140 (mt) REVERT: 0b 145 LYS cc_start: 0.7734 (tmtt) cc_final: 0.7508 (tptp) REVERT: 0b 186 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: 0b 194 ASP cc_start: 0.8618 (t0) cc_final: 0.7959 (t0) REVERT: 0b 220 GLU cc_start: 0.7551 (tp30) cc_final: 0.6941 (mt-10) REVERT: 0c 100 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.5804 (t80) REVERT: 0c 112 MET cc_start: 0.5918 (ppp) cc_final: 0.5667 (ppp) REVERT: 0c 140 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8650 (tm-30) REVERT: 0c 152 GLN cc_start: 0.7834 (pt0) cc_final: 0.7626 (pt0) REVERT: 0c 220 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6919 (mt-10) REVERT: 0c 221 MET cc_start: 0.7577 (tpp) cc_final: 0.7187 (tpp) REVERT: 0c 225 LEU cc_start: 0.7405 (mt) cc_final: 0.6931 (mp) REVERT: 0c 269 ASN cc_start: 0.8067 (t0) cc_final: 0.7856 (t0) REVERT: 0c 277 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5379 (mmmt) REVERT: 0d 18 GLN cc_start: 0.7920 (tp40) cc_final: 0.7441 (tp-100) REVERT: 0d 100 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5835 (t80) REVERT: 0d 151 ASN cc_start: 0.7915 (t0) cc_final: 0.7164 (t0) REVERT: 0d 186 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6576 (m-80) REVERT: 0d 213 GLN cc_start: 0.8199 (tp40) cc_final: 0.7858 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7087 (mt-10) REVERT: 0d 263 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6576 (tm-30) REVERT: 0e 30 TYR cc_start: 0.6653 (t80) cc_final: 0.6187 (t80) REVERT: 0e 32 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6703 (pt0) REVERT: 0e 37 GLN cc_start: 0.8136 (pp30) cc_final: 0.7595 (tt0) REVERT: 0e 65 PHE cc_start: 0.6593 (m-10) cc_final: 0.6346 (m-10) REVERT: 0e 186 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6497 (m-80) REVERT: 0e 194 ASP cc_start: 0.8536 (t70) cc_final: 0.7828 (t0) REVERT: 0e 213 GLN cc_start: 0.8136 (tp40) cc_final: 0.7694 (tm-30) REVERT: 0e 220 GLU cc_start: 0.7564 (tp30) cc_final: 0.6878 (mt-10) REVERT: 0e 225 LEU cc_start: 0.7931 (mt) cc_final: 0.7561 (mt) REVERT: 0f 22 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7633 (ttm110) REVERT: 0f 30 TYR cc_start: 0.6769 (t80) cc_final: 0.5877 (t80) REVERT: 0f 220 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6864 (mt-10) REVERT: 0f 269 ASN cc_start: 0.8061 (t0) cc_final: 0.7835 (t0) REVERT: 0f 281 ARG cc_start: 0.7706 (mmp80) cc_final: 0.7423 (mmp80) REVERT: 0g 40 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6751 (mm-30) REVERT: 0g 100 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5742 (t80) REVERT: 0g 112 MET cc_start: 0.6582 (ptm) cc_final: 0.5829 (ppp) REVERT: 0g 140 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8617 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8939 (tp) cc_final: 0.8551 (mt) REVERT: 0g 194 ASP cc_start: 0.8540 (t0) cc_final: 0.8043 (t0) REVERT: 0g 197 GLU cc_start: 0.7802 (pt0) cc_final: 0.7511 (pt0) REVERT: 0g 213 GLN cc_start: 0.8206 (tp40) cc_final: 0.7752 (tm-30) REVERT: 0h 18 GLN cc_start: 0.7811 (tp40) cc_final: 0.7594 (tp-100) REVERT: 0h 22 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7622 (tpp-160) REVERT: 0h 30 TYR cc_start: 0.7085 (t80) cc_final: 0.6591 (t80) REVERT: 0h 44 LEU cc_start: 0.7670 (mt) cc_final: 0.7280 (mt) REVERT: 0h 124 ASN cc_start: 0.7600 (p0) cc_final: 0.7170 (p0) REVERT: 0h 144 LEU cc_start: 0.7991 (tp) cc_final: 0.7572 (mt) REVERT: 0h 145 LYS cc_start: 0.7490 (tptp) cc_final: 0.7252 (tptp) REVERT: 0h 186 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: 0h 194 ASP cc_start: 0.8615 (t0) cc_final: 0.7977 (t0) REVERT: 0h 205 TYR cc_start: 0.8801 (t80) cc_final: 0.8595 (t80) REVERT: 0h 213 GLN cc_start: 0.8153 (tp40) cc_final: 0.7881 (tm-30) REVERT: 0h 220 GLU cc_start: 0.7349 (tp30) cc_final: 0.6790 (mt-10) REVERT: 0i 22 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7788 (ttm110) REVERT: 0i 40 GLU cc_start: 0.6740 (mm-30) cc_final: 0.6035 (mt-10) REVERT: 0i 112 MET cc_start: 0.5609 (ppp) cc_final: 0.3807 (mmp) REVERT: 0i 151 ASN cc_start: 0.7933 (t0) cc_final: 0.7664 (t0) REVERT: 0i 152 GLN cc_start: 0.7896 (pt0) cc_final: 0.7659 (pt0) REVERT: 0i 194 ASP cc_start: 0.8652 (t0) cc_final: 0.8001 (t0) REVERT: 0i 213 GLN cc_start: 0.8339 (tp40) cc_final: 0.7977 (tp40) REVERT: 0i 220 GLU cc_start: 0.7662 (mm-30) cc_final: 0.6910 (mt-10) REVERT: 0i 225 LEU cc_start: 0.7343 (mt) cc_final: 0.6905 (mp) REVERT: 0i 250 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7450 (mm) REVERT: 0i 262 GLU cc_start: 0.6886 (tp30) cc_final: 0.6643 (tp30) REVERT: 0j 18 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7313 (tp-100) REVERT: 0j 40 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6887 (mm-30) REVERT: 0j 100 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.5722 (t80) REVERT: 0j 140 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8702 (tm-30) REVERT: 0j 141 LEU cc_start: 0.8978 (mt) cc_final: 0.8624 (mt) REVERT: 0j 145 LYS cc_start: 0.7527 (tptp) cc_final: 0.7288 (tptp) REVERT: 0j 151 ASN cc_start: 0.8057 (t0) cc_final: 0.7438 (t0) REVERT: 0j 220 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6947 (mt-10) REVERT: 0k 18 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7501 (tp-100) REVERT: 0k 22 ARG cc_start: 0.7985 (tpp-160) cc_final: 0.7726 (tpp-160) REVERT: 0k 30 TYR cc_start: 0.6922 (t80) cc_final: 0.6322 (t80) REVERT: 0k 44 LEU cc_start: 0.7785 (mt) cc_final: 0.7391 (mt) REVERT: 0k 124 ASN cc_start: 0.7533 (p0) cc_final: 0.7269 (p0) REVERT: 0k 186 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: 0k 194 ASP cc_start: 0.8495 (t0) cc_final: 0.7935 (t0) REVERT: 0k 220 GLU cc_start: 0.7729 (tp30) cc_final: 0.6975 (mt-10) REVERT: 0l 18 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7617 (mm-40) REVERT: 0l 40 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6174 (mt-10) REVERT: 0l 100 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5867 (t80) REVERT: 0l 112 MET cc_start: 0.5534 (tpt) cc_final: 0.5325 (ttp) REVERT: 0l 140 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8609 (tm-30) REVERT: 0l 213 GLN cc_start: 0.8407 (tp40) cc_final: 0.7796 (tm-30) REVERT: 0l 214 LYS cc_start: 0.8241 (ttpp) cc_final: 0.7852 (ttpp) REVERT: 0l 218 TRP cc_start: 0.7103 (t-100) cc_final: 0.6660 (t60) outliers start: 106 outliers final: 69 residues processed: 786 average time/residue: 0.3737 time to fit residues: 452.3117 Evaluate side-chains 726 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 640 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 54 GLU Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU 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 54 GLU Chi-restraints excluded: chain 0c residue 63 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 185 ILE Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 277 LYS Chi-restraints excluded: chain 0d residue 31 LEU Chi-restraints excluded: chain 0d residue 52 PHE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 136 LEU Chi-restraints excluded: chain 0d residue 170 SER Chi-restraints excluded: chain 0d residue 186 PHE Chi-restraints excluded: chain 0d residue 217 VAL 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 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 54 GLU Chi-restraints excluded: chain 0f residue 100 TYR 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 0g residue 52 PHE Chi-restraints excluded: chain 0g residue 54 GLU Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 170 SER Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 277 LYS Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 136 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 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 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 54 GLU Chi-restraints excluded: chain 0j residue 100 TYR 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 277 LYS 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 185 ILE 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 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 136 LEU 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 223 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 211 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 168 GLN 0a 173 GLN ** 0b 37 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 59 GLN ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 173 GLN 0e 32 GLN ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 18 GLN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 173 GLN ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN 0j 21 ASN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 59 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 173 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25728 Z= 0.202 Angle : 0.742 9.109 34860 Z= 0.400 Chirality : 0.046 0.209 3756 Planarity : 0.005 0.059 4548 Dihedral : 7.080 36.160 3348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.88 % Favored : 84.72 % Rotamer: Outliers : 4.02 % Allowed : 23.25 % Favored : 72.73 % 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: -1.84 (0.17), residues: 3024 helix: 0.43 (0.16), residues: 1092 sheet: -3.42 (0.28), residues: 300 loop : -1.99 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP0k 218 HIS 0.007 0.001 HIS0h 58 PHE 0.030 0.002 PHE0h 65 TYR 0.018 0.002 TYR0a 205 ARG 0.007 0.000 ARG0c 22 *********************** 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 782 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 672 time to evaluate : 3.050 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 18 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7592 (tp-100) REVERT: 0a 22 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.7279 (tpp-160) REVERT: 0a 40 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6816 (mm-30) REVERT: 0a 54 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6428 (pm20) REVERT: 0a 100 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.5736 (t80) REVERT: 0a 106 LEU cc_start: 0.4641 (tp) cc_final: 0.4377 (mp) REVERT: 0a 126 MET cc_start: 0.8265 (mtm) cc_final: 0.8045 (mtt) REVERT: 0a 137 PHE cc_start: 0.7868 (m-80) cc_final: 0.7604 (m-80) REVERT: 0a 140 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8655 (tm-30) REVERT: 0a 141 LEU cc_start: 0.9012 (mt) cc_final: 0.8617 (mt) REVERT: 0a 145 LYS cc_start: 0.7722 (tptt) cc_final: 0.7483 (tptp) REVERT: 0a 153 ASN cc_start: 0.7153 (t0) cc_final: 0.6922 (t0) REVERT: 0a 194 ASP cc_start: 0.8159 (t0) cc_final: 0.7882 (t0) REVERT: 0a 213 GLN cc_start: 0.8199 (tp40) cc_final: 0.7792 (tm-30) REVERT: 0a 221 MET cc_start: 0.7526 (tpp) cc_final: 0.6758 (tpp) REVERT: 0a 225 LEU cc_start: 0.7609 (mt) cc_final: 0.6995 (mp) REVERT: 0b 30 TYR cc_start: 0.7238 (t80) cc_final: 0.6874 (t80) REVERT: 0b 37 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6807 (pt0) REVERT: 0b 44 LEU cc_start: 0.7568 (mt) cc_final: 0.7182 (mt) REVERT: 0b 145 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7550 (tptp) REVERT: 0b 186 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6585 (m-80) REVERT: 0b 194 ASP cc_start: 0.8621 (t0) cc_final: 0.8023 (t0) REVERT: 0b 220 GLU cc_start: 0.7536 (tp30) cc_final: 0.7020 (mt-10) REVERT: 0b 281 ARG cc_start: 0.7739 (mmp80) cc_final: 0.7510 (mmp80) REVERT: 0c 18 GLN cc_start: 0.7431 (tt0) cc_final: 0.7223 (tt0) REVERT: 0c 22 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7657 (ttm110) REVERT: 0c 100 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5855 (t80) REVERT: 0c 112 MET cc_start: 0.5939 (ppp) cc_final: 0.5661 (ppp) REVERT: 0c 140 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8632 (tm-30) REVERT: 0c 141 LEU cc_start: 0.9048 (mt) cc_final: 0.8650 (mt) REVERT: 0c 172 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6791 (mmtm) REVERT: 0c 194 ASP cc_start: 0.8768 (t0) cc_final: 0.7993 (t0) REVERT: 0c 220 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6998 (mt-10) REVERT: 0d 22 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7627 (tpp-160) REVERT: 0d 100 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.5913 (t80) REVERT: 0d 151 ASN cc_start: 0.7978 (t0) cc_final: 0.7429 (t0) REVERT: 0d 186 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: 0d 213 GLN cc_start: 0.8148 (tp40) cc_final: 0.7706 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7049 (mt-10) REVERT: 0d 263 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: 0e 18 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7567 (tp-100) REVERT: 0e 30 TYR cc_start: 0.7021 (t80) cc_final: 0.6430 (t80) REVERT: 0e 112 MET cc_start: 0.5514 (tpt) cc_final: 0.5172 (ttt) REVERT: 0e 194 ASP cc_start: 0.8648 (t70) cc_final: 0.8089 (t0) REVERT: 0e 213 GLN cc_start: 0.8001 (tp40) cc_final: 0.7627 (tm-30) REVERT: 0e 218 TRP cc_start: 0.7074 (t-100) cc_final: 0.6842 (t60) REVERT: 0e 220 GLU cc_start: 0.7521 (tp30) cc_final: 0.6947 (mt-10) REVERT: 0e 281 ARG cc_start: 0.7608 (mmp80) cc_final: 0.7341 (mmp80) REVERT: 0f 22 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7710 (ttm110) REVERT: 0f 30 TYR cc_start: 0.6747 (t80) cc_final: 0.5816 (t80) REVERT: 0f 213 GLN cc_start: 0.8346 (tp40) cc_final: 0.7673 (tm-30) REVERT: 0f 220 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6840 (mt-10) REVERT: 0f 269 ASN cc_start: 0.8149 (t0) cc_final: 0.7929 (t0) REVERT: 0f 281 ARG cc_start: 0.7678 (mmp80) cc_final: 0.7408 (mmp80) REVERT: 0g 40 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6800 (mm-30) REVERT: 0g 100 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.5902 (t80) REVERT: 0g 106 LEU cc_start: 0.4714 (tp) cc_final: 0.3857 (tt) REVERT: 0g 140 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8608 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8936 (tp) cc_final: 0.8644 (mt) REVERT: 0g 153 ASN cc_start: 0.7646 (t0) cc_final: 0.7179 (t0) REVERT: 0g 194 ASP cc_start: 0.8611 (t0) cc_final: 0.8188 (t0) REVERT: 0g 213 GLN cc_start: 0.8234 (tp40) cc_final: 0.7565 (tm-30) REVERT: 0h 30 TYR cc_start: 0.7075 (t80) cc_final: 0.6642 (t80) REVERT: 0h 44 LEU cc_start: 0.7767 (mt) cc_final: 0.7386 (mt) REVERT: 0h 112 MET cc_start: 0.5688 (tpt) cc_final: 0.5285 (ttt) REVERT: 0h 137 PHE cc_start: 0.7989 (m-80) cc_final: 0.7703 (m-80) REVERT: 0h 140 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8494 (tm-30) REVERT: 0h 145 LYS cc_start: 0.7553 (tptp) cc_final: 0.7310 (tptp) REVERT: 0h 194 ASP cc_start: 0.8622 (t0) cc_final: 0.8041 (t0) REVERT: 0h 220 GLU cc_start: 0.7380 (tp30) cc_final: 0.6863 (mt-10) REVERT: 0i 100 TYR cc_start: 0.6528 (OUTLIER) cc_final: 0.5885 (t80) REVERT: 0i 151 ASN cc_start: 0.7922 (t0) cc_final: 0.7605 (t0) REVERT: 0i 194 ASP cc_start: 0.8853 (t0) cc_final: 0.8273 (t0) REVERT: 0i 213 GLN cc_start: 0.8233 (tp40) cc_final: 0.7897 (tp40) REVERT: 0i 220 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6947 (mt-10) REVERT: 0i 250 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7372 (mm) REVERT: 0i 262 GLU cc_start: 0.6753 (tp30) cc_final: 0.6525 (tp30) REVERT: 0j 40 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7061 (mm-30) REVERT: 0j 100 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5797 (t80) REVERT: 0j 140 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8736 (tm-30) REVERT: 0j 145 LYS cc_start: 0.7560 (tptp) cc_final: 0.7327 (tptp) REVERT: 0j 151 ASN cc_start: 0.8066 (t0) cc_final: 0.7334 (t0) REVERT: 0j 153 ASN cc_start: 0.7676 (t0) cc_final: 0.7294 (t0) REVERT: 0j 194 ASP cc_start: 0.8658 (t0) cc_final: 0.8151 (t0) REVERT: 0j 213 GLN cc_start: 0.8225 (tp40) cc_final: 0.7833 (tm-30) REVERT: 0j 220 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6910 (mt-10) REVERT: 0j 225 LEU cc_start: 0.7719 (mt) cc_final: 0.7312 (mp) REVERT: 0k 18 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7677 (tp-100) REVERT: 0k 30 TYR cc_start: 0.6963 (t80) cc_final: 0.6407 (t80) REVERT: 0k 44 LEU cc_start: 0.7806 (mt) cc_final: 0.7393 (mt) REVERT: 0k 145 LYS cc_start: 0.7550 (tptp) cc_final: 0.7306 (tptp) REVERT: 0k 194 ASP cc_start: 0.8592 (t0) cc_final: 0.8080 (t0) REVERT: 0k 220 GLU cc_start: 0.7550 (tp30) cc_final: 0.6899 (mt-10) REVERT: 0l 18 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7672 (mm-40) REVERT: 0l 40 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6086 (mt-10) REVERT: 0l 100 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.5925 (t80) REVERT: 0l 140 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8641 (tm-30) REVERT: 0l 194 ASP cc_start: 0.8780 (t0) cc_final: 0.8174 (t0) REVERT: 0l 213 GLN cc_start: 0.8386 (tp40) cc_final: 0.7858 (tm-30) REVERT: 0l 214 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7864 (ttpp) REVERT: 0l 218 TRP cc_start: 0.6984 (t-100) cc_final: 0.6613 (t60) outliers start: 110 outliers final: 71 residues processed: 764 average time/residue: 0.3712 time to fit residues: 435.5028 Evaluate side-chains 708 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 622 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 54 GLU Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 170 SER Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 33 SER Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 54 GLU 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 54 GLU Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 172 LYS Chi-restraints excluded: chain 0c residue 185 ILE Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 31 LEU Chi-restraints excluded: chain 0d residue 52 PHE Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER 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 37 GLN Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU Chi-restraints excluded: chain 0e residue 136 LEU Chi-restraints excluded: chain 0e residue 141 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 63 VAL Chi-restraints excluded: chain 0f residue 100 TYR 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 52 PHE Chi-restraints excluded: chain 0g residue 100 TYR 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 277 LYS Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 37 GLN Chi-restraints excluded: chain 0h residue 52 PHE Chi-restraints excluded: chain 0h residue 100 TYR Chi-restraints excluded: chain 0h residue 186 PHE Chi-restraints excluded: chain 0h residue 198 VAL Chi-restraints excluded: chain 0i residue 33 SER Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 185 ILE 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 100 TYR 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 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 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 277 LYS Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 100 TYR 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 223 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 263 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 21 ASN ** 0a 123 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** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 21 ASN 0f 49 ASN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN 0j 21 ASN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 153 ASN ** 0k 249 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.7199 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= 0.206 Angle : 0.756 12.336 34860 Z= 0.404 Chirality : 0.047 0.218 3756 Planarity : 0.005 0.059 4548 Dihedral : 6.983 35.883 3348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.09 % Favored : 85.52 % Rotamer: Outliers : 3.69 % Allowed : 24.42 % Favored : 71.89 % 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: -1.81 (0.17), residues: 3024 helix: 0.44 (0.16), residues: 1092 sheet: -3.42 (0.28), residues: 300 loop : -1.96 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP0f 41 HIS 0.013 0.001 HIS0e 58 PHE 0.028 0.002 PHE0e 65 TYR 0.018 0.002 TYR0h 205 ARG 0.011 0.001 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 742 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 641 time to evaluate : 2.949 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: 0a 18 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7735 (tp-100) REVERT: 0a 22 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7248 (tpp-160) REVERT: 0a 54 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: 0a 100 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.5775 (t80) REVERT: 0a 141 LEU cc_start: 0.8969 (mt) cc_final: 0.8599 (mt) REVERT: 0a 145 LYS cc_start: 0.7742 (tptt) cc_final: 0.7517 (tptp) REVERT: 0a 153 ASN cc_start: 0.7185 (t0) cc_final: 0.6790 (t0) REVERT: 0a 194 ASP cc_start: 0.8181 (t0) cc_final: 0.7919 (t0) REVERT: 0a 213 GLN cc_start: 0.8199 (tp40) cc_final: 0.7659 (tm-30) REVERT: 0a 220 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: 0a 221 MET cc_start: 0.7488 (tpp) cc_final: 0.6781 (tpp) REVERT: 0a 225 LEU cc_start: 0.7624 (mt) cc_final: 0.7027 (mp) REVERT: 0b 30 TYR cc_start: 0.7247 (t80) cc_final: 0.6954 (t80) REVERT: 0b 37 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: 0b 44 LEU cc_start: 0.7601 (mt) cc_final: 0.7196 (mt) REVERT: 0b 145 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7559 (tptp) REVERT: 0b 194 ASP cc_start: 0.8717 (t0) cc_final: 0.8070 (t0) REVERT: 0b 213 GLN cc_start: 0.8342 (tp40) cc_final: 0.7989 (tm-30) REVERT: 0b 220 GLU cc_start: 0.7408 (tp30) cc_final: 0.6858 (mt-10) REVERT: 0b 267 LYS cc_start: 0.2826 (mtpt) cc_final: 0.2119 (mmmt) REVERT: 0c 100 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5937 (t80) REVERT: 0c 123 ASN cc_start: 0.8276 (t0) cc_final: 0.8044 (t0) REVERT: 0c 140 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8641 (tm-30) REVERT: 0c 141 LEU cc_start: 0.9073 (mt) cc_final: 0.8666 (mt) REVERT: 0c 172 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6775 (mmtm) REVERT: 0c 194 ASP cc_start: 0.8683 (t0) cc_final: 0.7933 (t0) REVERT: 0c 213 GLN cc_start: 0.8374 (tp40) cc_final: 0.7622 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6999 (mt-10) REVERT: 0c 225 LEU cc_start: 0.7433 (mt) cc_final: 0.7055 (mp) REVERT: 0d 18 GLN cc_start: 0.7702 (tp40) cc_final: 0.7234 (tp-100) REVERT: 0d 22 ARG cc_start: 0.7853 (tpp-160) cc_final: 0.7523 (tpp-160) REVERT: 0d 100 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5903 (t80) REVERT: 0d 112 MET cc_start: 0.6256 (ptm) cc_final: 0.5885 (ppp) REVERT: 0d 151 ASN cc_start: 0.7945 (t0) cc_final: 0.7401 (t0) REVERT: 0d 153 ASN cc_start: 0.7570 (t0) cc_final: 0.7148 (t0) REVERT: 0d 186 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: 0d 213 GLN cc_start: 0.8138 (tp40) cc_final: 0.7677 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7071 (mt-10) REVERT: 0e 18 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7666 (tp-100) REVERT: 0e 30 TYR cc_start: 0.6981 (t80) cc_final: 0.6446 (t80) REVERT: 0e 37 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: 0e 144 LEU cc_start: 0.8023 (tp) cc_final: 0.7678 (mt) REVERT: 0e 185 ILE cc_start: 0.7221 (pt) cc_final: 0.6900 (pt) REVERT: 0e 194 ASP cc_start: 0.8643 (t70) cc_final: 0.8106 (t0) REVERT: 0e 209 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8447 (mmtm) REVERT: 0e 213 GLN cc_start: 0.8014 (tp40) cc_final: 0.7628 (tm-30) REVERT: 0e 218 TRP cc_start: 0.7062 (t-100) cc_final: 0.6746 (t60) REVERT: 0e 220 GLU cc_start: 0.7511 (tp30) cc_final: 0.6961 (mt-10) REVERT: 0f 22 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7584 (ttm110) REVERT: 0f 30 TYR cc_start: 0.6841 (t80) cc_final: 0.6077 (t80) REVERT: 0f 213 GLN cc_start: 0.8344 (tp40) cc_final: 0.7736 (tm-30) REVERT: 0f 220 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6921 (mt-10) REVERT: 0f 281 ARG cc_start: 0.7714 (mmp80) cc_final: 0.7476 (mmp80) REVERT: 0g 22 ARG cc_start: 0.7807 (ttm110) cc_final: 0.7247 (ttm110) REVERT: 0g 100 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5792 (t80) REVERT: 0g 140 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8704 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8965 (tp) cc_final: 0.8653 (mt) REVERT: 0g 194 ASP cc_start: 0.8803 (t0) cc_final: 0.8323 (t0) REVERT: 0g 213 GLN cc_start: 0.8237 (tp40) cc_final: 0.7586 (tm-30) REVERT: 0h 18 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7506 (tp-100) REVERT: 0h 30 TYR cc_start: 0.7071 (t80) cc_final: 0.6693 (t80) REVERT: 0h 44 LEU cc_start: 0.7794 (mt) cc_final: 0.7393 (mt) REVERT: 0h 126 MET cc_start: 0.8904 (mtm) cc_final: 0.8603 (mtp) REVERT: 0h 145 LYS cc_start: 0.7665 (tptp) cc_final: 0.7370 (tptp) REVERT: 0h 194 ASP cc_start: 0.8645 (t0) cc_final: 0.8082 (t0) REVERT: 0h 220 GLU cc_start: 0.7416 (tp30) cc_final: 0.6923 (mt-10) REVERT: 0i 112 MET cc_start: 0.5251 (ppp) cc_final: 0.3618 (mmp) REVERT: 0i 194 ASP cc_start: 0.8802 (t0) cc_final: 0.8268 (t0) REVERT: 0i 213 GLN cc_start: 0.8329 (tp40) cc_final: 0.7939 (tp40) REVERT: 0i 220 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6959 (mt-10) REVERT: 0i 222 MET cc_start: 0.7627 (mmm) cc_final: 0.7305 (mmm) REVERT: 0i 225 LEU cc_start: 0.7337 (mt) cc_final: 0.6942 (mp) REVERT: 0i 250 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7349 (mm) REVERT: 0i 262 GLU cc_start: 0.6777 (tp30) cc_final: 0.6531 (tp30) REVERT: 0i 269 ASN cc_start: 0.8255 (t0) cc_final: 0.8042 (t0) REVERT: 0j 40 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7048 (mm-30) REVERT: 0j 100 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.5932 (t80) REVERT: 0j 112 MET cc_start: 0.5230 (ppp) cc_final: 0.4829 (ppp) REVERT: 0j 140 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8886 (tm-30) REVERT: 0j 141 LEU cc_start: 0.9044 (mt) cc_final: 0.8527 (mt) REVERT: 0j 153 ASN cc_start: 0.7721 (t0) cc_final: 0.7369 (t0) REVERT: 0j 194 ASP cc_start: 0.8651 (t0) cc_final: 0.8197 (t0) REVERT: 0j 213 GLN cc_start: 0.8190 (tp40) cc_final: 0.7812 (tm-30) REVERT: 0j 225 LEU cc_start: 0.7651 (mt) cc_final: 0.7365 (mp) REVERT: 0k 30 TYR cc_start: 0.6935 (t80) cc_final: 0.6444 (t80) REVERT: 0k 44 LEU cc_start: 0.7739 (mt) cc_final: 0.7363 (mt) REVERT: 0k 145 LYS cc_start: 0.7555 (tptp) cc_final: 0.7284 (tptp) REVERT: 0k 194 ASP cc_start: 0.8619 (t0) cc_final: 0.8141 (t0) REVERT: 0k 220 GLU cc_start: 0.7532 (tp30) cc_final: 0.7157 (mt-10) REVERT: 0l 18 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7878 (mm-40) REVERT: 0l 100 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.5858 (t80) REVERT: 0l 128 PHE cc_start: 0.7110 (m-80) cc_final: 0.6890 (m-80) REVERT: 0l 140 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8656 (tm-30) REVERT: 0l 146 GLU cc_start: 0.7306 (tt0) cc_final: 0.7067 (tt0) REVERT: 0l 194 ASP cc_start: 0.8782 (t0) cc_final: 0.8268 (t0) outliers start: 101 outliers final: 71 residues processed: 727 average time/residue: 0.3766 time to fit residues: 418.9642 Evaluate side-chains 701 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 616 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 54 GLU Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 220 GLU Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 33 SER Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 185 ILE 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 54 GLU Chi-restraints excluded: chain 0c residue 63 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 136 LEU Chi-restraints excluded: chain 0c residue 172 LYS Chi-restraints excluded: chain 0c residue 185 ILE Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0d residue 31 LEU Chi-restraints excluded: chain 0d residue 54 GLU Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER 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 37 GLN Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU 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 24 PHE Chi-restraints excluded: chain 0f residue 54 GLU Chi-restraints excluded: chain 0f residue 63 VAL Chi-restraints excluded: chain 0f residue 100 TYR 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 223 THR Chi-restraints excluded: chain 0g residue 100 TYR Chi-restraints excluded: chain 0g residue 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 277 LYS Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 100 TYR 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 223 THR Chi-restraints excluded: chain 0i residue 63 VAL Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 170 SER Chi-restraints excluded: chain 0i residue 185 ILE 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 100 TYR 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 277 LYS Chi-restraints excluded: chain 0k residue 33 SER Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 100 TYR 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 277 LYS Chi-restraints excluded: chain 0k residue 278 VAL Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 223 THR 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: 2.9990 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 0.9990 chunk 162 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 243 optimal weight: 8.9990 chunk 254 optimal weight: 0.5980 chunk 268 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 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** ** 0c 123 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 58 HIS ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 58 HIS ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN 0j 58 HIS ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 59 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.7480 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= 0.198 Angle : 0.761 11.142 34860 Z= 0.404 Chirality : 0.047 0.248 3756 Planarity : 0.005 0.061 4548 Dihedral : 6.799 36.684 3348 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.46 % Favored : 86.14 % Rotamer: Outliers : 3.33 % Allowed : 25.22 % Favored : 71.45 % 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: -1.68 (0.17), residues: 3024 helix: 0.57 (0.16), residues: 1092 sheet: -3.41 (0.28), residues: 300 loop : -1.88 (0.18), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP0a 41 HIS 0.013 0.001 HIS0e 58 PHE 0.029 0.002 PHE0e 65 TYR 0.018 0.001 TYR0e 205 ARG 0.012 0.001 ARG0b 22 *********************** 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 753 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 662 time to evaluate : 2.590 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: 0a 22 ARG cc_start: 0.7805 (tpp-160) cc_final: 0.7211 (tpp-160) REVERT: 0a 54 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6415 (pm20) REVERT: 0a 124 ASN cc_start: 0.7555 (p0) cc_final: 0.7213 (p0) REVERT: 0a 145 LYS cc_start: 0.7778 (tptt) cc_final: 0.7549 (tptp) REVERT: 0a 153 ASN cc_start: 0.7227 (t0) cc_final: 0.6965 (t0) REVERT: 0a 194 ASP cc_start: 0.8216 (t0) cc_final: 0.7975 (t0) REVERT: 0a 213 GLN cc_start: 0.8110 (tp40) cc_final: 0.7642 (tm-30) REVERT: 0a 220 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6950 (mt-10) REVERT: 0a 281 ARG cc_start: 0.7540 (mmp80) cc_final: 0.7249 (mmm-85) REVERT: 0b 37 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6914 (pt0) REVERT: 0b 44 LEU cc_start: 0.7426 (mt) cc_final: 0.7065 (mt) REVERT: 0b 145 LYS cc_start: 0.7973 (tmtt) cc_final: 0.7649 (tptp) REVERT: 0b 194 ASP cc_start: 0.8725 (t0) cc_final: 0.8114 (t0) REVERT: 0b 213 GLN cc_start: 0.8221 (tp40) cc_final: 0.8009 (tm-30) REVERT: 0b 220 GLU cc_start: 0.7363 (tp30) cc_final: 0.6871 (mt-10) REVERT: 0c 100 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.5927 (t80) REVERT: 0c 123 ASN cc_start: 0.8011 (t0) cc_final: 0.7590 (p0) REVERT: 0c 140 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8636 (tm-30) REVERT: 0c 153 ASN cc_start: 0.7717 (t0) cc_final: 0.7327 (t0) REVERT: 0c 194 ASP cc_start: 0.8713 (t0) cc_final: 0.8014 (t0) REVERT: 0c 213 GLN cc_start: 0.8354 (tp40) cc_final: 0.7559 (tm-30) REVERT: 0c 220 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7036 (mt-10) REVERT: 0c 263 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5804 (tm-30) REVERT: 0d 18 GLN cc_start: 0.7722 (tp40) cc_final: 0.7305 (tp-100) REVERT: 0d 100 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6135 (t80) REVERT: 0d 112 MET cc_start: 0.6328 (ptm) cc_final: 0.6094 (ppp) REVERT: 0d 151 ASN cc_start: 0.7939 (t0) cc_final: 0.7160 (t0) REVERT: 0d 186 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: 0d 213 GLN cc_start: 0.8145 (tp40) cc_final: 0.7710 (tm-30) REVERT: 0d 220 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6836 (mt-10) REVERT: 0e 18 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7708 (tp-100) REVERT: 0e 30 TYR cc_start: 0.7140 (t80) cc_final: 0.6631 (t80) REVERT: 0e 37 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: 0e 144 LEU cc_start: 0.8006 (tp) cc_final: 0.7677 (mt) REVERT: 0e 185 ILE cc_start: 0.7471 (pt) cc_final: 0.7036 (pt) REVERT: 0e 194 ASP cc_start: 0.8633 (t70) cc_final: 0.8160 (t70) REVERT: 0e 213 GLN cc_start: 0.8003 (tp40) cc_final: 0.7629 (tm-30) REVERT: 0e 220 GLU cc_start: 0.7540 (tp30) cc_final: 0.7001 (mt-10) REVERT: 0f 22 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7538 (ttm110) REVERT: 0f 30 TYR cc_start: 0.7025 (t80) cc_final: 0.6278 (t80) REVERT: 0f 125 ASP cc_start: 0.8016 (p0) cc_final: 0.7658 (p0) REVERT: 0f 213 GLN cc_start: 0.8375 (tp40) cc_final: 0.7780 (tm-30) REVERT: 0f 220 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7080 (mt-10) REVERT: 0f 225 LEU cc_start: 0.7132 (mt) cc_final: 0.6902 (mm) REVERT: 0g 22 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7500 (ttm110) REVERT: 0g 100 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.5735 (t80) REVERT: 0g 140 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8735 (tm-30) REVERT: 0g 141 LEU cc_start: 0.8961 (tp) cc_final: 0.8723 (mt) REVERT: 0g 153 ASN cc_start: 0.7611 (t0) cc_final: 0.7115 (t0) REVERT: 0g 194 ASP cc_start: 0.8746 (t0) cc_final: 0.8312 (t0) REVERT: 0g 213 GLN cc_start: 0.8316 (tp40) cc_final: 0.7633 (tm-30) REVERT: 0h 18 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7600 (tp-100) REVERT: 0h 30 TYR cc_start: 0.6978 (t80) cc_final: 0.6713 (t80) REVERT: 0h 44 LEU cc_start: 0.7769 (mt) cc_final: 0.7395 (mt) REVERT: 0h 112 MET cc_start: 0.5833 (tpt) cc_final: 0.4748 (ptm) REVERT: 0h 145 LYS cc_start: 0.7622 (tptp) cc_final: 0.7338 (tptp) REVERT: 0h 194 ASP cc_start: 0.8619 (t0) cc_final: 0.8155 (t0) REVERT: 0h 220 GLU cc_start: 0.7367 (tp30) cc_final: 0.6924 (mt-10) REVERT: 0i 100 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5896 (t80) REVERT: 0i 112 MET cc_start: 0.5417 (ppp) cc_final: 0.3683 (mmp) REVERT: 0i 194 ASP cc_start: 0.8795 (t0) cc_final: 0.8274 (t0) REVERT: 0i 213 GLN cc_start: 0.8272 (tp40) cc_final: 0.7821 (tm-30) REVERT: 0i 220 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6958 (mt-10) REVERT: 0i 250 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7361 (mm) REVERT: 0j 100 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.6006 (t80) REVERT: 0j 112 MET cc_start: 0.5190 (ppp) cc_final: 0.4873 (ppp) REVERT: 0j 140 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8862 (tm-30) REVERT: 0j 172 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6591 (mmtm) REVERT: 0j 194 ASP cc_start: 0.8739 (t0) cc_final: 0.8317 (t0) REVERT: 0j 213 GLN cc_start: 0.8223 (tp40) cc_final: 0.7908 (tm-30) REVERT: 0k 18 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7684 (tp-100) REVERT: 0k 22 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7621 (tpp-160) REVERT: 0k 44 LEU cc_start: 0.7563 (mt) cc_final: 0.7233 (mt) REVERT: 0k 112 MET cc_start: 0.5932 (tpt) cc_final: 0.5128 (ptm) REVERT: 0k 145 LYS cc_start: 0.7533 (tptp) cc_final: 0.7282 (tptp) REVERT: 0k 194 ASP cc_start: 0.8623 (t0) cc_final: 0.8256 (t0) REVERT: 0k 220 GLU cc_start: 0.7329 (tp30) cc_final: 0.6999 (mt-10) REVERT: 0l 18 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8080 (tp40) REVERT: 0l 40 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6821 (mm-30) REVERT: 0l 100 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.5888 (t80) REVERT: 0l 140 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8654 (tm-30) REVERT: 0l 145 LYS cc_start: 0.7659 (tptp) cc_final: 0.7397 (tptp) REVERT: 0l 146 GLU cc_start: 0.7318 (tt0) cc_final: 0.7093 (tt0) REVERT: 0l 194 ASP cc_start: 0.8800 (t0) cc_final: 0.8316 (t0) REVERT: 0l 213 GLN cc_start: 0.8416 (tp40) cc_final: 0.7883 (tm-30) outliers start: 91 outliers final: 67 residues processed: 734 average time/residue: 0.3724 time to fit residues: 417.5709 Evaluate side-chains 704 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 623 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 54 GLU Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0a residue 220 GLU Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 185 ILE 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 54 GLU Chi-restraints excluded: chain 0c residue 63 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 185 ILE Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 263 GLU Chi-restraints excluded: chain 0d residue 31 LEU Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER 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 24 PHE Chi-restraints excluded: chain 0e residue 37 GLN Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU 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 24 PHE Chi-restraints excluded: chain 0f residue 54 GLU Chi-restraints excluded: chain 0f residue 63 VAL Chi-restraints excluded: chain 0f residue 100 TYR 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 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 277 LYS Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE 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 223 THR Chi-restraints excluded: chain 0i residue 24 PHE Chi-restraints excluded: chain 0i residue 63 VAL Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 185 ILE Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 227 ILE Chi-restraints excluded: chain 0i residue 250 ILE Chi-restraints excluded: chain 0j residue 52 PHE Chi-restraints excluded: chain 0j residue 100 TYR 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 277 LYS Chi-restraints excluded: chain 0k residue 52 PHE Chi-restraints excluded: chain 0k residue 100 TYR 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 278 VAL Chi-restraints excluded: chain 0l residue 37 GLN Chi-restraints excluded: chain 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 223 THR 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: 0.9990 chunk 173 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 chunk 275 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 183 optimal weight: 0.0870 chunk 145 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 123 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** ** 0c 123 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 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 58 HIS ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 173 GLN ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 58 HIS ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 211 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.7703 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= 0.204 Angle : 0.784 11.537 34860 Z= 0.413 Chirality : 0.048 0.259 3756 Planarity : 0.005 0.060 4548 Dihedral : 6.756 35.929 3348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.72 % Favored : 85.88 % Rotamer: Outliers : 3.14 % Allowed : 25.99 % 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: -1.70 (0.17), residues: 3024 helix: 0.56 (0.16), residues: 1092 sheet: -3.44 (0.28), residues: 300 loop : -1.90 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP0e 41 HIS 0.012 0.001 HIS0e 58 PHE 0.030 0.002 PHE0e 65 TYR 0.021 0.001 TYR0b 205 ARG 0.009 0.001 ARG0j 22 ********************** 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 719 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 633 time to evaluate : 2.898 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 18 GLN cc_start: 0.7931 (tp-100) cc_final: 0.7559 (tp-100) REVERT: 0a 22 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7509 (tpp-160) REVERT: 0a 54 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: 0a 144 LEU cc_start: 0.8212 (tp) cc_final: 0.7905 (mt) REVERT: 0a 145 LYS cc_start: 0.7676 (tptt) cc_final: 0.7456 (tptp) REVERT: 0a 153 ASN cc_start: 0.7232 (t0) cc_final: 0.6996 (t0) REVERT: 0a 194 ASP cc_start: 0.8249 (t0) cc_final: 0.7971 (t0) REVERT: 0a 213 GLN cc_start: 0.8109 (tp40) cc_final: 0.7633 (tm-30) REVERT: 0a 281 ARG cc_start: 0.7622 (mmp80) cc_final: 0.7117 (mmm-85) REVERT: 0b 44 LEU cc_start: 0.7488 (mt) cc_final: 0.7098 (mt) REVERT: 0b 112 MET cc_start: 0.5855 (tpt) cc_final: 0.5380 (ptm) REVERT: 0b 145 LYS cc_start: 0.7979 (tmtt) cc_final: 0.7637 (tptp) REVERT: 0b 194 ASP cc_start: 0.8749 (t0) cc_final: 0.8149 (t0) REVERT: 0b 220 GLU cc_start: 0.7378 (tp30) cc_final: 0.6920 (mt-10) REVERT: 0c 22 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7593 (ttm110) REVERT: 0c 100 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.5989 (t80) REVERT: 0c 172 LYS cc_start: 0.7589 (mmmt) cc_final: 0.6867 (mmtm) REVERT: 0c 194 ASP cc_start: 0.8706 (t0) cc_final: 0.8008 (t0) REVERT: 0c 220 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7042 (mt-10) REVERT: 0c 263 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6338 (tm-30) REVERT: 0d 112 MET cc_start: 0.6392 (ptm) cc_final: 0.6116 (ppp) REVERT: 0d 151 ASN cc_start: 0.8031 (t0) cc_final: 0.7478 (t0) REVERT: 0d 186 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: 0d 213 GLN cc_start: 0.8135 (tp40) cc_final: 0.7766 (tm-30) REVERT: 0d 225 LEU cc_start: 0.7667 (mt) cc_final: 0.7352 (mp) REVERT: 0e 18 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7707 (tp-100) REVERT: 0e 30 TYR cc_start: 0.7155 (t80) cc_final: 0.6729 (t80) REVERT: 0e 37 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: 0e 144 LEU cc_start: 0.8136 (tp) cc_final: 0.7795 (mt) REVERT: 0e 194 ASP cc_start: 0.8605 (t70) cc_final: 0.8143 (t70) REVERT: 0e 213 GLN cc_start: 0.8162 (tp40) cc_final: 0.7714 (tm-30) REVERT: 0e 220 GLU cc_start: 0.7377 (tp30) cc_final: 0.6956 (mt-10) REVERT: 0f 30 TYR cc_start: 0.7105 (t80) cc_final: 0.6382 (t80) REVERT: 0f 125 ASP cc_start: 0.7975 (p0) cc_final: 0.7704 (p0) REVERT: 0f 213 GLN cc_start: 0.8382 (tp40) cc_final: 0.7802 (tm-30) REVERT: 0f 220 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7060 (mt-10) REVERT: 0g 22 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7474 (ttm110) REVERT: 0g 141 LEU cc_start: 0.8952 (tp) cc_final: 0.8681 (mt) REVERT: 0g 194 ASP cc_start: 0.8700 (t0) cc_final: 0.8320 (t0) REVERT: 0g 213 GLN cc_start: 0.8318 (tp40) cc_final: 0.7619 (tm-30) REVERT: 0h 18 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7740 (tp-100) REVERT: 0h 30 TYR cc_start: 0.6915 (t80) cc_final: 0.6573 (t80) REVERT: 0h 44 LEU cc_start: 0.7528 (mt) cc_final: 0.7184 (mt) REVERT: 0h 112 MET cc_start: 0.5975 (tpt) cc_final: 0.4817 (ptm) REVERT: 0h 145 LYS cc_start: 0.7619 (tptp) cc_final: 0.7348 (tptp) REVERT: 0h 194 ASP cc_start: 0.8613 (t0) cc_final: 0.8265 (t0) REVERT: 0h 220 GLU cc_start: 0.7385 (tp30) cc_final: 0.6970 (mt-10) REVERT: 0i 194 ASP cc_start: 0.8811 (t0) cc_final: 0.8296 (t0) REVERT: 0i 213 GLN cc_start: 0.8271 (tp40) cc_final: 0.8009 (tm-30) REVERT: 0i 220 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7041 (mt-10) REVERT: 0i 250 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7393 (mm) REVERT: 0j 22 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: 0j 100 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.6075 (t80) REVERT: 0j 140 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8849 (tm-30) REVERT: 0j 141 LEU cc_start: 0.8886 (mt) cc_final: 0.8466 (mt) REVERT: 0j 172 LYS cc_start: 0.6932 (mmtt) cc_final: 0.6521 (mmtm) REVERT: 0j 213 GLN cc_start: 0.8229 (tp40) cc_final: 0.7921 (tm-30) REVERT: 0k 18 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7846 (tp-100) REVERT: 0k 22 ARG cc_start: 0.7912 (tpp-160) cc_final: 0.7507 (tpp-160) REVERT: 0k 26 HIS cc_start: 0.8386 (OUTLIER) cc_final: 0.8157 (t-90) REVERT: 0k 112 MET cc_start: 0.5866 (tpt) cc_final: 0.5070 (ptm) REVERT: 0k 145 LYS cc_start: 0.7676 (tptp) cc_final: 0.7337 (tptp) REVERT: 0k 194 ASP cc_start: 0.8633 (t0) cc_final: 0.8202 (t0) REVERT: 0l 18 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7949 (tp40) REVERT: 0l 22 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7273 (tpp-160) REVERT: 0l 100 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.6025 (t80) REVERT: 0l 140 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8619 (tm-30) REVERT: 0l 146 GLU cc_start: 0.7398 (tt0) cc_final: 0.7169 (tt0) REVERT: 0l 194 ASP cc_start: 0.8828 (t0) cc_final: 0.8354 (t0) REVERT: 0l 213 GLN cc_start: 0.8448 (tp40) cc_final: 0.7943 (tm-30) REVERT: 0l 218 TRP cc_start: 0.6720 (t-100) cc_final: 0.6507 (t-100) outliers start: 86 outliers final: 67 residues processed: 700 average time/residue: 0.3755 time to fit residues: 402.9631 Evaluate side-chains 680 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 604 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0a residue 52 PHE Chi-restraints excluded: chain 0a residue 54 GLU Chi-restraints excluded: chain 0a residue 100 TYR Chi-restraints excluded: chain 0a residue 186 PHE Chi-restraints excluded: chain 0b residue 24 PHE Chi-restraints excluded: chain 0b residue 37 GLN Chi-restraints excluded: chain 0b residue 52 PHE Chi-restraints excluded: chain 0b residue 185 ILE Chi-restraints excluded: chain 0b residue 186 PHE Chi-restraints excluded: chain 0b residue 198 VAL Chi-restraints excluded: chain 0b residue 278 VAL Chi-restraints excluded: chain 0c residue 54 GLU Chi-restraints excluded: chain 0c residue 63 VAL Chi-restraints excluded: chain 0c residue 100 TYR Chi-restraints excluded: chain 0c residue 170 SER Chi-restraints excluded: chain 0c residue 185 ILE Chi-restraints excluded: chain 0c residue 186 PHE Chi-restraints excluded: chain 0c residue 198 VAL Chi-restraints excluded: chain 0c residue 227 ILE Chi-restraints excluded: chain 0c residue 263 GLU Chi-restraints excluded: chain 0d residue 31 LEU Chi-restraints excluded: chain 0d residue 100 TYR Chi-restraints excluded: chain 0d residue 170 SER 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 37 GLN Chi-restraints excluded: chain 0e residue 52 PHE Chi-restraints excluded: chain 0e residue 54 GLU 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 54 GLU Chi-restraints excluded: chain 0f residue 63 VAL Chi-restraints excluded: chain 0f residue 100 TYR 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 186 PHE Chi-restraints excluded: chain 0g residue 198 VAL Chi-restraints excluded: chain 0g residue 277 LYS Chi-restraints excluded: chain 0h residue 33 SER Chi-restraints excluded: chain 0h residue 52 PHE 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 223 THR Chi-restraints excluded: chain 0i residue 24 PHE Chi-restraints excluded: chain 0i residue 63 VAL Chi-restraints excluded: chain 0i residue 100 TYR Chi-restraints excluded: chain 0i residue 136 LEU Chi-restraints excluded: chain 0i residue 185 ILE Chi-restraints excluded: chain 0i residue 186 PHE Chi-restraints excluded: chain 0i residue 198 VAL Chi-restraints excluded: chain 0i residue 227 ILE Chi-restraints excluded: chain 0i residue 250 ILE Chi-restraints excluded: chain 0j residue 100 TYR 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 277 LYS Chi-restraints excluded: chain 0k residue 26 HIS Chi-restraints excluded: chain 0k residue 170 SER 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 0l residue 54 GLU Chi-restraints excluded: chain 0l residue 63 VAL Chi-restraints excluded: chain 0l residue 100 TYR Chi-restraints excluded: chain 0l residue 123 ASN Chi-restraints excluded: chain 0l residue 186 PHE Chi-restraints excluded: chain 0l residue 198 VAL Chi-restraints excluded: chain 0l residue 223 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 58 HIS ** 0a 123 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** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 211 ASN ** 0d 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 49 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 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.234669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.228544 restraints weight = 57179.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.229363 restraints weight = 37407.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.230188 restraints weight = 26979.843| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.7809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25728 Z= 0.279 Angle : 0.843 11.056 34860 Z= 0.447 Chirality : 0.051 0.274 3756 Planarity : 0.005 0.058 4548 Dihedral : 7.140 36.076 3348 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.71 % Favored : 83.90 % Rotamer: Outliers : 3.07 % Allowed : 26.86 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.34 (0.16), residues: 1080 sheet: -3.35 (0.28), residues: 300 loop : -1.97 (0.17), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP0e 218 HIS 0.046 0.002 HIS0k 26 PHE 0.033 0.002 PHE0k 199 TYR 0.031 0.002 TYR0k 27 ARG 0.013 0.001 ARG0l 281 =============================================================================== Job complete usr+sys time: 7319.47 seconds wall clock time: 129 minutes 48.23 seconds (7788.23 seconds total)