Starting phenix.real_space_refine (version: dev) on Sat Feb 25 09:55:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/02_2023/6qx7_4662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/02_2023/6qx7_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_4662/02_2023/6qx7_4662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/02_2023/6qx7_4662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/02_2023/6qx7_4662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx7_4662/02_2023/6qx7_4662.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Process input model Symmetric amino acids flipped Residue "0a PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0a TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0a TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0b TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0b TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0c PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0c TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0c TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0d PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0d TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0d TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0e PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0e TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0e TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0f PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0f TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0f TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0g PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0g TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0g TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0h PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0h TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0h TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0i PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0i TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0i TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0j PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0j TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0j TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0k PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0k TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0k TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0l PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0l TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0l TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 25164 Number of models: 1 Model: "" Number of chains: 12 Chain: "0a" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0b" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0c" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0d" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0e" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0f" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0g" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0h" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0i" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0j" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0k" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Chain: "0l" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2097 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 1 Time building chain proxies: 14.81, per 1000 atoms: 0.59 Number of scatterers: 25164 At special positions: 0 Unit cell: (159.728, 159.728, 91.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 4764 8.00 N 4152 7.00 C 16164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.85 Conformation dependent library (CDL) restraints added in 3.6 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: 1.05 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: 7.58 Time building geometry restraints manager: 13.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6951 1.33 - 1.45: 4657 1.45 - 1.57: 13976 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 25728 Sorted by residual: bond pdb=" N ILE0c 227 " pdb=" CA ILE0c 227 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.11e-02 8.12e+03 1.50e+01 bond pdb=" N ILE0k 227 " pdb=" CA ILE0k 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.48e+01 bond pdb=" N ILE0f 227 " pdb=" CA ILE0f 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 bond pdb=" N ILE0b 227 " pdb=" CA ILE0b 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 bond pdb=" N ILE0i 227 " pdb=" CA ILE0i 227 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.11e-02 8.12e+03 1.47e+01 ... (remaining 25723 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 934 107.44 - 114.08: 13755 114.08 - 120.71: 11509 120.71 - 127.35: 8405 127.35 - 133.98: 257 Bond angle restraints: 34860 Sorted by residual: angle pdb=" N ALA0j 187 " pdb=" CA ALA0j 187 " pdb=" C ALA0j 187 " ideal model delta sigma weight residual 108.07 116.19 -8.12 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0f 187 " pdb=" CA ALA0f 187 " pdb=" C ALA0f 187 " ideal model delta sigma weight residual 108.07 116.19 -8.12 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0h 187 " pdb=" CA ALA0h 187 " pdb=" C ALA0h 187 " ideal model delta sigma weight residual 108.07 116.18 -8.11 1.38e+00 5.25e-01 3.46e+01 angle pdb=" N ALA0i 187 " pdb=" CA ALA0i 187 " pdb=" C ALA0i 187 " ideal model delta sigma weight residual 108.07 116.18 -8.11 1.38e+00 5.25e-01 3.45e+01 angle pdb=" N ALA0a 187 " pdb=" CA ALA0a 187 " pdb=" C ALA0a 187 " ideal model delta sigma weight residual 108.07 116.15 -8.08 1.38e+00 5.25e-01 3.43e+01 ... (remaining 34855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.44: 12962 10.44 - 20.88: 1811 20.88 - 31.33: 407 31.33 - 41.77: 204 41.77 - 52.21: 84 Dihedral angle restraints: 15468 sinusoidal: 6300 harmonic: 9168 Sorted by residual: dihedral pdb=" CA THR0b 91 " pdb=" C THR0b 91 " pdb=" N VAL0b 92 " pdb=" CA VAL0b 92 " ideal model delta harmonic sigma weight residual 180.00 -137.44 -42.56 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" CA THR0k 91 " pdb=" C THR0k 91 " pdb=" N VAL0k 92 " pdb=" CA VAL0k 92 " ideal model delta harmonic sigma weight residual 180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 dihedral pdb=" CA THR0j 91 " pdb=" C THR0j 91 " pdb=" N VAL0j 92 " pdb=" CA VAL0j 92 " ideal model delta harmonic sigma weight residual 180.00 -137.51 -42.49 0 5.00e+00 4.00e-02 7.22e+01 ... (remaining 15465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2347 0.048 - 0.096: 918 0.096 - 0.144: 313 0.144 - 0.192: 154 0.192 - 0.240: 24 Chirality restraints: 3756 Sorted by residual: chirality pdb=" CB VAL0d 70 " pdb=" CA VAL0d 70 " pdb=" CG1 VAL0d 70 " pdb=" CG2 VAL0d 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL0c 70 " pdb=" CA VAL0c 70 " pdb=" CG1 VAL0c 70 " pdb=" CG2 VAL0c 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB VAL0g 70 " pdb=" CA VAL0g 70 " pdb=" CG1 VAL0g 70 " pdb=" CG2 VAL0g 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3753 not shown) Planarity restraints: 4548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN0e 59 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C GLN0e 59 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN0e 59 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE0e 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN0b 59 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C GLN0b 59 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN0b 59 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE0b 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN0l 59 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C GLN0l 59 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN0l 59 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE0l 60 " -0.017 2.00e-02 2.50e+03 ... (remaining 4545 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.56: 36 1.56 - 2.40: 172 2.40 - 3.23: 25127 3.23 - 4.07: 62972 4.07 - 4.90: 114396 Warning: very small nonbonded interaction distances. Nonbonded interactions: 202703 Sorted by model distance: nonbonded pdb=" CD GLU0f 248 " pdb=" O LYS0g 228 " model vdw 0.726 3.270 nonbonded pdb=" CD GLU0j 248 " pdb=" O LYS0k 228 " model vdw 0.734 3.270 nonbonded pdb=" CD GLU0i 248 " pdb=" O LYS0j 228 " model vdw 0.739 3.270 nonbonded pdb=" CD GLU0e 248 " pdb=" O LYS0f 228 " model vdw 0.740 3.270 nonbonded pdb=" CD GLU0k 248 " pdb=" O LYS0l 228 " model vdw 0.742 3.270 ... (remaining 202698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0a' selection = chain '0b' selection = chain '0c' selection = chain '0d' selection = chain '0e' selection = chain '0f' selection = chain '0g' selection = chain '0h' selection = chain '0i' selection = chain '0j' selection = chain '0k' selection = chain '0l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 2.470 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: 0.010 Extract box with map and model: 9.140 Check model and map are aligned: 0.000 Process input model: 67.100 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 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 % 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 *********************** 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 : 3.086 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 outliers start: 48 outliers final: 20 residues processed: 1144 average time/residue: 0.4049 time to fit residues: 697.5877 Evaluate side-chains 723 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 703 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2155 time to fit residues: 12.3997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.0980 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 272 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 88 ASN 0a 89 GLN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 173 GLN 0a 188 HIS 0b 88 ASN 0b 89 GLN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 153 ASN ** 0b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 173 GLN 0b 188 HIS ** 0c 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 88 ASN 0c 89 GLN 0c 123 ASN ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 173 GLN 0c 188 HIS 0d 26 HIS 0d 88 ASN 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 173 GLN 0d 188 HIS ** 0e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 26 HIS ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 88 ASN 0e 89 GLN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 167 ASN 0e 168 GLN 0e 188 HIS ** 0f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 88 ASN 0f 89 GLN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 167 ASN 0f 173 GLN 0f 188 HIS 0g 26 HIS 0g 88 ASN 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 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 173 GLN 0h 188 HIS 0i 29 ASN 0i 32 GLN 0i 88 ASN 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 88 ASN 0j 89 GLN 0j 123 ASN 0j 153 ASN 0j 167 ASN 0j 173 GLN 0j 188 HIS ** 0k 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 88 ASN 0k 89 GLN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 153 ASN 0k 167 ASN 0k 168 GLN 0k 188 HIS ** 0l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 88 ASN 0l 89 GLN 0l 123 ASN ** 0l 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 168 GLN 0l 173 GLN 0l 188 HIS Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 25728 Z= 0.224 Angle : 0.823 7.332 34860 Z= 0.451 Chirality : 0.049 0.171 3756 Planarity : 0.005 0.045 4548 Dihedral : 8.364 38.479 3348 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 1.59 % Allowed : 15.71 % Favored : 82.71 % Rotamer Outliers : 4.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.92 % 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: -3.58 (0.14), residues: 3024 helix: -1.60 (0.14), residues: 1068 sheet: -3.47 (0.24), residues: 372 loop : -2.68 (0.15), residues: 1584 *********************** 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 898 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 771 time to evaluate : 2.732 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 outliers start: 127 outliers final: 56 residues processed: 846 average time/residue: 0.4420 time to fit residues: 549.4849 Evaluate side-chains 701 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 645 time to evaluate : 3.096 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2352 time to fit residues: 29.0503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 272 optimal weight: 0.3980 chunk 294 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 270 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 88 ASN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 167 ASN 0a 168 GLN 0b 21 ASN 0b 88 ASN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 168 GLN 0b 249 GLN 0c 29 ASN 0c 32 GLN 0c 88 ASN 0c 152 GLN 0c 167 ASN 0c 168 GLN 0d 88 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 167 ASN 0d 168 GLN ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 88 ASN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 173 GLN 0f 29 ASN 0f 32 GLN ** 0f 88 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** ** 0f 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 168 GLN ** 0g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 88 ASN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 167 ASN 0g 168 GLN ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 88 ASN ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 168 GLN 0i 88 ASN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 167 ASN 0i 173 GLN 0j 88 ASN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 168 GLN 0k 88 ASN ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 29 ASN 0l 32 GLN ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 88 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 167 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25728 Z= 0.202 Angle : 0.766 7.503 34860 Z= 0.419 Chirality : 0.046 0.145 3756 Planarity : 0.005 0.051 4548 Dihedral : 7.885 37.165 3348 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.43 % Allowed : 16.20 % Favored : 83.37 % Rotamer Outliers : 3.18 % 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: -2.79 (0.15), residues: 3024 helix: -0.59 (0.15), residues: 1080 sheet: -3.93 (0.25), residues: 300 loop : -2.36 (0.16), residues: 1644 *********************** 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 831 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 744 time to evaluate : 2.952 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 outliers start: 87 outliers final: 36 residues processed: 792 average time/residue: 0.4232 time to fit residues: 503.1439 Evaluate side-chains 696 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 660 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2402 time to fit residues: 20.2018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 21 ASN 0a 59 GLN 0a 88 ASN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 153 ASN 0a 211 ASN 0a 213 GLN ** 0b 32 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** 0b 167 ASN 0b 211 ASN ** 0c 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 58 HIS ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN 0c 153 ASN ** 0d 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 21 ASN 0d 59 GLN ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN 0d 211 ASN ** 0d 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 26 HIS ** 0e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 211 ASN 0f 58 HIS ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 153 ASN ** 0g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 59 GLN ** 0g 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN 0h 26 HIS ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 32 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 0h 167 ASN ** 0h 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 58 HIS ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 151 ASN ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 59 GLN ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 151 ASN ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 26 HIS ** 0k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 25728 Z= 0.285 Angle : 0.827 8.516 34860 Z= 0.448 Chirality : 0.048 0.153 3756 Planarity : 0.005 0.054 4548 Dihedral : 7.837 36.481 3348 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.43 % Allowed : 16.80 % Favored : 82.77 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -2.52 (0.15), residues: 3024 helix: -0.28 (0.15), residues: 1044 sheet: -3.68 (0.25), residues: 300 loop : -2.25 (0.16), residues: 1680 *********************** 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 799 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 704 time to evaluate : 2.944 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 outliers start: 95 outliers final: 44 residues processed: 780 average time/residue: 0.4006 time to fit residues: 473.2068 Evaluate side-chains 696 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 652 time to evaluate : 3.145 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2464 time to fit residues: 23.9447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 215 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 260 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 58 HIS 0a 59 GLN 0a 88 ASN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 58 HIS ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 59 GLN ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 123 ASN 0c 173 GLN 0c 211 ASN 0d 21 ASN ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 59 GLN ** 0d 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN ** 0f 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 173 GLN 0f 211 ASN 0g 49 ASN 0g 59 GLN ** 0g 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 213 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 151 ASN ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 211 ASN ** 0i 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 58 HIS 0j 59 GLN ** 0j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 173 GLN ** 0k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** 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 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 211 ASN ** 0l 29 ASN ** 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** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 25728 Z= 0.313 Angle : 0.845 8.567 34860 Z= 0.459 Chirality : 0.049 0.149 3756 Planarity : 0.005 0.054 4548 Dihedral : 7.967 36.938 3348 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 16.87 % Favored : 82.74 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.82 % 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: -2.58 (0.15), residues: 3024 helix: -0.38 (0.15), residues: 1044 sheet: -3.59 (0.25), residues: 300 loop : -2.29 (0.16), residues: 1680 *********************** 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 761 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 697 time to evaluate : 2.901 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 outliers start: 64 outliers final: 37 residues processed: 741 average time/residue: 0.4231 time to fit residues: 473.6966 Evaluate side-chains 694 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 657 time to evaluate : 3.028 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2683 time to fit residues: 21.7001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 59 GLN ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 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 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 59 GLN ** 0c 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 151 ASN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 88 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 173 GLN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 151 ASN ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 173 GLN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN 0f 88 ASN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 151 ASN ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 59 GLN 0g 88 ASN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 249 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 29 ASN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 151 ASN ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 88 ASN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** 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 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 59 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 211 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 25728 Z= 0.216 Angle : 0.790 10.146 34860 Z= 0.423 Chirality : 0.047 0.199 3756 Planarity : 0.005 0.055 4548 Dihedral : 7.406 36.194 3348 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.24 % Favored : 84.36 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -2.38 (0.16), residues: 3024 helix: -0.14 (0.15), residues: 1068 sheet: -3.63 (0.26), residues: 300 loop : -2.21 (0.17), residues: 1656 *********************** 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 746 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 667 time to evaluate : 3.046 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 outliers start: 79 outliers final: 54 residues processed: 713 average time/residue: 0.4096 time to fit residues: 443.4377 Evaluate side-chains 664 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 610 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2403 time to fit residues: 28.0188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 165 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 153 ASN 0b 32 GLN ** 0b 108 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 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 59 GLN 0c 88 ASN 0c 152 GLN ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 88 ASN ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 152 GLN ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 59 GLN 0f 88 ASN ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 152 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 249 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 21 ASN 0i 59 GLN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 211 ASN ** 0k 37 GLN ** 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 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 25728 Z= 0.213 Angle : 0.797 10.688 34860 Z= 0.426 Chirality : 0.048 0.205 3756 Planarity : 0.005 0.058 4548 Dihedral : 7.196 36.227 3348 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.18 % Favored : 84.42 % Rotamer Outliers : 1.28 % 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: -2.17 (0.16), residues: 3024 helix: 0.16 (0.15), residues: 1056 sheet: -3.69 (0.26), residues: 300 loop : -2.12 (0.17), residues: 1668 *********************** 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 660 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 625 time to evaluate : 3.031 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 outliers start: 35 outliers final: 20 residues processed: 647 average time/residue: 0.4048 time to fit residues: 399.5953 Evaluate side-chains 606 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 586 time to evaluate : 3.063 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2650 time to fit residues: 13.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.0370 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 227 optimal weight: 0.2980 chunk 263 optimal weight: 0.8980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 153 ASN 0a 173 GLN ** 0a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 21 ASN ** 0b 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 29 ASN ** 0c 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 181 ASN ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 153 ASN ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 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** 0f 181 ASN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 211 ASN ** 0g 249 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 21 ASN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 173 GLN 0i 211 ASN ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 59 GLN ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN 0l 152 GLN 0l 215 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.7722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25728 Z= 0.199 Angle : 0.787 11.634 34860 Z= 0.417 Chirality : 0.047 0.216 3756 Planarity : 0.005 0.059 4548 Dihedral : 6.891 35.530 3348 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.89 % Favored : 85.71 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 3024 helix: 0.41 (0.16), residues: 1068 sheet: -3.59 (0.39), residues: 132 loop : -2.39 (0.16), residues: 1824 *********************** 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 664 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 637 time to evaluate : 2.805 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 outliers start: 27 outliers final: 15 residues processed: 644 average time/residue: 0.4100 time to fit residues: 405.5147 Evaluate side-chains 595 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 580 time to evaluate : 2.807 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2360 time to fit residues: 10.4314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 254 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 173 GLN ** 0b 108 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 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 58 HIS ** 0d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 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 58 HIS ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** 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 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.7896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 25728 Z= 0.238 Angle : 0.818 11.495 34860 Z= 0.431 Chirality : 0.048 0.261 3756 Planarity : 0.005 0.074 4548 Dihedral : 6.982 35.468 3348 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.34 % Favored : 84.26 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.16), residues: 3024 helix: 0.39 (0.16), residues: 1068 sheet: -3.63 (0.26), residues: 300 loop : -2.23 (0.17), residues: 1656 *********************** 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 633 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 607 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 620 average time/residue: 0.3996 time to fit residues: 377.0685 Evaluate side-chains 583 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 574 time to evaluate : 3.130 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3082 time to fit residues: 9.1183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 chunk 275 optimal weight: 4.9990 chunk 237 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 183 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 215 ASN ** 0a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 108 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 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 49 ASN ** 0d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 58 HIS ** 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** 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 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.8138 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= 0.229 Angle : 0.829 12.407 34860 Z= 0.438 Chirality : 0.048 0.272 3756 Planarity : 0.005 0.061 4548 Dihedral : 6.960 35.616 3348 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.11 % Favored : 84.49 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -2.12 (0.16), residues: 3024 helix: 0.41 (0.16), residues: 1056 sheet: -3.57 (0.26), residues: 300 loop : -2.29 (0.17), residues: 1668 ********************** 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 615 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 608 time to evaluate : 3.365 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 outliers start: 7 outliers final: 5 residues processed: 611 average time/residue: 0.4120 time to fit residues: 382.4158 Evaluate side-chains 591 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 586 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2347 time to fit residues: 6.6655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 219 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 108 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 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 215 ASN ** 0d 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 155 GLN ** 0e 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 21 ASN ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** 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** ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.238048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.232371 restraints weight = 56821.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.233357 restraints weight = 36440.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.234098 restraints weight = 25011.291| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.8301 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= 0.238 Angle : 0.853 12.181 34860 Z= 0.446 Chirality : 0.048 0.263 3756 Planarity : 0.005 0.060 4548 Dihedral : 6.960 36.940 3348 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.40 % Allowed : 15.31 % Favored : 84.29 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -2.07 (0.16), residues: 3024 helix: 0.44 (0.15), residues: 1068 sheet: -3.53 (0.27), residues: 300 loop : -2.26 (0.17), residues: 1656 =============================================================================== Job complete usr+sys time: 7158.81 seconds wall clock time: 130 minutes 27.72 seconds (7827.72 seconds total)