Starting phenix.real_space_refine on Wed Mar 4 18:58:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xno_33321/03_2026/7xno_33321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xno_33321/03_2026/7xno_33321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xno_33321/03_2026/7xno_33321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xno_33321/03_2026/7xno_33321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xno_33321/03_2026/7xno_33321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xno_33321/03_2026/7xno_33321.map" } resolution = 2.54 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= 0.019 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10398 2.51 5 N 2613 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15888 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 299 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "Y" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1785 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "Z" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "B" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 865 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 299 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "D" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1785 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "E" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "F" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 865 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 299 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1785 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 8, 'TRANS': 238} Chain: "I" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain: "J" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 865 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.62, per 1000 atoms: 0.23 Number of scatterers: 15888 At special positions: 0 Unit cell: (130.711, 124.808, 100.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2790 8.00 N 2613 7.00 C 10398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 15 " distance=2.03 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: 1.19 Conformation dependent library (CDL) restraints added in 634.2 milliseconds 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 6 sheets defined 77.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 18 through 40 Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.735A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 Processing helix chain 'Y' and resid 45 through 60 Processing helix chain 'Y' and resid 73 through 88 removed outlier: 3.636A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 132 removed outlier: 4.177A pdb=" N VAL Y 103 " --> pdb=" O ILE Y 99 " (cutoff:3.500A) Proline residue: Y 104 - end of helix removed outlier: 4.118A pdb=" N THR Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY Y 122 " --> pdb=" O THR Y 118 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE Y 123 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 164 removed outlier: 3.636A pdb=" N ILE Y 139 " --> pdb=" O ASN Y 135 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE Y 154 " --> pdb=" O GLN Y 150 " (cutoff:3.500A) Proline residue: Y 157 - end of helix Processing helix chain 'Y' and resid 165 through 175 Processing helix chain 'Y' and resid 177 through 204 removed outlier: 4.484A pdb=" N VAL Y 192 " --> pdb=" O GLY Y 188 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA Y 193 " --> pdb=" O GLY Y 189 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL Y 194 " --> pdb=" O MET Y 190 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY Y 195 " --> pdb=" O VAL Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 219 Processing helix chain 'Y' and resid 225 through 246 removed outlier: 3.925A pdb=" N GLN Y 246 " --> pdb=" O ALA Y 242 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 19 Processing helix chain 'Z' and resid 20 through 24 removed outlier: 4.596A pdb=" N GLN Z 23 " --> pdb=" O THR Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 40 Processing helix chain 'Z' and resid 40 through 48 Processing helix chain 'Z' and resid 52 through 62 Processing helix chain 'Z' and resid 71 through 88 removed outlier: 4.377A pdb=" N ILE Z 75 " --> pdb=" O VAL Z 71 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 117 removed outlier: 3.600A pdb=" N GLN Z 98 " --> pdb=" O ASP Z 94 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) Proline residue: Z 107 - end of helix Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 134 removed outlier: 3.705A pdb=" N ILE Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER Z 134 " --> pdb=" O SER Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 166 removed outlier: 3.857A pdb=" N ILE Z 141 " --> pdb=" O ILE Z 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 173 removed outlier: 3.632A pdb=" N GLU Z 171 " --> pdb=" O SER Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 201 removed outlier: 3.708A pdb=" N ASP Z 180 " --> pdb=" O GLY Z 176 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL Z 201 " --> pdb=" O VAL Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 219 removed outlier: 3.950A pdb=" N PHE Z 219 " --> pdb=" O LYS Z 216 " (cutoff:3.500A) Processing helix chain 'Z' and resid 228 through 241 Processing helix chain 'Z' and resid 253 through 261 removed outlier: 3.642A pdb=" N LEU Z 260 " --> pdb=" O ASN Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 300 Processing helix chain 'B' and resid -14 through -3 Processing helix chain 'B' and resid 4 through 20 Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.625A pdb=" N GLN B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'C' and resid 18 through 40 Processing helix chain 'D' and resid 4 through 25 removed outlier: 3.713A pdb=" N ILE D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 44 Processing helix chain 'D' and resid 45 through 60 Processing helix chain 'D' and resid 73 through 88 removed outlier: 3.629A pdb=" N ALA D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 132 removed outlier: 4.179A pdb=" N VAL D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Proline residue: D 104 - end of helix removed outlier: 4.144A pdb=" N THR D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLY D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 164 removed outlier: 3.607A pdb=" N ILE D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 165 through 175 Processing helix chain 'D' and resid 177 through 204 removed outlier: 4.505A pdb=" N VAL D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 225 through 246 removed outlier: 3.925A pdb=" N GLN D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'E' and resid 20 through 24 removed outlier: 4.586A pdb=" N GLN E 23 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 40 removed outlier: 3.544A pdb=" N LEU E 40 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 71 through 88 removed outlier: 4.363A pdb=" N ILE E 75 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 117 removed outlier: 3.579A pdb=" N GLN E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY E 106 " --> pdb=" O VAL E 102 " (cutoff:3.500A) Proline residue: E 107 - end of helix Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 119 through 134 removed outlier: 3.677A pdb=" N ILE E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 166 removed outlier: 3.855A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.517A pdb=" N GLU E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 201 removed outlier: 3.615A pdb=" N ASP E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 removed outlier: 3.957A pdb=" N PHE E 219 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 241 Processing helix chain 'E' and resid 253 through 261 removed outlier: 3.627A pdb=" N LEU E 260 " --> pdb=" O ASN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 279 Processing helix chain 'E' and resid 282 through 300 Processing helix chain 'F' and resid -14 through -3 Processing helix chain 'F' and resid 4 through 20 Processing helix chain 'F' and resid 21 through 26 Processing helix chain 'F' and resid 27 through 43 removed outlier: 3.575A pdb=" N GLN F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'F' and resid 70 through 77 Processing helix chain 'G' and resid 18 through 40 Processing helix chain 'H' and resid 4 through 25 removed outlier: 3.702A pdb=" N ILE H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 44 Processing helix chain 'H' and resid 45 through 60 Processing helix chain 'H' and resid 73 through 88 removed outlier: 3.632A pdb=" N ALA H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 132 removed outlier: 4.175A pdb=" N VAL H 103 " --> pdb=" O ILE H 99 " (cutoff:3.500A) Proline residue: H 104 - end of helix removed outlier: 4.186A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLY H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 164 removed outlier: 3.650A pdb=" N ILE H 139 " --> pdb=" O ASN H 135 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 154 " --> pdb=" O GLN H 150 " (cutoff:3.500A) Proline residue: H 157 - end of helix Processing helix chain 'H' and resid 165 through 175 Processing helix chain 'H' and resid 177 through 204 removed outlier: 4.509A pdb=" N VAL H 192 " --> pdb=" O GLY H 188 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ALA H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 225 through 246 removed outlier: 3.861A pdb=" N GLN H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'I' and resid 20 through 24 removed outlier: 4.591A pdb=" N GLN I 23 " --> pdb=" O THR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 40 removed outlier: 3.567A pdb=" N LEU I 40 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 48 Processing helix chain 'I' and resid 52 through 62 Processing helix chain 'I' and resid 71 through 88 removed outlier: 4.371A pdb=" N ILE I 75 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 117 removed outlier: 3.635A pdb=" N GLN I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY I 106 " --> pdb=" O VAL I 102 " (cutoff:3.500A) Proline residue: I 107 - end of helix Proline residue: I 114 - end of helix Processing helix chain 'I' and resid 119 through 134 removed outlier: 3.653A pdb=" N ILE I 123 " --> pdb=" O THR I 119 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER I 134 " --> pdb=" O SER I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 166 removed outlier: 3.849A pdb=" N ILE I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 173 removed outlier: 3.603A pdb=" N GLU I 171 " --> pdb=" O SER I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 201 removed outlier: 3.707A pdb=" N ASP I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL I 201 " --> pdb=" O VAL I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 219 removed outlier: 3.971A pdb=" N PHE I 219 " --> pdb=" O LYS I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 241 Processing helix chain 'I' and resid 253 through 261 removed outlier: 3.654A pdb=" N LEU I 260 " --> pdb=" O ASN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 279 Processing helix chain 'I' and resid 282 through 300 Processing helix chain 'J' and resid -14 through -3 Processing helix chain 'J' and resid 4 through 20 Processing helix chain 'J' and resid 21 through 26 Processing helix chain 'J' and resid 27 through 43 removed outlier: 3.629A pdb=" N GLN J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'J' and resid 70 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'Z' and resid 208 through 213 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AA4, first strand: chain 'E' and resid 208 through 213 Processing sheet with id=AA5, first strand: chain 'G' and resid 2 through 3 Processing sheet with id=AA6, first strand: chain 'I' and resid 208 through 213 1129 hydrogen bonds defined for protein. 3360 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: 2.60 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4903 1.34 - 1.46: 2977 1.46 - 1.58: 8173 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 16209 Sorted by residual: bond pdb=" C THR J 82 " pdb=" N PRO J 83 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.04e+00 bond pdb=" C THR B 82 " pdb=" N PRO B 83 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 1.00e+00 bond pdb=" C THR F 82 " pdb=" N PRO F 83 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.85e-01 bond pdb=" C2 MAN I 401 " pdb=" O2 MAN I 401 " ideal model delta sigma weight residual 1.407 1.426 -0.019 2.00e-02 2.50e+03 9.26e-01 bond pdb=" C2 MAN E 401 " pdb=" O2 MAN E 401 " ideal model delta sigma weight residual 1.407 1.426 -0.019 2.00e-02 2.50e+03 9.06e-01 ... (remaining 16204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 21442 1.38 - 2.76: 415 2.76 - 4.13: 90 4.13 - 5.51: 38 5.51 - 6.89: 8 Bond angle restraints: 21993 Sorted by residual: angle pdb=" N ASP Y 73 " pdb=" CA ASP Y 73 " pdb=" C ASP Y 73 " ideal model delta sigma weight residual 111.02 115.78 -4.76 1.25e+00 6.40e-01 1.45e+01 angle pdb=" N MET E 31 " pdb=" CA MET E 31 " pdb=" C MET E 31 " ideal model delta sigma weight residual 111.02 114.75 -3.73 1.22e+00 6.72e-01 9.34e+00 angle pdb=" N MET I 31 " pdb=" CA MET I 31 " pdb=" C MET I 31 " ideal model delta sigma weight residual 111.02 114.64 -3.62 1.22e+00 6.72e-01 8.80e+00 angle pdb=" N THR Z 206 " pdb=" CA THR Z 206 " pdb=" C THR Z 206 " ideal model delta sigma weight residual 109.81 115.51 -5.70 2.21e+00 2.05e-01 6.66e+00 angle pdb=" N THR I 206 " pdb=" CA THR I 206 " pdb=" C THR I 206 " ideal model delta sigma weight residual 109.81 115.51 -5.70 2.21e+00 2.05e-01 6.65e+00 ... (remaining 21988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8828 17.76 - 35.51: 627 35.51 - 53.27: 99 53.27 - 71.02: 19 71.02 - 88.78: 12 Dihedral angle restraints: 9585 sinusoidal: 3696 harmonic: 5889 Sorted by residual: dihedral pdb=" CA PRO J 83 " pdb=" C PRO J 83 " pdb=" N LYS J 84 " pdb=" CA LYS J 84 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA PRO F 83 " pdb=" C PRO F 83 " pdb=" N LYS F 84 " pdb=" CA LYS F 84 " ideal model delta harmonic sigma weight residual -180.00 -154.27 -25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA PRO B 83 " pdb=" C PRO B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1553 0.027 - 0.054: 595 0.054 - 0.081: 331 0.081 - 0.108: 112 0.108 - 0.135: 31 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE Z 92 " pdb=" N ILE Z 92 " pdb=" C ILE Z 92 " pdb=" CB ILE Z 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE I 92 " pdb=" N ILE I 92 " pdb=" C ILE I 92 " pdb=" CB ILE I 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 2619 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 86 " 0.031 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" CG TRP J 86 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP J 86 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP J 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP J 86 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 86 " 0.031 2.00e-02 2.50e+03 2.91e-02 2.12e+01 pdb=" CG TRP F 86 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP F 86 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP F 86 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP F 86 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 86 " 0.030 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP B 86 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 86 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 86 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 86 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 86 " 0.001 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2006 2.75 - 3.29: 16260 3.29 - 3.83: 28296 3.83 - 4.36: 32947 4.36 - 4.90: 57398 Nonbonded interactions: 136907 Sorted by model distance: nonbonded pdb=" OD2 ASP D 128 " pdb=" NH2 ARG E 30 " model vdw 2.215 3.120 nonbonded pdb=" O VAL D 217 " pdb=" OG1 THR D 220 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR I 48 " pdb=" OE1 GLU I 83 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR Z 48 " pdb=" OE1 GLU Z 83 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR E 48 " pdb=" OE1 GLU E 83 " model vdw 2.242 3.040 ... (remaining 136902 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 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.190 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 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:9.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.002 0.024 16212 Z= 0.120 Angle : 0.527 6.889 21999 Z= 0.283 Chirality : 0.039 0.135 2622 Planarity : 0.004 0.042 2691 Dihedral : 12.886 88.781 5814 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 0.12 % Allowed : 0.06 % Favored : 99.82 % 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 are not related in a simple way. whole: 1.92 (0.19), residues: 2061 helix: 2.15 (0.14), residues: 1494 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 86 TYR 0.008 0.001 TYR F 14 PHE 0.009 0.001 PHE E 219 TRP 0.078 0.002 TRP J 86 HIS 0.003 0.001 HIS I 68 Details of bonding type rmsd covalent geometry : bond 0.00244 (16209) covalent geometry : angle 0.52699 (21993) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.24914 ( 6) hydrogen bonds : bond 0.11973 ( 1129) hydrogen bonds : angle 4.75682 ( 3360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.620 Fit side-chains REVERT: A 13 LYS cc_start: 0.8306 (pptt) cc_final: 0.7788 (pmtt) REVERT: B 4 ASP cc_start: 0.7964 (p0) cc_final: 0.7580 (p0) REVERT: D 246 GLN cc_start: 0.7588 (pt0) cc_final: 0.7058 (pp30) REVERT: E 52 GLU cc_start: 0.7236 (mp0) cc_final: 0.6764 (mp0) REVERT: J 65 ASN cc_start: 0.7427 (t0) cc_final: 0.7063 (t0) outliers start: 2 outliers final: 2 residues processed: 189 average time/residue: 0.7525 time to fit residues: 154.2644 Evaluate side-chains 154 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 TYR Chi-restraints excluded: chain J residue 5 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN B -6 ASN F -6 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN J -6 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075844 restraints weight = 28116.262| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.75 r_work: 0.3136 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16212 Z= 0.140 Angle : 0.526 6.515 21999 Z= 0.281 Chirality : 0.041 0.145 2622 Planarity : 0.005 0.058 2691 Dihedral : 4.531 28.809 2254 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 1.39 % Allowed : 5.85 % Favored : 92.77 % 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 are not related in a simple way. whole: 2.00 (0.19), residues: 2061 helix: 2.16 (0.13), residues: 1503 sheet: None (None), residues: 0 loop : -1.06 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 30 TYR 0.005 0.001 TYR F 14 PHE 0.008 0.001 PHE I 219 TRP 0.030 0.002 TRP J 86 HIS 0.003 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00308 (16209) covalent geometry : angle 0.52627 (21993) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.76574 ( 6) hydrogen bonds : bond 0.04543 ( 1129) hydrogen bonds : angle 4.01959 ( 3360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.614 Fit side-chains REVERT: A 13 LYS cc_start: 0.8245 (pptt) cc_final: 0.7556 (ptpp) REVERT: Y 128 ASP cc_start: 0.7126 (m-30) cc_final: 0.6623 (m-30) REVERT: Z 169 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6459 (pp) REVERT: D 128 ASP cc_start: 0.7100 (m-30) cc_final: 0.6717 (m-30) REVERT: D 246 GLN cc_start: 0.7672 (pt0) cc_final: 0.6983 (pp30) REVERT: E 52 GLU cc_start: 0.7355 (mp0) cc_final: 0.6849 (mp0) REVERT: E 169 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6554 (pp) REVERT: F 65 ASN cc_start: 0.7383 (t0) cc_final: 0.7130 (t0) REVERT: J 4 ASP cc_start: 0.6621 (p0) cc_final: 0.6319 (p0) REVERT: J 65 ASN cc_start: 0.7307 (t0) cc_final: 0.6876 (t0) outliers start: 23 outliers final: 3 residues processed: 179 average time/residue: 0.7552 time to fit residues: 146.7592 Evaluate side-chains 163 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain I residue 117 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 57 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075671 restraints weight = 28397.935| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.77 r_work: 0.3135 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16212 Z= 0.132 Angle : 0.506 6.226 21999 Z= 0.271 Chirality : 0.041 0.144 2622 Planarity : 0.005 0.046 2691 Dihedral : 4.405 24.974 2250 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.12 % Favored : 95.73 % Rotamer: Outliers : 1.33 % Allowed : 9.04 % Favored : 89.63 % 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 are not related in a simple way. whole: 1.97 (0.19), residues: 2061 helix: 2.17 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 86 TYR 0.006 0.001 TYR J 14 PHE 0.007 0.001 PHE I 219 TRP 0.019 0.001 TRP I 26 HIS 0.003 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00289 (16209) covalent geometry : angle 0.50608 (21993) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.86192 ( 6) hydrogen bonds : bond 0.04416 ( 1129) hydrogen bonds : angle 3.93285 ( 3360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.561 Fit side-chains REVERT: A 13 LYS cc_start: 0.8285 (pptt) cc_final: 0.7594 (ptpp) REVERT: Y 128 ASP cc_start: 0.7097 (m-30) cc_final: 0.6654 (m-30) REVERT: Z 169 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6421 (pp) REVERT: D 128 ASP cc_start: 0.7009 (m-30) cc_final: 0.6613 (m-30) REVERT: D 246 GLN cc_start: 0.7720 (pt0) cc_final: 0.7011 (pp30) REVERT: E 52 GLU cc_start: 0.7333 (mp0) cc_final: 0.6986 (mp0) REVERT: E 169 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6508 (pp) REVERT: F 65 ASN cc_start: 0.7357 (t0) cc_final: 0.7122 (t0) REVERT: J 65 ASN cc_start: 0.7351 (t0) cc_final: 0.6914 (t0) outliers start: 22 outliers final: 3 residues processed: 177 average time/residue: 0.7150 time to fit residues: 137.6393 Evaluate side-chains 160 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 117 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 173 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 167 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN D 246 GLN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076640 restraints weight = 28049.981| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.74 r_work: 0.3149 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16212 Z= 0.122 Angle : 0.490 8.000 21999 Z= 0.262 Chirality : 0.040 0.145 2622 Planarity : 0.004 0.045 2691 Dihedral : 4.300 24.128 2250 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.25 % Rotamer: Outliers : 1.39 % Allowed : 10.25 % Favored : 88.37 % 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 are not related in a simple way. whole: 2.05 (0.19), residues: 2061 helix: 2.24 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 86 TYR 0.006 0.001 TYR J 14 PHE 0.007 0.001 PHE I 219 TRP 0.013 0.001 TRP I 26 HIS 0.002 0.000 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00260 (16209) covalent geometry : angle 0.49030 (21993) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.72034 ( 6) hydrogen bonds : bond 0.04147 ( 1129) hydrogen bonds : angle 3.84135 ( 3360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.567 Fit side-chains REVERT: A 13 LYS cc_start: 0.8355 (pptt) cc_final: 0.7625 (ptpp) REVERT: Y 128 ASP cc_start: 0.6929 (m-30) cc_final: 0.6461 (m-30) REVERT: Y 137 ARG cc_start: 0.7472 (mmp80) cc_final: 0.7229 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6425 (pp) REVERT: B -7 GLU cc_start: 0.6597 (tt0) cc_final: 0.6333 (tt0) REVERT: E 52 GLU cc_start: 0.7302 (mp0) cc_final: 0.6968 (mp0) REVERT: E 169 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6381 (pp) REVERT: F 1 MET cc_start: 0.6102 (mmm) cc_final: 0.5874 (mpt) REVERT: F 65 ASN cc_start: 0.7331 (t0) cc_final: 0.7113 (t0) REVERT: J 65 ASN cc_start: 0.7411 (t0) cc_final: 0.6995 (t0) REVERT: J 68 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8494 (mt-10) outliers start: 23 outliers final: 12 residues processed: 176 average time/residue: 0.7242 time to fit residues: 138.7751 Evaluate side-chains 171 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 27 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN C 11 ASN F -2 GLN F 66 ASN I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076801 restraints weight = 28047.096| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.75 r_work: 0.3154 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16212 Z= 0.120 Angle : 0.485 6.753 21999 Z= 0.259 Chirality : 0.040 0.142 2622 Planarity : 0.004 0.045 2691 Dihedral : 4.252 23.206 2250 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.51 % Favored : 95.34 % Rotamer: Outliers : 1.39 % Allowed : 10.85 % Favored : 87.76 % 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 are not related in a simple way. whole: 2.13 (0.19), residues: 2061 helix: 2.29 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.23 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 86 TYR 0.006 0.001 TYR J 14 PHE 0.007 0.001 PHE I 219 TRP 0.011 0.001 TRP E 26 HIS 0.002 0.000 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00255 (16209) covalent geometry : angle 0.48510 (21993) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.73940 ( 6) hydrogen bonds : bond 0.04083 ( 1129) hydrogen bonds : angle 3.79915 ( 3360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.516 Fit side-chains REVERT: A 13 LYS cc_start: 0.8372 (pptt) cc_final: 0.7661 (ptpp) REVERT: Y 128 ASP cc_start: 0.6882 (m-30) cc_final: 0.6430 (m-30) REVERT: Y 137 ARG cc_start: 0.7493 (mmp80) cc_final: 0.7251 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6368 (pp) REVERT: B -7 GLU cc_start: 0.6735 (tt0) cc_final: 0.6460 (tt0) REVERT: E 52 GLU cc_start: 0.7334 (mp0) cc_final: 0.6728 (mp0) REVERT: E 169 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6328 (pp) REVERT: F 65 ASN cc_start: 0.7348 (t0) cc_final: 0.7115 (t0) REVERT: H 137 ARG cc_start: 0.7482 (mmp-170) cc_final: 0.7065 (mmp-170) REVERT: J 65 ASN cc_start: 0.7422 (t0) cc_final: 0.7026 (t0) REVERT: J 68 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8542 (mt-10) outliers start: 23 outliers final: 13 residues processed: 177 average time/residue: 0.7200 time to fit residues: 138.5389 Evaluate side-chains 173 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 144 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 246 GLN I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076446 restraints weight = 28004.660| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.74 r_work: 0.3146 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16212 Z= 0.126 Angle : 0.493 6.053 21999 Z= 0.263 Chirality : 0.040 0.151 2622 Planarity : 0.004 0.045 2691 Dihedral : 4.281 22.954 2250 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.15 % Rotamer: Outliers : 1.69 % Allowed : 11.21 % Favored : 87.10 % 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 are not related in a simple way. whole: 2.09 (0.19), residues: 2061 helix: 2.27 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 86 TYR 0.006 0.001 TYR J 14 PHE 0.007 0.001 PHE I 219 TRP 0.011 0.001 TRP E 26 HIS 0.003 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00275 (16209) covalent geometry : angle 0.49247 (21993) SS BOND : bond 0.00148 ( 3) SS BOND : angle 0.81326 ( 6) hydrogen bonds : bond 0.04198 ( 1129) hydrogen bonds : angle 3.81611 ( 3360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.588 Fit side-chains REVERT: A 13 LYS cc_start: 0.8345 (pptt) cc_final: 0.7607 (ptpp) REVERT: Y 128 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6445 (m-30) REVERT: Y 137 ARG cc_start: 0.7479 (mmp80) cc_final: 0.7240 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6446 (pp) REVERT: D 245 LYS cc_start: 0.7814 (mmtp) cc_final: 0.6984 (mttp) REVERT: E 52 GLU cc_start: 0.7333 (mp0) cc_final: 0.6614 (mp0) REVERT: E 169 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6312 (pp) REVERT: F 65 ASN cc_start: 0.7373 (t0) cc_final: 0.7142 (t0) REVERT: H 137 ARG cc_start: 0.7439 (mmp-170) cc_final: 0.7009 (mmp-170) REVERT: J 4 ASP cc_start: 0.6934 (p0) cc_final: 0.6573 (p0) REVERT: J 65 ASN cc_start: 0.7429 (t0) cc_final: 0.7025 (t0) REVERT: J 68 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8527 (mt-10) outliers start: 28 outliers final: 13 residues processed: 183 average time/residue: 0.7448 time to fit residues: 148.1132 Evaluate side-chains 174 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 128 ASP Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 246 GLN I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.074721 restraints weight = 28173.881| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.73 r_work: 0.3113 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16212 Z= 0.161 Angle : 0.535 6.512 21999 Z= 0.285 Chirality : 0.042 0.154 2622 Planarity : 0.005 0.045 2691 Dihedral : 4.495 24.359 2250 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 1.69 % Allowed : 11.45 % Favored : 86.86 % 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 are not related in a simple way. whole: 1.88 (0.19), residues: 2061 helix: 2.10 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 86 TYR 0.007 0.001 TYR J 14 PHE 0.008 0.001 PHE I 219 TRP 0.014 0.001 TRP I 26 HIS 0.004 0.001 HIS Z 61 Details of bonding type rmsd covalent geometry : bond 0.00376 (16209) covalent geometry : angle 0.53503 (21993) SS BOND : bond 0.00154 ( 3) SS BOND : angle 1.14851 ( 6) hydrogen bonds : bond 0.04770 ( 1129) hydrogen bonds : angle 3.95481 ( 3360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.531 Fit side-chains REVERT: A 13 LYS cc_start: 0.8451 (pptt) cc_final: 0.7727 (ptpp) REVERT: Y 128 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6482 (m-30) REVERT: Y 137 ARG cc_start: 0.7540 (mmp80) cc_final: 0.7301 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6594 (pp) REVERT: D 128 ASP cc_start: 0.7066 (m-30) cc_final: 0.6736 (m-30) REVERT: E 52 GLU cc_start: 0.7382 (mp0) cc_final: 0.6676 (mp0) REVERT: E 169 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6517 (pp) REVERT: F 65 ASN cc_start: 0.7418 (t0) cc_final: 0.7178 (t0) REVERT: H 137 ARG cc_start: 0.7479 (mmp-170) cc_final: 0.7026 (mmp-170) REVERT: I 168 LYS cc_start: 0.6313 (ttpt) cc_final: 0.5925 (ttpt) REVERT: J 65 ASN cc_start: 0.7473 (t0) cc_final: 0.7030 (t0) REVERT: J 68 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8533 (mt-10) outliers start: 28 outliers final: 17 residues processed: 183 average time/residue: 0.7259 time to fit residues: 144.3070 Evaluate side-chains 180 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 128 ASP Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain F residue -6 ASN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 246 GLN I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.074605 restraints weight = 28221.158| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.74 r_work: 0.3116 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16212 Z= 0.160 Angle : 0.533 6.272 21999 Z= 0.285 Chirality : 0.042 0.155 2622 Planarity : 0.005 0.046 2691 Dihedral : 4.523 25.340 2250 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.34 % Favored : 94.52 % Rotamer: Outliers : 1.93 % Allowed : 11.21 % Favored : 86.86 % 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 are not related in a simple way. whole: 1.82 (0.19), residues: 2061 helix: 2.06 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 86 TYR 0.007 0.001 TYR J 14 PHE 0.007 0.001 PHE I 219 TRP 0.013 0.001 TRP I 26 HIS 0.004 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00372 (16209) covalent geometry : angle 0.53251 (21993) SS BOND : bond 0.00169 ( 3) SS BOND : angle 1.14735 ( 6) hydrogen bonds : bond 0.04724 ( 1129) hydrogen bonds : angle 3.96056 ( 3360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.578 Fit side-chains REVERT: A 13 LYS cc_start: 0.8448 (pptt) cc_final: 0.7723 (ptpp) REVERT: Y 128 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6450 (m-30) REVERT: Y 137 ARG cc_start: 0.7438 (mmp80) cc_final: 0.7207 (mmp-170) REVERT: Z 169 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6596 (pp) REVERT: D 128 ASP cc_start: 0.7063 (m-30) cc_final: 0.6649 (m-30) REVERT: D 206 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.5831 (tptp) REVERT: E 52 GLU cc_start: 0.7419 (mp0) cc_final: 0.6720 (mp0) REVERT: E 169 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6577 (pp) REVERT: F 4 ASP cc_start: 0.6888 (p0) cc_final: 0.6551 (p0) REVERT: F 65 ASN cc_start: 0.7456 (t0) cc_final: 0.7230 (t0) REVERT: H 137 ARG cc_start: 0.7478 (mmp-170) cc_final: 0.7014 (mmp-170) REVERT: I 168 LYS cc_start: 0.6324 (ttpt) cc_final: 0.5922 (ttpt) REVERT: J 4 ASP cc_start: 0.6973 (p0) cc_final: 0.6610 (p0) REVERT: J 65 ASN cc_start: 0.7433 (t0) cc_final: 0.7026 (t0) REVERT: J 68 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8555 (mt-10) outliers start: 32 outliers final: 16 residues processed: 181 average time/residue: 0.7093 time to fit residues: 139.7533 Evaluate side-chains 178 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 128 ASP Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 34 optimal weight: 0.3980 chunk 161 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 246 GLN I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.095572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076793 restraints weight = 28115.785| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.73 r_work: 0.3157 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16212 Z= 0.117 Angle : 0.487 7.492 21999 Z= 0.260 Chirality : 0.040 0.142 2622 Planarity : 0.004 0.046 2691 Dihedral : 4.295 24.807 2250 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.15 % Rotamer: Outliers : 1.63 % Allowed : 11.51 % Favored : 86.86 % 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 are not related in a simple way. whole: 2.06 (0.19), residues: 2061 helix: 2.25 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 86 TYR 0.005 0.001 TYR B 50 PHE 0.006 0.001 PHE I 219 TRP 0.010 0.001 TRP E 26 HIS 0.002 0.000 HIS Z 298 Details of bonding type rmsd covalent geometry : bond 0.00242 (16209) covalent geometry : angle 0.48705 (21993) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.69428 ( 6) hydrogen bonds : bond 0.04017 ( 1129) hydrogen bonds : angle 3.81589 ( 3360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.479 Fit side-chains REVERT: A 13 LYS cc_start: 0.8359 (pptt) cc_final: 0.7622 (ptpp) REVERT: Y 128 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6449 (m-30) REVERT: Y 137 ARG cc_start: 0.7364 (mmp80) cc_final: 0.7132 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6573 (pp) REVERT: D 246 GLN cc_start: 0.7491 (pt0) cc_final: 0.6878 (pp30) REVERT: E 52 GLU cc_start: 0.7382 (mp0) cc_final: 0.7137 (mp0) REVERT: E 169 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6443 (pp) REVERT: F 65 ASN cc_start: 0.7402 (t0) cc_final: 0.7181 (t0) REVERT: J 4 ASP cc_start: 0.6831 (p0) cc_final: 0.6455 (p0) REVERT: J 65 ASN cc_start: 0.7383 (t0) cc_final: 0.6989 (t0) REVERT: J 68 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8481 (mt-10) outliers start: 27 outliers final: 15 residues processed: 176 average time/residue: 0.7040 time to fit residues: 134.7226 Evaluate side-chains 170 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 128 ASP Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 131 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 246 GLN I 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076088 restraints weight = 28084.918| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.73 r_work: 0.3143 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16212 Z= 0.132 Angle : 0.505 7.514 21999 Z= 0.269 Chirality : 0.041 0.149 2622 Planarity : 0.004 0.047 2691 Dihedral : 4.339 23.329 2250 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.45 % Allowed : 11.81 % Favored : 86.74 % 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 are not related in a simple way. whole: 2.04 (0.19), residues: 2061 helix: 2.22 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.22 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 86 TYR 0.007 0.001 TYR J 14 PHE 0.007 0.001 PHE I 219 TRP 0.011 0.001 TRP E 26 HIS 0.003 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00292 (16209) covalent geometry : angle 0.50500 (21993) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.85550 ( 6) hydrogen bonds : bond 0.04270 ( 1129) hydrogen bonds : angle 3.83718 ( 3360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.601 Fit side-chains REVERT: A 13 LYS cc_start: 0.8403 (pptt) cc_final: 0.7679 (ptpp) REVERT: Y 128 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: Y 137 ARG cc_start: 0.7390 (mmp80) cc_final: 0.7157 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6564 (pp) REVERT: D 246 GLN cc_start: 0.7525 (pt0) cc_final: 0.6916 (pp30) REVERT: E 52 GLU cc_start: 0.7367 (mp0) cc_final: 0.7119 (mp0) REVERT: E 169 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6461 (pp) REVERT: F 4 ASP cc_start: 0.6909 (p0) cc_final: 0.6630 (p0) REVERT: F 65 ASN cc_start: 0.7419 (t0) cc_final: 0.7191 (t0) REVERT: I 168 LYS cc_start: 0.6279 (ttpt) cc_final: 0.5921 (ttpt) REVERT: J 4 ASP cc_start: 0.6808 (p0) cc_final: 0.6445 (p0) REVERT: J 65 ASN cc_start: 0.7406 (t0) cc_final: 0.7001 (t0) REVERT: J 68 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8485 (mt-10) outliers start: 24 outliers final: 15 residues processed: 175 average time/residue: 0.7396 time to fit residues: 140.8460 Evaluate side-chains 173 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 25 ASP Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 128 ASP Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue -14 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 246 GLN I 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.093946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074889 restraints weight = 28100.219| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.75 r_work: 0.3119 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16212 Z= 0.155 Angle : 0.535 7.404 21999 Z= 0.285 Chirality : 0.042 0.154 2622 Planarity : 0.005 0.046 2691 Dihedral : 4.483 24.837 2250 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.69 % Allowed : 11.45 % Favored : 86.86 % 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 are not related in a simple way. whole: 1.90 (0.19), residues: 2061 helix: 2.06 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.14 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 86 TYR 0.008 0.001 TYR J 14 PHE 0.007 0.001 PHE I 219 TRP 0.012 0.001 TRP I 26 HIS 0.004 0.001 HIS I 61 Details of bonding type rmsd covalent geometry : bond 0.00357 (16209) covalent geometry : angle 0.53455 (21993) SS BOND : bond 0.00177 ( 3) SS BOND : angle 1.08202 ( 6) hydrogen bonds : bond 0.04648 ( 1129) hydrogen bonds : angle 3.93126 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.12 seconds wall clock time: 86 minutes 57.47 seconds (5217.47 seconds total)