Starting phenix.real_space_refine on Mon Aug 25 08:30:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dn1_47023/08_2025/9dn1_47023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dn1_47023/08_2025/9dn1_47023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dn1_47023/08_2025/9dn1_47023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dn1_47023/08_2025/9dn1_47023.map" model { file = "/net/cci-nas-00/data/ceres_data/9dn1_47023/08_2025/9dn1_47023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dn1_47023/08_2025/9dn1_47023.cif" } resolution = 2.9 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 8745 2.51 5 N 2189 2.21 5 O 2387 1.98 5 H 13486 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26895 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "I" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "J" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "K" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "L" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "M" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "N" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "O" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "P" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "R" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2445 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Time building chain proxies: 4.12, per 1000 atoms: 0.15 Number of scatterers: 26895 At special positions: 0 Unit cell: (143.055, 143.922, 65.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 O 2387 8.00 N 2189 7.00 C 8745 6.00 H 13486 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 810.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 1 sheets defined 74.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 79 through 89 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 112 through 117 Processing helix chain 'H' and resid 124 through 153 removed outlier: 3.890A pdb=" N SER H 129 " --> pdb=" O PRO H 125 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE H 136 " --> pdb=" O LYS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 175 removed outlier: 3.657A pdb=" N ILE H 159 " --> pdb=" O PHE H 155 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 189 removed outlier: 3.650A pdb=" N PHE H 179 " --> pdb=" O MET H 175 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 210 removed outlier: 3.825A pdb=" N TRP H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 201 " --> pdb=" O PHE H 197 " (cutoff:3.500A) Proline residue: H 204 - end of helix removed outlier: 3.560A pdb=" N GLY H 209 " --> pdb=" O ILE H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 214 Processing helix chain 'I' and resid 80 through 89 Processing helix chain 'I' and resid 105 through 109 Processing helix chain 'I' and resid 112 through 117 Processing helix chain 'I' and resid 124 through 153 removed outlier: 3.881A pdb=" N SER I 129 " --> pdb=" O PRO I 125 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL I 130 " --> pdb=" O ALA I 126 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 175 removed outlier: 3.907A pdb=" N ILE I 159 " --> pdb=" O PHE I 155 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE I 164 " --> pdb=" O THR I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 189 removed outlier: 3.703A pdb=" N PHE I 179 " --> pdb=" O MET I 175 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER I 189 " --> pdb=" O LEU I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 203 removed outlier: 3.817A pdb=" N TRP I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY I 201 " --> pdb=" O PHE I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 209 removed outlier: 3.573A pdb=" N GLY I 209 " --> pdb=" O ILE I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 214 removed outlier: 3.505A pdb=" N LEU I 213 " --> pdb=" O SER I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 105 through 109 Processing helix chain 'J' and resid 112 through 117 Processing helix chain 'J' and resid 124 through 153 removed outlier: 3.868A pdb=" N SER J 129 " --> pdb=" O PRO J 125 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE J 136 " --> pdb=" O LYS J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 175 removed outlier: 3.704A pdb=" N ILE J 159 " --> pdb=" O PHE J 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE J 164 " --> pdb=" O THR J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 189 removed outlier: 3.646A pdb=" N PHE J 179 " --> pdb=" O MET J 175 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 210 removed outlier: 3.821A pdb=" N TRP J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY J 201 " --> pdb=" O PHE J 197 " (cutoff:3.500A) Proline residue: J 204 - end of helix removed outlier: 3.561A pdb=" N GLY J 209 " --> pdb=" O ILE J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 214 Processing helix chain 'K' and resid 80 through 89 Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 112 through 117 Processing helix chain 'K' and resid 124 through 153 removed outlier: 3.886A pdb=" N SER K 129 " --> pdb=" O PRO K 125 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL K 130 " --> pdb=" O ALA K 126 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 175 removed outlier: 3.706A pdb=" N ILE K 159 " --> pdb=" O PHE K 155 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE K 164 " --> pdb=" O THR K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 189 removed outlier: 3.698A pdb=" N PHE K 179 " --> pdb=" O MET K 175 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 209 removed outlier: 3.818A pdb=" N TRP K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY K 201 " --> pdb=" O PHE K 197 " (cutoff:3.500A) Proline residue: K 204 - end of helix removed outlier: 3.561A pdb=" N GLY K 209 " --> pdb=" O ILE K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 214 Processing helix chain 'L' and resid 80 through 89 Processing helix chain 'L' and resid 105 through 109 Processing helix chain 'L' and resid 112 through 117 Processing helix chain 'L' and resid 124 through 153 removed outlier: 3.878A pdb=" N SER L 129 " --> pdb=" O PRO L 125 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL L 130 " --> pdb=" O ALA L 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE L 136 " --> pdb=" O LYS L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 175 removed outlier: 3.712A pdb=" N ILE L 159 " --> pdb=" O PHE L 155 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 189 removed outlier: 3.660A pdb=" N PHE L 179 " --> pdb=" O MET L 175 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER L 189 " --> pdb=" O LEU L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 209 removed outlier: 3.817A pdb=" N TRP L 194 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY L 201 " --> pdb=" O PHE L 197 " (cutoff:3.500A) Proline residue: L 204 - end of helix removed outlier: 3.556A pdb=" N GLY L 209 " --> pdb=" O ILE L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 214 Processing helix chain 'M' and resid 80 through 89 Processing helix chain 'M' and resid 105 through 109 Processing helix chain 'M' and resid 112 through 117 Processing helix chain 'M' and resid 124 through 153 removed outlier: 3.887A pdb=" N SER M 129 " --> pdb=" O PRO M 125 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL M 130 " --> pdb=" O ALA M 126 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE M 136 " --> pdb=" O LYS M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 175 removed outlier: 3.743A pdb=" N ILE M 159 " --> pdb=" O PHE M 155 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE M 164 " --> pdb=" O THR M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 189 removed outlier: 3.655A pdb=" N PHE M 179 " --> pdb=" O MET M 175 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 189 " --> pdb=" O LEU M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 210 removed outlier: 3.822A pdb=" N TRP M 194 " --> pdb=" O LEU M 190 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY M 201 " --> pdb=" O PHE M 197 " (cutoff:3.500A) Proline residue: M 204 - end of helix removed outlier: 3.573A pdb=" N GLY M 209 " --> pdb=" O ILE M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 214 Processing helix chain 'N' and resid 80 through 89 Processing helix chain 'N' and resid 105 through 109 Processing helix chain 'N' and resid 112 through 117 Processing helix chain 'N' and resid 124 through 153 removed outlier: 3.884A pdb=" N SER N 129 " --> pdb=" O PRO N 125 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL N 130 " --> pdb=" O ALA N 126 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE N 136 " --> pdb=" O LYS N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 175 removed outlier: 3.713A pdb=" N ILE N 159 " --> pdb=" O PHE N 155 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE N 164 " --> pdb=" O THR N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 189 removed outlier: 3.676A pdb=" N PHE N 179 " --> pdb=" O MET N 175 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER N 189 " --> pdb=" O LEU N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 210 removed outlier: 3.817A pdb=" N TRP N 194 " --> pdb=" O LEU N 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY N 201 " --> pdb=" O PHE N 197 " (cutoff:3.500A) Proline residue: N 204 - end of helix removed outlier: 3.564A pdb=" N GLY N 209 " --> pdb=" O ILE N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 214 Processing helix chain 'O' and resid 80 through 89 Processing helix chain 'O' and resid 105 through 109 Processing helix chain 'O' and resid 112 through 117 Processing helix chain 'O' and resid 124 through 153 removed outlier: 3.903A pdb=" N SER O 129 " --> pdb=" O PRO O 125 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL O 130 " --> pdb=" O ALA O 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE O 136 " --> pdb=" O LYS O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 175 removed outlier: 3.702A pdb=" N ILE O 159 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE O 164 " --> pdb=" O THR O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 189 removed outlier: 3.700A pdb=" N PHE O 179 " --> pdb=" O MET O 175 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER O 189 " --> pdb=" O LEU O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 210 removed outlier: 3.820A pdb=" N TRP O 194 " --> pdb=" O LEU O 190 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY O 201 " --> pdb=" O PHE O 197 " (cutoff:3.500A) Proline residue: O 204 - end of helix removed outlier: 3.554A pdb=" N GLY O 209 " --> pdb=" O ILE O 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 214 Processing helix chain 'P' and resid 80 through 89 Processing helix chain 'P' and resid 105 through 109 Processing helix chain 'P' and resid 112 through 117 Processing helix chain 'P' and resid 124 through 153 removed outlier: 3.893A pdb=" N SER P 129 " --> pdb=" O PRO P 125 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL P 130 " --> pdb=" O ALA P 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE P 136 " --> pdb=" O LYS P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 175 removed outlier: 3.728A pdb=" N ILE P 159 " --> pdb=" O PHE P 155 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE P 164 " --> pdb=" O THR P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 189 removed outlier: 3.678A pdb=" N PHE P 179 " --> pdb=" O MET P 175 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER P 189 " --> pdb=" O LEU P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 209 removed outlier: 3.820A pdb=" N TRP P 194 " --> pdb=" O LEU P 190 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY P 201 " --> pdb=" O PHE P 197 " (cutoff:3.500A) Proline residue: P 204 - end of helix removed outlier: 3.550A pdb=" N GLY P 209 " --> pdb=" O ILE P 205 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 214 Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 105 through 109 Processing helix chain 'Q' and resid 112 through 117 Processing helix chain 'Q' and resid 124 through 153 removed outlier: 3.891A pdb=" N SER Q 129 " --> pdb=" O PRO Q 125 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL Q 130 " --> pdb=" O ALA Q 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE Q 136 " --> pdb=" O LYS Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 175 removed outlier: 3.739A pdb=" N ILE Q 159 " --> pdb=" O PHE Q 155 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE Q 164 " --> pdb=" O THR Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 189 removed outlier: 3.663A pdb=" N PHE Q 179 " --> pdb=" O MET Q 175 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER Q 189 " --> pdb=" O LEU Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 209 removed outlier: 3.820A pdb=" N TRP Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY Q 201 " --> pdb=" O PHE Q 197 " (cutoff:3.500A) Proline residue: Q 204 - end of helix removed outlier: 3.552A pdb=" N GLY Q 209 " --> pdb=" O ILE Q 205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 214 Processing helix chain 'R' and resid 80 through 89 Processing helix chain 'R' and resid 105 through 109 Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 124 through 153 removed outlier: 3.886A pdb=" N SER R 129 " --> pdb=" O PRO R 125 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL R 130 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE R 136 " --> pdb=" O LYS R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 175 removed outlier: 3.844A pdb=" N ILE R 159 " --> pdb=" O PHE R 155 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE R 164 " --> pdb=" O THR R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 189 removed outlier: 3.696A pdb=" N PHE R 179 " --> pdb=" O MET R 175 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER R 189 " --> pdb=" O LEU R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 3.819A pdb=" N TRP R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY R 201 " --> pdb=" O PHE R 197 " (cutoff:3.500A) Proline residue: R 204 - end of helix removed outlier: 3.565A pdb=" N GLY R 209 " --> pdb=" O ILE R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 214 Processing sheet with id=AA1, first strand: chain 'H' and resid 216 through 230 removed outlier: 6.672A pdb=" N GLN K 217 " --> pdb=" O ILE L 216 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL L 218 " --> pdb=" O GLN K 217 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG K 219 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU L 220 " --> pdb=" O ARG K 219 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY K 221 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N MET L 222 " --> pdb=" O GLY K 221 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU K 223 " --> pdb=" O MET L 222 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY L 224 " --> pdb=" O GLU K 223 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS K 225 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA L 226 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG K 227 " --> pdb=" O ALA L 226 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N HIS L 228 " --> pdb=" O ARG K 227 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS K 229 " --> pdb=" O HIS L 228 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N GLU L 230 " --> pdb=" O LYS K 229 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN J 217 " --> pdb=" O ILE K 216 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL K 218 " --> pdb=" O GLN J 217 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG J 219 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU K 220 " --> pdb=" O ARG J 219 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY J 221 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N MET K 222 " --> pdb=" O GLY J 221 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU J 223 " --> pdb=" O MET K 222 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N GLY K 224 " --> pdb=" O GLU J 223 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS J 225 " --> pdb=" O GLY K 224 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ALA K 226 " --> pdb=" O LYS J 225 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG J 227 " --> pdb=" O ALA K 226 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N HIS K 228 " --> pdb=" O ARG J 227 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS J 229 " --> pdb=" O HIS K 228 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N GLU K 230 " --> pdb=" O LYS J 229 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN I 217 " --> pdb=" O ILE J 216 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N VAL J 218 " --> pdb=" O GLN I 217 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG I 219 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU J 220 " --> pdb=" O ARG I 219 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY I 221 " --> pdb=" O LEU J 220 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N MET J 222 " --> pdb=" O GLY I 221 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU I 223 " --> pdb=" O MET J 222 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY J 224 " --> pdb=" O GLU I 223 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS I 225 " --> pdb=" O GLY J 224 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ALA J 226 " --> pdb=" O LYS I 225 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG I 227 " --> pdb=" O ALA J 226 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N HIS J 228 " --> pdb=" O ARG I 227 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LYS I 229 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N GLU J 230 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN H 217 " --> pdb=" O ILE R 216 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL R 218 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG H 219 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU R 220 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY H 221 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET R 222 " --> pdb=" O GLY H 221 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU H 223 " --> pdb=" O MET R 222 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N GLY R 224 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS H 225 " --> pdb=" O GLY R 224 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ALA R 226 " --> pdb=" O LYS H 225 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG H 227 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS R 228 " --> pdb=" O ARG H 227 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS H 229 " --> pdb=" O HIS R 228 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU R 230 " --> pdb=" O LYS H 229 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2484 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: 5.89 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13486 1.03 - 1.23: 92 1.23 - 1.43: 5750 1.43 - 1.62: 7710 1.62 - 1.82: 176 Bond restraints: 27214 Sorted by residual: bond pdb=" CG LEU R 156 " pdb=" CD1 LEU R 156 " ideal model delta sigma weight residual 1.521 1.382 0.139 3.30e-02 9.18e+02 1.78e+01 bond pdb=" N GLU O 79 " pdb=" CA GLU O 79 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.30e+00 bond pdb=" N GLU I 79 " pdb=" CA GLU I 79 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.27e+00 bond pdb=" N GLU M 79 " pdb=" CA GLU M 79 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N GLU R 79 " pdb=" CA GLU R 79 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.23e+00 ... (remaining 27209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 47025 1.39 - 2.79: 1933 2.79 - 4.18: 161 4.18 - 5.57: 27 5.57 - 6.97: 13 Bond angle restraints: 49159 Sorted by residual: angle pdb=" N GLY Q 224 " pdb=" CA GLY Q 224 " pdb=" C GLY Q 224 " ideal model delta sigma weight residual 110.87 117.06 -6.19 1.54e+00 4.22e-01 1.61e+01 angle pdb=" N GLY H 224 " pdb=" CA GLY H 224 " pdb=" C GLY H 224 " ideal model delta sigma weight residual 110.87 117.04 -6.17 1.54e+00 4.22e-01 1.60e+01 angle pdb=" N GLY M 224 " pdb=" CA GLY M 224 " pdb=" C GLY M 224 " ideal model delta sigma weight residual 110.87 117.01 -6.14 1.54e+00 4.22e-01 1.59e+01 angle pdb=" N GLY P 224 " pdb=" CA GLY P 224 " pdb=" C GLY P 224 " ideal model delta sigma weight residual 110.87 116.98 -6.11 1.54e+00 4.22e-01 1.58e+01 angle pdb=" N GLY O 224 " pdb=" CA GLY O 224 " pdb=" C GLY O 224 " ideal model delta sigma weight residual 110.87 116.98 -6.11 1.54e+00 4.22e-01 1.58e+01 ... (remaining 49154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 11653 17.74 - 35.48: 687 35.48 - 53.23: 351 53.23 - 70.97: 119 70.97 - 88.71: 27 Dihedral angle restraints: 12837 sinusoidal: 6864 harmonic: 5973 Sorted by residual: dihedral pdb=" CA ASP L 115 " pdb=" CB ASP L 115 " pdb=" CG ASP L 115 " pdb=" OD1 ASP L 115 " ideal model delta sinusoidal sigma weight residual -30.00 -88.93 58.93 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA LEU R 213 " pdb=" C LEU R 213 " pdb=" N SER R 214 " pdb=" CA SER R 214 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LEU Q 213 " pdb=" C LEU Q 213 " pdb=" N SER Q 214 " pdb=" CA SER Q 214 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 12834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1074 0.026 - 0.052: 543 0.052 - 0.077: 233 0.077 - 0.103: 98 0.103 - 0.129: 43 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA ILE N 159 " pdb=" N ILE N 159 " pdb=" C ILE N 159 " pdb=" CB ILE N 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE K 159 " pdb=" N ILE K 159 " pdb=" C ILE K 159 " pdb=" CB ILE K 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE Q 159 " pdb=" N ILE Q 159 " pdb=" C ILE Q 159 " pdb=" CB ILE Q 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1988 not shown) Planarity restraints: 3949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS M 122 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO M 123 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO M 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO M 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 122 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO L 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 123 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 122 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO Q 123 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO Q 123 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO Q 123 " 0.020 5.00e-02 4.00e+02 ... (remaining 3946 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 3368 2.27 - 2.85: 57711 2.85 - 3.44: 64863 3.44 - 4.02: 86659 4.02 - 4.60: 136274 Nonbonded interactions: 348875 Sorted by model distance: nonbonded pdb=" OD1 ASP K 100 " pdb=" H TYR K 102 " model vdw 1.689 2.450 nonbonded pdb=" OD1 ASP O 100 " pdb=" H TYR O 102 " model vdw 1.723 2.450 nonbonded pdb=" OD1 ASP P 100 " pdb=" H TYR P 102 " model vdw 1.732 2.450 nonbonded pdb=" OD1 ASP H 100 " pdb=" H TYR H 102 " model vdw 1.800 2.450 nonbonded pdb=" OD1 ASP Q 100 " pdb=" H TYR Q 102 " model vdw 1.838 2.450 ... (remaining 348870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.150 Extract box with map and model: 0.240 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.120 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 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 : 0.003 0.139 13728 Z= 0.174 Angle : 0.660 6.967 18480 Z= 0.371 Chirality : 0.040 0.129 1991 Planarity : 0.005 0.036 2354 Dihedral : 16.000 88.709 5093 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.64 % Allowed : 10.37 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1661 helix: 0.98 (0.16), residues: 1078 sheet: None (None), residues: 0 loop : -1.18 (0.21), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 87 TYR 0.007 0.001 TYR I 174 PHE 0.017 0.002 PHE H 155 TRP 0.002 0.001 TRP K 194 HIS 0.002 0.001 HIS J 228 Details of bonding type rmsd covalent geometry : bond 0.00346 (13728) covalent geometry : angle 0.65981 (18480) hydrogen bonds : bond 0.19030 ( 872) hydrogen bonds : angle 5.23927 ( 2484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 307 time to evaluate : 0.444 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: I 215 ASN cc_start: 0.8581 (t0) cc_final: 0.8042 (t0) REVERT: J 186 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8574 (tp) REVERT: J 215 ASN cc_start: 0.8582 (t0) cc_final: 0.8035 (t0) REVERT: K 115 ASP cc_start: 0.9033 (m-30) cc_final: 0.8710 (m-30) REVERT: K 215 ASN cc_start: 0.8545 (t0) cc_final: 0.8144 (t0) REVERT: L 155 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7893 (t80) REVERT: L 186 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8516 (tp) REVERT: L 215 ASN cc_start: 0.8567 (t0) cc_final: 0.8040 (t0) REVERT: M 171 MET cc_start: 0.8480 (mtt) cc_final: 0.8265 (mtm) REVERT: M 215 ASN cc_start: 0.8631 (t0) cc_final: 0.8109 (t0) REVERT: N 186 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8368 (tp) REVERT: N 215 ASN cc_start: 0.8651 (t0) cc_final: 0.8112 (t0) REVERT: O 215 ASN cc_start: 0.8591 (t0) cc_final: 0.8065 (t0) REVERT: P 215 ASN cc_start: 0.8583 (t0) cc_final: 0.8144 (t0) REVERT: Q 215 ASN cc_start: 0.8609 (t0) cc_final: 0.8155 (t0) REVERT: R 215 ASN cc_start: 0.8553 (t0) cc_final: 0.8006 (t0) outliers start: 9 outliers final: 5 residues processed: 313 average time/residue: 1.2827 time to fit residues: 434.1906 Evaluate side-chains 314 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 305 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain N residue 141 MET Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain P residue 141 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.088989 restraints weight = 52410.630| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.30 r_work: 0.2891 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13728 Z= 0.148 Angle : 0.571 4.455 18480 Z= 0.312 Chirality : 0.037 0.112 1991 Planarity : 0.005 0.033 2354 Dihedral : 5.825 54.493 1859 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.78 % Allowed : 11.08 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.20), residues: 1661 helix: 1.90 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 87 TYR 0.007 0.001 TYR N 138 PHE 0.016 0.001 PHE R 155 TRP 0.002 0.000 TRP O 194 HIS 0.002 0.001 HIS I 228 Details of bonding type rmsd covalent geometry : bond 0.00313 (13728) covalent geometry : angle 0.57051 (18480) hydrogen bonds : bond 0.06974 ( 872) hydrogen bonds : angle 4.00272 ( 2484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 300 time to evaluate : 0.762 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: I 215 ASN cc_start: 0.8483 (t0) cc_final: 0.8089 (t0) REVERT: J 186 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8528 (tp) REVERT: K 186 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8386 (tp) REVERT: L 186 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8561 (tp) REVERT: M 186 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8470 (tp) REVERT: M 215 ASN cc_start: 0.8467 (t0) cc_final: 0.8045 (t0) REVERT: N 186 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8385 (tp) REVERT: N 215 ASN cc_start: 0.8520 (t0) cc_final: 0.8031 (t0) REVERT: O 215 ASN cc_start: 0.8499 (t0) cc_final: 0.8065 (t0) REVERT: P 215 ASN cc_start: 0.8624 (t0) cc_final: 0.8247 (t0) REVERT: Q 215 ASN cc_start: 0.8644 (t0) cc_final: 0.8283 (t0) REVERT: R 186 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8436 (tp) outliers start: 11 outliers final: 0 residues processed: 308 average time/residue: 1.2173 time to fit residues: 406.4261 Evaluate side-chains 296 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 290 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 142 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 228 HIS O 228 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.087525 restraints weight = 52758.163| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.29 r_work: 0.2865 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13728 Z= 0.148 Angle : 0.540 4.573 18480 Z= 0.298 Chirality : 0.037 0.119 1991 Planarity : 0.004 0.032 2354 Dihedral : 4.927 53.754 1845 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.92 % Allowed : 12.93 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1661 helix: 2.05 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.14 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 87 TYR 0.009 0.001 TYR N 138 PHE 0.008 0.001 PHE J 170 TRP 0.003 0.001 TRP K 194 HIS 0.004 0.001 HIS O 228 Details of bonding type rmsd covalent geometry : bond 0.00324 (13728) covalent geometry : angle 0.54004 (18480) hydrogen bonds : bond 0.06923 ( 872) hydrogen bonds : angle 3.91957 ( 2484) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 299 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 215 ASN cc_start: 0.8567 (t0) cc_final: 0.8206 (t0) REVERT: J 186 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8502 (tp) REVERT: K 186 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8373 (tp) REVERT: L 186 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8551 (tp) REVERT: M 186 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8481 (tp) REVERT: M 215 ASN cc_start: 0.8530 (t0) cc_final: 0.8047 (t0) REVERT: N 186 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8354 (tp) REVERT: N 215 ASN cc_start: 0.8573 (t0) cc_final: 0.8079 (t0) REVERT: O 97 GLN cc_start: 0.8300 (tt0) cc_final: 0.8088 (tt0) REVERT: O 215 ASN cc_start: 0.8533 (t0) cc_final: 0.8083 (t0) REVERT: P 87 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8024 (ttp80) REVERT: P 215 ASN cc_start: 0.8638 (t0) cc_final: 0.8178 (t0) REVERT: Q 215 ASN cc_start: 0.8668 (t0) cc_final: 0.8239 (t0) REVERT: R 186 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8412 (tp) outliers start: 13 outliers final: 3 residues processed: 305 average time/residue: 1.2238 time to fit residues: 404.2529 Evaluate side-chains 300 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 290 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain P residue 87 ARG Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.087364 restraints weight = 52727.927| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.30 r_work: 0.2868 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13728 Z= 0.146 Angle : 0.524 4.566 18480 Z= 0.287 Chirality : 0.036 0.120 1991 Planarity : 0.004 0.031 2354 Dihedral : 4.863 55.235 1845 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.21 % Allowed : 14.91 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.20), residues: 1661 helix: 2.16 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.20 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.009 0.001 TYR M 138 PHE 0.016 0.001 PHE R 155 TRP 0.003 0.001 TRP M 194 HIS 0.003 0.001 HIS I 228 Details of bonding type rmsd covalent geometry : bond 0.00324 (13728) covalent geometry : angle 0.52401 (18480) hydrogen bonds : bond 0.06539 ( 872) hydrogen bonds : angle 3.83610 ( 2484) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 298 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 155 PHE cc_start: 0.8558 (t80) cc_final: 0.8334 (t80) REVERT: I 215 ASN cc_start: 0.8519 (t0) cc_final: 0.8162 (t0) REVERT: J 186 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8482 (tp) REVERT: K 175 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8675 (mtt) REVERT: K 186 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8353 (tp) REVERT: L 86 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8262 (mm-30) REVERT: L 186 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8528 (tp) REVERT: M 186 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (tp) REVERT: M 215 ASN cc_start: 0.8533 (t0) cc_final: 0.8064 (t0) REVERT: N 186 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8363 (tp) REVERT: N 215 ASN cc_start: 0.8552 (t0) cc_final: 0.8070 (t0) REVERT: O 97 GLN cc_start: 0.8312 (tt0) cc_final: 0.8098 (tt0) REVERT: O 175 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: O 215 ASN cc_start: 0.8530 (t0) cc_final: 0.8070 (t0) REVERT: P 215 ASN cc_start: 0.8631 (t0) cc_final: 0.8214 (t0) REVERT: Q 186 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8314 (tp) REVERT: Q 215 ASN cc_start: 0.8676 (t0) cc_final: 0.8376 (t0) REVERT: R 186 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8389 (tp) outliers start: 17 outliers final: 4 residues processed: 306 average time/residue: 1.5355 time to fit residues: 508.4941 Evaluate side-chains 301 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 288 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 229 LYS Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 222 MET Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.084289 restraints weight = 53170.305| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.29 r_work: 0.2816 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13728 Z= 0.212 Angle : 0.587 5.018 18480 Z= 0.325 Chirality : 0.038 0.122 1991 Planarity : 0.005 0.054 2354 Dihedral : 5.021 56.290 1845 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.78 % Allowed : 14.56 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.20), residues: 1661 helix: 1.92 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -1.36 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 87 TYR 0.012 0.002 TYR N 138 PHE 0.014 0.001 PHE R 155 TRP 0.003 0.001 TRP K 194 HIS 0.004 0.002 HIS Q 228 Details of bonding type rmsd covalent geometry : bond 0.00494 (13728) covalent geometry : angle 0.58666 (18480) hydrogen bonds : bond 0.07744 ( 872) hydrogen bonds : angle 3.98191 ( 2484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 230 GLU cc_start: 0.8891 (tp30) cc_final: 0.8247 (tp30) REVERT: J 186 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8526 (tp) REVERT: K 175 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8695 (mtt) REVERT: L 86 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8261 (mm-30) REVERT: L 175 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8778 (mtt) REVERT: L 186 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8556 (tp) REVERT: M 186 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8496 (tp) REVERT: N 186 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8388 (tp) REVERT: O 175 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8793 (mtt) REVERT: Q 186 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8366 (tp) REVERT: Q 230 GLU cc_start: 0.8641 (tp30) cc_final: 0.7704 (tp30) REVERT: R 186 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8434 (tp) outliers start: 25 outliers final: 7 residues processed: 290 average time/residue: 1.3871 time to fit residues: 434.8011 Evaluate side-chains 291 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 167 MET Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 32 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.111225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086400 restraints weight = 52869.628| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.29 r_work: 0.2856 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13728 Z= 0.149 Angle : 0.532 4.615 18480 Z= 0.290 Chirality : 0.036 0.122 1991 Planarity : 0.004 0.047 2354 Dihedral : 4.928 57.424 1845 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.42 % Allowed : 15.41 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.20), residues: 1661 helix: 2.09 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 87 TYR 0.008 0.001 TYR M 138 PHE 0.013 0.001 PHE R 155 TRP 0.002 0.001 TRP I 194 HIS 0.003 0.001 HIS M 228 Details of bonding type rmsd covalent geometry : bond 0.00332 (13728) covalent geometry : angle 0.53221 (18480) hydrogen bonds : bond 0.06666 ( 872) hydrogen bonds : angle 3.87246 ( 2484) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 294 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 215 ASN cc_start: 0.8601 (t0) cc_final: 0.8230 (t0) REVERT: I 230 GLU cc_start: 0.8846 (tp30) cc_final: 0.8240 (tp30) REVERT: J 186 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8475 (tp) REVERT: K 175 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8658 (mtt) REVERT: L 86 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8250 (mm-30) REVERT: L 175 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8759 (mtt) REVERT: L 186 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (tp) REVERT: M 215 ASN cc_start: 0.8589 (t0) cc_final: 0.8142 (t0) REVERT: N 186 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8348 (tp) REVERT: N 215 ASN cc_start: 0.8579 (t0) cc_final: 0.8105 (t0) REVERT: O 175 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (mtt) REVERT: O 215 ASN cc_start: 0.8566 (t0) cc_final: 0.8124 (t0) REVERT: P 215 ASN cc_start: 0.8623 (t0) cc_final: 0.8218 (t0) REVERT: Q 186 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8306 (tp) REVERT: Q 215 ASN cc_start: 0.8708 (t0) cc_final: 0.8412 (t0) REVERT: Q 230 GLU cc_start: 0.8437 (tp30) cc_final: 0.7561 (tp30) REVERT: R 175 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8720 (mtt) REVERT: R 186 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8375 (tp) outliers start: 20 outliers final: 6 residues processed: 304 average time/residue: 1.2575 time to fit residues: 414.2939 Evaluate side-chains 301 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 286 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain R residue 175 MET Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 158 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086425 restraints weight = 52432.419| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.29 r_work: 0.2854 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13728 Z= 0.149 Angle : 0.530 4.583 18480 Z= 0.289 Chirality : 0.036 0.124 1991 Planarity : 0.004 0.054 2354 Dihedral : 4.874 58.235 1845 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.99 % Allowed : 16.19 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.20), residues: 1661 helix: 2.12 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -1.07 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 87 TYR 0.009 0.001 TYR R 138 PHE 0.012 0.001 PHE R 155 TRP 0.003 0.001 TRP M 194 HIS 0.003 0.001 HIS O 228 Details of bonding type rmsd covalent geometry : bond 0.00333 (13728) covalent geometry : angle 0.52985 (18480) hydrogen bonds : bond 0.06617 ( 872) hydrogen bonds : angle 3.86173 ( 2484) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 291 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 215 ASN cc_start: 0.8616 (t0) cc_final: 0.8276 (t0) REVERT: J 186 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8490 (tp) REVERT: K 175 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8680 (mtt) REVERT: L 86 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8288 (mm-30) REVERT: L 186 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8502 (tp) REVERT: M 215 ASN cc_start: 0.8594 (t0) cc_final: 0.8154 (t0) REVERT: N 186 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8352 (tp) REVERT: N 215 ASN cc_start: 0.8574 (t0) cc_final: 0.8117 (t0) REVERT: O 175 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8749 (mtt) REVERT: O 215 ASN cc_start: 0.8533 (t0) cc_final: 0.8121 (t0) REVERT: P 215 ASN cc_start: 0.8623 (t0) cc_final: 0.8236 (t0) REVERT: Q 186 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8308 (tp) REVERT: Q 215 ASN cc_start: 0.8700 (t0) cc_final: 0.8435 (t0) REVERT: R 186 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8371 (tp) outliers start: 14 outliers final: 7 residues processed: 300 average time/residue: 1.4620 time to fit residues: 475.5150 Evaluate side-chains 299 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 285 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 171 MET Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 96 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.087888 restraints weight = 52519.301| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.29 r_work: 0.2878 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13728 Z= 0.123 Angle : 0.510 4.610 18480 Z= 0.276 Chirality : 0.036 0.124 1991 Planarity : 0.004 0.056 2354 Dihedral : 4.801 58.860 1845 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.14 % Allowed : 16.19 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.20), residues: 1661 helix: 2.26 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.92 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 87 TYR 0.008 0.001 TYR H 138 PHE 0.011 0.001 PHE R 155 TRP 0.002 0.000 TRP M 194 HIS 0.002 0.001 HIS O 228 Details of bonding type rmsd covalent geometry : bond 0.00261 (13728) covalent geometry : angle 0.50994 (18480) hydrogen bonds : bond 0.06064 ( 872) hydrogen bonds : angle 3.81055 ( 2484) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 303 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 186 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8383 (tp) REVERT: H 215 ASN cc_start: 0.8569 (t0) cc_final: 0.8120 (t0) REVERT: I 215 ASN cc_start: 0.8521 (t0) cc_final: 0.8185 (t0) REVERT: K 175 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8663 (mtt) REVERT: L 86 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8272 (mm-30) REVERT: L 186 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8474 (tp) REVERT: L 215 ASN cc_start: 0.8619 (t0) cc_final: 0.8407 (t160) REVERT: M 215 ASN cc_start: 0.8485 (t0) cc_final: 0.8102 (t0) REVERT: N 186 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8335 (tp) REVERT: N 215 ASN cc_start: 0.8519 (t0) cc_final: 0.8027 (t0) REVERT: O 175 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8721 (mtt) REVERT: O 215 ASN cc_start: 0.8499 (t0) cc_final: 0.8071 (t0) REVERT: P 215 ASN cc_start: 0.8586 (t0) cc_final: 0.8155 (t0) REVERT: Q 186 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8303 (tp) REVERT: Q 215 ASN cc_start: 0.8646 (t0) cc_final: 0.8327 (t0) REVERT: R 186 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8356 (tp) outliers start: 16 outliers final: 5 residues processed: 313 average time/residue: 1.2672 time to fit residues: 431.3407 Evaluate side-chains 307 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 295 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 215 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085413 restraints weight = 52688.293| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.29 r_work: 0.2838 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13728 Z= 0.177 Angle : 0.554 4.996 18480 Z= 0.303 Chirality : 0.037 0.123 1991 Planarity : 0.005 0.060 2354 Dihedral : 4.913 59.530 1845 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.14 % Allowed : 16.55 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.20), residues: 1661 helix: 2.13 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -1.00 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 87 TYR 0.011 0.001 TYR N 138 PHE 0.009 0.001 PHE R 155 TRP 0.003 0.001 TRP I 194 HIS 0.003 0.001 HIS R 228 Details of bonding type rmsd covalent geometry : bond 0.00406 (13728) covalent geometry : angle 0.55431 (18480) hydrogen bonds : bond 0.06971 ( 872) hydrogen bonds : angle 3.90251 ( 2484) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 285 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 215 ASN cc_start: 0.8699 (t0) cc_final: 0.8384 (t0) REVERT: K 175 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8721 (mtt) REVERT: L 86 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8264 (mm-30) REVERT: L 186 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8533 (tp) REVERT: N 186 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8358 (tp) REVERT: N 215 ASN cc_start: 0.8626 (t0) cc_final: 0.8200 (t0) REVERT: O 175 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8759 (mtt) REVERT: O 215 ASN cc_start: 0.8572 (t0) cc_final: 0.8206 (t0) REVERT: Q 186 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8327 (tp) REVERT: Q 215 ASN cc_start: 0.8777 (t0) cc_final: 0.8512 (t0) REVERT: R 186 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8389 (tp) outliers start: 16 outliers final: 7 residues processed: 296 average time/residue: 1.2531 time to fit residues: 401.3738 Evaluate side-chains 295 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 282 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.087554 restraints weight = 52429.543| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.30 r_work: 0.2873 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13728 Z= 0.128 Angle : 0.517 4.933 18480 Z= 0.278 Chirality : 0.036 0.124 1991 Planarity : 0.004 0.061 2354 Dihedral : 4.834 59.993 1845 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.14 % Allowed : 16.90 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1661 helix: 2.29 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.87 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 87 TYR 0.007 0.001 TYR L 138 PHE 0.010 0.001 PHE R 155 TRP 0.002 0.000 TRP M 194 HIS 0.003 0.001 HIS O 228 Details of bonding type rmsd covalent geometry : bond 0.00278 (13728) covalent geometry : angle 0.51673 (18480) hydrogen bonds : bond 0.06112 ( 872) hydrogen bonds : angle 3.82175 ( 2484) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3322 Ramachandran restraints generated. 1661 Oldfield, 0 Emsley, 1661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 186 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8385 (tp) REVERT: H 215 ASN cc_start: 0.8609 (t0) cc_final: 0.8170 (t0) REVERT: I 215 ASN cc_start: 0.8551 (t0) cc_final: 0.8215 (t0) REVERT: K 175 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8689 (mtt) REVERT: L 86 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8299 (mm-30) REVERT: L 186 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8502 (tp) REVERT: L 215 ASN cc_start: 0.8630 (t0) cc_final: 0.8424 (OUTLIER) REVERT: M 215 ASN cc_start: 0.8499 (t0) cc_final: 0.8122 (t0) REVERT: N 171 MET cc_start: 0.8536 (mtt) cc_final: 0.8286 (mtm) REVERT: N 186 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8351 (tp) REVERT: N 215 ASN cc_start: 0.8532 (t0) cc_final: 0.8046 (t0) REVERT: O 175 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: O 215 ASN cc_start: 0.8507 (t0) cc_final: 0.8127 (t0) REVERT: P 215 ASN cc_start: 0.8615 (t0) cc_final: 0.8194 (t0) REVERT: Q 186 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8311 (tp) REVERT: Q 215 ASN cc_start: 0.8654 (t0) cc_final: 0.8309 (t0) REVERT: R 175 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8720 (mtt) REVERT: R 186 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8361 (tp) outliers start: 16 outliers final: 7 residues processed: 304 average time/residue: 1.1973 time to fit residues: 395.7489 Evaluate side-chains 305 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 291 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 222 MET Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain R residue 175 MET Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.087974 restraints weight = 52139.760| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.29 r_work: 0.2879 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13728 Z= 0.128 Angle : 0.513 4.887 18480 Z= 0.276 Chirality : 0.036 0.125 1991 Planarity : 0.004 0.060 2354 Dihedral : 4.770 59.744 1845 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.99 % Allowed : 17.12 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.20), residues: 1661 helix: 2.36 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.86 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 87 TYR 0.009 0.001 TYR H 138 PHE 0.010 0.001 PHE R 155 TRP 0.003 0.000 TRP I 194 HIS 0.003 0.001 HIS O 228 Details of bonding type rmsd covalent geometry : bond 0.00279 (13728) covalent geometry : angle 0.51342 (18480) hydrogen bonds : bond 0.05988 ( 872) hydrogen bonds : angle 3.80320 ( 2484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9413.24 seconds wall clock time: 159 minutes 21.73 seconds (9561.73 seconds total)