Starting phenix.real_space_refine on Fri Jul 3 19:00:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xno_33321/07_2026/7xno_33321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xno_33321/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xno_33321/07_2026/7xno_33321.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xno_33321/07_2026/7xno_33321.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xno_33321/07_2026/7xno_33321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xno_33321/07_2026/7xno_33321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xno_33321/07_2026/7xno_33321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xno_33321/07_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-6108/lib/python3.11/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: 3.33, per 1000 atoms: 0.21 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: 1.16 Conformation dependent library (CDL) restraints added in 508.9 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: 0.32 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: 2.46 Time building geometry restraints manager: 1.58 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: 8762 17.76 - 35.51: 627 35.51 - 53.27: 99 53.27 - 71.02: 19 71.02 - 88.78: 12 Dihedral angle restraints: 9519 sinusoidal: 3630 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 9516 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.230 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 12.942 88.781 5748 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/Z covalent geometry : bond 0.00244 / 0.12 (16209) covalent geometry : angle 0.52699 / 0.28 (21993) SS BOND : bond 0.00087 / 0.04 ( 3) SS BOND : angle 0.24914 / 0.13 ( 6) hydrogen bonds : bond 0.11973 / 8.32 ( 1129) hydrogen bonds : angle 4.75682 / 3.45 ( 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 : 0.605 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: 0.6317 time to fit residues: 130.1309 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 : 0.649 ------------------------------------------------------------------------------- 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... 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 = 0.094742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075840 restraints weight = 28114.451| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.75 r_work: 0.3137 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0952 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= 0.139 Angle : 0.527 6.470 21999 Z= 0.281 Chirality : 0.041 0.143 2622 Planarity : 0.005 0.057 2691 Dihedral : 4.543 28.906 2188 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 1.33 % Allowed : 5.91 % 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: 2.01 (0.19), residues: 2061 helix: 2.11 (0.13), residues: 1518 sheet: None (None), residues: 0 loop : -0.96 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 30 TYR 0.006 0.001 TYR F 14 PHE 0.008 0.001 PHE I 219 TRP 0.032 0.002 TRP B 86 HIS 0.002 0.001 HIS I 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (16209) covalent geometry : angle 0.52703 / 0.28 (21993) SS BOND : bond 0.00147 / 0.06 ( 3) SS BOND : angle 0.74965 / 0.43 ( 6) hydrogen bonds : bond 0.04574 / 3.15 ( 1129) hydrogen bonds : angle 4.01764 / 2.92 ( 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 190 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.653 Fit side-chains REVERT: A 13 LYS cc_start: 0.8246 (pptt) cc_final: 0.7554 (pmtt) REVERT: Y 128 ASP cc_start: 0.7128 (m-30) cc_final: 0.6629 (m-30) REVERT: Z 169 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6456 (pp) REVERT: D 128 ASP cc_start: 0.7106 (m-30) cc_final: 0.6720 (m-30) REVERT: D 246 GLN cc_start: 0.7680 (pt0) cc_final: 0.6994 (pp30) REVERT: E 52 GLU cc_start: 0.7357 (mp0) cc_final: 0.6853 (mp0) REVERT: E 169 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6478 (pp) REVERT: F 65 ASN cc_start: 0.7386 (t0) cc_final: 0.7138 (t0) REVERT: J 4 ASP cc_start: 0.6605 (p0) cc_final: 0.6307 (p0) REVERT: J 65 ASN cc_start: 0.7310 (t0) cc_final: 0.6879 (t0) outliers start: 22 outliers final: 3 residues processed: 178 average time/residue: 0.6611 time to fit residues: 128.4163 Evaluate side-chains 162 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 10.0000 chunk 148 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3548 r_free = 0.3548 target = 0.093701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074679 restraints weight = 28433.418| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.75 r_work: 0.3112 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16212 Z= 0.156 Angle : 0.533 6.107 21999 Z= 0.285 Chirality : 0.042 0.149 2622 Planarity : 0.005 0.045 2691 Dihedral : 4.524 24.626 2184 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 1.27 % Allowed : 8.98 % Favored : 89.75 % 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: 1.83 (0.19), residues: 2061 helix: 2.01 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.19 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 117 TYR 0.007 0.001 TYR E 157 PHE 0.008 0.001 PHE I 219 TRP 0.021 0.002 TRP E 26 HIS 0.003 0.001 HIS E 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16209) covalent geometry : angle 0.53289 / 0.29 (21993) SS BOND : bond 0.00177 / 0.07 ( 3) SS BOND : angle 1.08424 / 0.63 ( 6) hydrogen bonds : bond 0.04796 / 3.30 ( 1129) hydrogen bonds : angle 4.02080 / 2.93 ( 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 186 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.421 Fit side-chains REVERT: A 13 LYS cc_start: 0.8378 (pptt) cc_final: 0.7679 (ptpp) REVERT: Y 128 ASP cc_start: 0.7144 (m-30) cc_final: 0.6633 (m-30) REVERT: Y 137 ARG cc_start: 0.7634 (mmp-170) cc_final: 0.7376 (mmp80) REVERT: Z 169 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6438 (pp) REVERT: B 1 MET cc_start: 0.6153 (mmm) cc_final: 0.5936 (mpt) REVERT: D 128 ASP cc_start: 0.7116 (m-30) cc_final: 0.6688 (m-30) REVERT: D 246 GLN cc_start: 0.7738 (pt0) cc_final: 0.7008 (pp30) REVERT: E 50 THR cc_start: 0.8025 (t) cc_final: 0.7760 (t) REVERT: E 52 GLU cc_start: 0.7361 (mp0) cc_final: 0.7029 (mp0) REVERT: E 169 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6643 (pp) REVERT: F 65 ASN cc_start: 0.7374 (t0) cc_final: 0.7122 (t0) REVERT: H 203 MET cc_start: 0.8942 (ptt) cc_final: 0.8738 (ptt) REVERT: J 65 ASN cc_start: 0.7375 (t0) cc_final: 0.6953 (t0) outliers start: 21 outliers final: 4 residues processed: 180 average time/residue: 0.6082 time to fit residues: 119.4845 Evaluate side-chains 166 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 11 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3551 r_free = 0.3551 target = 0.093825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.074965 restraints weight = 28231.384| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.74 r_work: 0.3119 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16212 Z= 0.147 Angle : 0.519 6.389 21999 Z= 0.278 Chirality : 0.041 0.147 2622 Planarity : 0.005 0.047 2691 Dihedral : 4.493 25.143 2184 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.05 % Favored : 94.81 % Rotamer: Outliers : 1.75 % Allowed : 9.70 % Favored : 88.55 % 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: 1.85 (0.19), residues: 2061 helix: 2.09 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 86 TYR 0.006 0.001 TYR E 157 PHE 0.007 0.001 PHE I 219 TRP 0.015 0.001 TRP I 26 HIS 0.003 0.001 HIS I 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16209) covalent geometry : angle 0.51858 / 0.28 (21993) SS BOND : bond 0.00194 / 0.08 ( 3) SS BOND : angle 1.01286 / 0.59 ( 6) hydrogen bonds : bond 0.04624 / 3.19 ( 1129) hydrogen bonds : angle 3.97319 / 2.89 ( 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 193 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.632 Fit side-chains REVERT: A 13 LYS cc_start: 0.8357 (pptt) cc_final: 0.7643 (ptpp) REVERT: Y 128 ASP cc_start: 0.7105 (m-30) cc_final: 0.6647 (m-30) REVERT: Z 169 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6440 (pp) REVERT: D 128 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: E 50 THR cc_start: 0.8065 (t) cc_final: 0.7797 (t) REVERT: E 52 GLU cc_start: 0.7375 (mp0) cc_final: 0.7052 (mp0) REVERT: E 169 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6575 (pp) REVERT: F 1 MET cc_start: 0.6084 (mmm) cc_final: 0.5857 (mpt) REVERT: F 65 ASN cc_start: 0.7422 (t0) cc_final: 0.7161 (t0) REVERT: J 1 MET cc_start: 0.5787 (mmm) cc_final: 0.5505 (mmt) REVERT: J 65 ASN cc_start: 0.7374 (t0) cc_final: 0.6964 (t0) REVERT: J 68 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8534 (mt-10) outliers start: 29 outliers final: 12 residues processed: 184 average time/residue: 0.6002 time to fit residues: 121.0506 Evaluate side-chains 171 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL 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 B residue 27 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 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 152 VAL Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN Y 246 GLN Z 98 GLN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073252 restraints weight = 28080.707| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.74 r_work: 0.3083 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16212 Z= 0.207 Angle : 0.581 7.613 21999 Z= 0.309 Chirality : 0.044 0.181 2622 Planarity : 0.005 0.051 2691 Dihedral : 4.684 25.919 2184 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.69 % Allowed : 9.95 % 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: 1.57 (0.19), residues: 2061 helix: 1.82 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 117 TYR 0.010 0.002 TYR E 157 PHE 0.009 0.001 PHE Y 211 TRP 0.016 0.002 TRP I 26 HIS 0.004 0.001 HIS E 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (16209) covalent geometry : angle 0.58056 / 0.31 (21993) SS BOND : bond 0.00225 / 0.10 ( 3) SS BOND : angle 1.44687 / 0.83 ( 6) hydrogen bonds : bond 0.05340 / 3.67 ( 1129) hydrogen bonds : angle 4.12950 / 3.01 ( 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 189 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.642 Fit side-chains REVERT: A 13 LYS cc_start: 0.8463 (pptt) cc_final: 0.7732 (ptpp) REVERT: Y 128 ASP cc_start: 0.7216 (m-30) cc_final: 0.6696 (m-30) REVERT: Y 137 ARG cc_start: 0.7555 (mmp80) cc_final: 0.7325 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6510 (pp) REVERT: D 128 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6928 (m-30) REVERT: D 171 GLU cc_start: 0.6608 (pt0) cc_final: 0.6405 (pt0) REVERT: E 169 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6631 (pp) REVERT: F 65 ASN cc_start: 0.7461 (t0) cc_final: 0.7193 (t0) REVERT: H 137 ARG cc_start: 0.7525 (mmp-170) cc_final: 0.7104 (mmp-170) REVERT: I 168 LYS cc_start: 0.6339 (ttpt) cc_final: 0.5998 (tttm) REVERT: J 4 ASP cc_start: 0.6986 (p0) cc_final: 0.6620 (p0) REVERT: J 65 ASN cc_start: 0.7446 (t0) cc_final: 0.7023 (t0) outliers start: 28 outliers final: 15 residues processed: 183 average time/residue: 0.6016 time to fit residues: 120.4073 Evaluate side-chains 176 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL 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 D residue 25 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 117 TRP 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 117 TRP 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: 0.9990 chunk 189 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 181 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN Y 246 GLN Z 98 GLN 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 = 0.3581 r_free = 0.3581 target = 0.095546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076613 restraints weight = 28014.888| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.74 r_work: 0.3152 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16212 Z= 0.115 Angle : 0.487 7.196 21999 Z= 0.261 Chirality : 0.040 0.139 2622 Planarity : 0.005 0.047 2691 Dihedral : 4.419 26.097 2184 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.00 % Rotamer: Outliers : 1.33 % Allowed : 11.21 % Favored : 87.46 % 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: 1.99 (0.19), residues: 2061 helix: 2.20 (0.13), residues: 1515 sheet: None (None), residues: 0 loop : -1.32 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 2 TYR 0.006 0.001 TYR F 50 PHE 0.006 0.001 PHE I 219 TRP 0.010 0.001 TRP Y 142 HIS 0.002 0.000 HIS I 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (16209) covalent geometry : angle 0.48674 / 0.26 (21993) SS BOND : bond 0.00202 / 0.09 ( 3) SS BOND : angle 0.69941 / 0.41 ( 6) hydrogen bonds : bond 0.04041 / 2.79 ( 1129) hydrogen bonds : angle 3.87370 / 2.83 ( 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 185 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.605 Fit side-chains REVERT: A 13 LYS cc_start: 0.8343 (pptt) cc_final: 0.7626 (ptpp) REVERT: Y 128 ASP cc_start: 0.6948 (m-30) cc_final: 0.6472 (m-30) REVERT: Y 137 ARG cc_start: 0.7324 (mmp80) cc_final: 0.7104 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6438 (pp) REVERT: D 206 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.5871 (tptp) REVERT: E 52 GLU cc_start: 0.7223 (mp0) cc_final: 0.6840 (mp0) REVERT: E 169 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6480 (pp) REVERT: F 65 ASN cc_start: 0.7427 (t0) cc_final: 0.7168 (t0) REVERT: H 137 ARG cc_start: 0.7429 (mmp-170) cc_final: 0.6995 (mmp-170) REVERT: I 168 LYS cc_start: 0.6303 (ttpt) cc_final: 0.6076 (tmtp) REVERT: J 65 ASN cc_start: 0.7389 (t0) cc_final: 0.6982 (t0) REVERT: J 68 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8541 (mt-10) outliers start: 22 outliers final: 11 residues processed: 177 average time/residue: 0.6406 time to fit residues: 123.7333 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 : 0.508 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 177 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN 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 = 0.3596 r_free = 0.3596 target = 0.096429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077536 restraints weight = 27915.129| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.75 r_work: 0.3170 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1370 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= 0.112 Angle : 0.480 6.760 21999 Z= 0.255 Chirality : 0.040 0.153 2622 Planarity : 0.004 0.047 2691 Dihedral : 4.257 23.694 2184 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 1.15 % Allowed : 11.87 % Favored : 86.98 % 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: 2.16 (0.19), residues: 2061 helix: 2.37 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.27 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 86 TYR 0.006 0.001 TYR J 50 PHE 0.006 0.001 PHE I 219 TRP 0.010 0.001 TRP Y 142 HIS 0.002 0.000 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (16209) covalent geometry : angle 0.47968 / 0.26 (21993) SS BOND : bond 0.00160 / 0.07 ( 3) SS BOND : angle 0.59663 / 0.36 ( 6) hydrogen bonds : bond 0.03879 / 2.69 ( 1129) hydrogen bonds : angle 3.75950 / 2.74 ( 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 183 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.618 Fit side-chains REVERT: A 13 LYS cc_start: 0.8370 (pptt) cc_final: 0.7645 (ptpp) REVERT: Y 137 ARG cc_start: 0.7340 (mmp80) cc_final: 0.7115 (mmp-170) REVERT: Z 169 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6384 (pp) REVERT: D 206 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.5857 (tptp) REVERT: E 169 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6352 (pp) REVERT: F 65 ASN cc_start: 0.7383 (t0) cc_final: 0.7143 (t0) REVERT: H 137 ARG cc_start: 0.7409 (mmp-170) cc_final: 0.6935 (mmp-170) REVERT: J 4 ASP cc_start: 0.6756 (p0) cc_final: 0.6416 (p0) REVERT: J 65 ASN cc_start: 0.7371 (t0) cc_final: 0.6993 (t0) REVERT: J 68 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8523 (mt-10) outliers start: 19 outliers final: 11 residues processed: 177 average time/residue: 0.6718 time to fit residues: 129.7086 Evaluate side-chains 169 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 D residue 206 LYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 214 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 31 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN H 150 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 = 0.3515 r_free = 0.3515 target = 0.091743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072587 restraints weight = 28358.188| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.74 r_work: 0.3074 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16212 Z= 0.247 Angle : 0.622 7.009 21999 Z= 0.329 Chirality : 0.047 0.194 2622 Planarity : 0.005 0.051 2691 Dihedral : 4.743 25.323 2184 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.05 % Favored : 94.76 % Rotamer: Outliers : 1.93 % Allowed : 11.27 % Favored : 86.80 % 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: 1.49 (0.19), residues: 2061 helix: 1.75 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.27 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 86 TYR 0.011 0.002 TYR I 70 PHE 0.010 0.002 PHE I 65 TRP 0.015 0.002 TRP I 26 HIS 0.004 0.001 HIS E 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.25 (16209) covalent geometry : angle 0.62106 / 0.33 (21993) SS BOND : bond 0.00211 / 0.09 ( 3) SS BOND : angle 1.67787 / 0.98 ( 6) hydrogen bonds : bond 0.05655 / 3.88 ( 1129) hydrogen bonds : angle 4.15960 / 3.03 ( 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 189 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.572 Fit side-chains REVERT: A 13 LYS cc_start: 0.8484 (pptt) cc_final: 0.7766 (ptpp) REVERT: Y 128 ASP cc_start: 0.7391 (m-30) cc_final: 0.6929 (m-30) REVERT: Y 137 ARG cc_start: 0.7585 (mmp80) cc_final: 0.7349 (mmp-170) REVERT: Z 169 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6581 (pp) REVERT: D 128 ASP cc_start: 0.7374 (m-30) cc_final: 0.7033 (m-30) REVERT: D 206 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6000 (tptp) REVERT: E 52 GLU cc_start: 0.7249 (mp0) cc_final: 0.6803 (mp0) REVERT: E 169 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6700 (pp) REVERT: F 4 ASP cc_start: 0.6844 (p0) cc_final: 0.6512 (p0) REVERT: F 65 ASN cc_start: 0.7477 (t0) cc_final: 0.7257 (t0) REVERT: I 168 LYS cc_start: 0.6342 (ttpt) cc_final: 0.5991 (ttpt) REVERT: J 4 ASP cc_start: 0.6991 (p0) cc_final: 0.6613 (p0) REVERT: J 65 ASN cc_start: 0.7496 (t0) cc_final: 0.7094 (t0) outliers start: 32 outliers final: 14 residues processed: 178 average time/residue: 0.6124 time to fit residues: 119.0639 Evaluate side-chains 174 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 152 VAL Chi-restraints excluded: chain Y residue 203 MET Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 169 ILE 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 D residue 206 LYS Chi-restraints excluded: chain E residue 117 TRP 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 152 VAL 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: 0.2980 chunk 161 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 129 optimal weight: 0.0980 chunk 184 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN I 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.095989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077249 restraints weight = 27931.780| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.73 r_work: 0.3164 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16212 Z= 0.112 Angle : 0.486 6.060 21999 Z= 0.261 Chirality : 0.040 0.137 2622 Planarity : 0.005 0.047 2691 Dihedral : 4.425 26.831 2184 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.51 % Favored : 95.34 % Rotamer: Outliers : 0.90 % Allowed : 12.30 % Favored : 86.80 % 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: 2.01 (0.19), residues: 2061 helix: 2.26 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.32 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 117 TYR 0.006 0.001 TYR F 50 PHE 0.006 0.001 PHE I 219 TRP 0.011 0.001 TRP Y 142 HIS 0.002 0.000 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (16209) covalent geometry : angle 0.48550 / 0.26 (21993) SS BOND : bond 0.00196 / 0.08 ( 3) SS BOND : angle 0.66218 / 0.39 ( 6) hydrogen bonds : bond 0.03893 / 2.70 ( 1129) hydrogen bonds : angle 3.84091 / 2.80 ( 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 174 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.534 Fit side-chains REVERT: A 13 LYS cc_start: 0.8362 (pptt) cc_final: 0.7630 (ptpp) REVERT: Y 128 ASP cc_start: 0.7158 (m-30) cc_final: 0.6792 (m-30) REVERT: Z 169 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6481 (pp) REVERT: B 4 ASP cc_start: 0.6721 (p0) cc_final: 0.6373 (p0) REVERT: D 206 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.5861 (tptp) REVERT: D 245 LYS cc_start: 0.7819 (mmtp) cc_final: 0.6959 (mttt) REVERT: E 169 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6520 (pp) REVERT: F 4 ASP cc_start: 0.6851 (p0) cc_final: 0.6511 (p0) REVERT: F 65 ASN cc_start: 0.7412 (t0) cc_final: 0.7174 (t0) REVERT: I 168 LYS cc_start: 0.6300 (ttpt) cc_final: 0.5956 (ttpt) REVERT: J 4 ASP cc_start: 0.6978 (p0) cc_final: 0.6611 (p0) REVERT: J 65 ASN cc_start: 0.7401 (t0) cc_final: 0.6997 (t0) REVERT: J 68 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8524 (mt-10) outliers start: 15 outliers final: 7 residues processed: 171 average time/residue: 0.6393 time to fit residues: 119.0095 Evaluate side-chains 165 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain D residue 33 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 H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU 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: 5.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 113 optimal weight: 0.0050 chunk 186 optimal weight: 0.0570 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 1.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN I 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.095326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076546 restraints weight = 28100.098| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.73 r_work: 0.3153 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16212 Z= 0.122 Angle : 0.498 6.027 21999 Z= 0.265 Chirality : 0.040 0.147 2622 Planarity : 0.005 0.046 2691 Dihedral : 4.336 23.644 2184 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.66 % Favored : 95.20 % Rotamer: Outliers : 1.02 % Allowed : 12.24 % 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: 2.06 (0.19), residues: 2061 helix: 2.29 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Z 86 TYR 0.005 0.001 TYR B 50 PHE 0.007 0.001 PHE I 219 TRP 0.011 0.001 TRP Y 142 HIS 0.002 0.000 HIS I 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16209) covalent geometry : angle 0.49755 / 0.27 (21993) SS BOND : bond 0.00150 / 0.06 ( 3) SS BOND : angle 0.70716 / 0.42 ( 6) hydrogen bonds : bond 0.04099 / 2.84 ( 1129) hydrogen bonds : angle 3.80519 / 2.77 ( 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 171 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.604 Fit side-chains REVERT: A 13 LYS cc_start: 0.8400 (pptt) cc_final: 0.7672 (ptpp) REVERT: Y 128 ASP cc_start: 0.7053 (m-30) cc_final: 0.6632 (m-30) REVERT: Z 169 ILE cc_start: 0.6848 (OUTLIER) cc_final: 0.6454 (pp) REVERT: D 206 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.5898 (tptp) REVERT: E 52 GLU cc_start: 0.7042 (mp0) cc_final: 0.6633 (mp0) REVERT: E 169 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6566 (pp) REVERT: F -7 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: F 65 ASN cc_start: 0.7408 (t0) cc_final: 0.7185 (t0) REVERT: I 168 LYS cc_start: 0.6311 (ttpt) cc_final: 0.5949 (ttpt) REVERT: J 65 ASN cc_start: 0.7379 (t0) cc_final: 0.6970 (t0) REVERT: J 68 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8490 (mt-10) outliers start: 17 outliers final: 9 residues processed: 167 average time/residue: 0.6760 time to fit residues: 122.7279 Evaluate side-chains 167 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain D residue 33 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 F residue -7 GLU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU 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: 0.8980 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 109 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 246 GLN Z 98 GLN C 11 ASN F 66 ASN I 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076896 restraints weight = 27909.523| |-----------------------------------------------------------------------------| 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: 0.8637 moved from start: 0.1409 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= 0.121 Angle : 0.497 5.941 21999 Z= 0.265 Chirality : 0.040 0.164 2622 Planarity : 0.005 0.046 2691 Dihedral : 4.335 23.673 2184 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.56 % Favored : 95.29 % Rotamer: Outliers : 1.15 % Allowed : 12.36 % Favored : 86.50 % 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: 2.07 (0.19), residues: 2061 helix: 2.30 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.28 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 86 TYR 0.005 0.001 TYR J 14 PHE 0.007 0.001 PHE Z 219 TRP 0.011 0.001 TRP H 142 HIS 0.002 0.000 HIS I 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (16209) covalent geometry : angle 0.49663 / 0.26 (21993) SS BOND : bond 0.00154 / 0.06 ( 3) SS BOND : angle 0.70918 / 0.42 ( 6) hydrogen bonds : bond 0.04060 / 2.81 ( 1129) hydrogen bonds : angle 3.79052 / 2.76 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4591.62 seconds wall clock time: 79 minutes 5.58 seconds (4745.58 seconds total)