Starting phenix.real_space_refine on Sat Jun 14 02:48:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xno_33321/06_2025/7xno_33321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xno_33321/06_2025/7xno_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xno_33321/06_2025/7xno_33321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xno_33321/06_2025/7xno_33321.map" model { file = "/net/cci-nas-00/data/ceres_data/7xno_33321/06_2025/7xno_33321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xno_33321/06_2025/7xno_33321.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.14, per 1000 atoms: 0.64 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: 4.25 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.57 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: 4.58 Time building geometry restraints manager: 4.99 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: 0.07 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: 2.730 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: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 37.680 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:14.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.760 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (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 TRP 0.078 0.002 TRP J 86 HIS 0.003 0.001 HIS I 68 PHE 0.009 0.001 PHE E 219 TYR 0.008 0.001 TYR F 14 ARG 0.002 0.000 ARG Z 86 Details of bonding type rmsd hydrogen bonds : bond 0.11973 ( 1129) hydrogen bonds : angle 4.75682 ( 3360) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.24914 ( 6) covalent geometry : bond 0.00244 (16209) covalent geometry : angle 0.52699 (21993) *********************** 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 : 1.648 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: 1.7647 time to fit residues: 363.6509 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 : 1.897 ------------------------------------------------------------------------------- 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 172 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F -6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN ** J -6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070939 restraints weight = 28342.940| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.74 r_work: 0.3035 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 16212 Z= 0.352 Angle : 0.730 8.001 21999 Z= 0.386 Chirality : 0.052 0.231 2622 Planarity : 0.006 0.057 2691 Dihedral : 5.381 29.180 2254 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 1.93 % Allowed : 7.23 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2061 helix: 1.22 (0.13), residues: 1530 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 26 HIS 0.006 0.001 HIS I 61 PHE 0.014 0.002 PHE I 65 TYR 0.016 0.002 TYR E 157 ARG 0.004 0.001 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.06808 ( 1129) hydrogen bonds : angle 4.54026 ( 3360) SS BOND : bond 0.00242 ( 3) SS BOND : angle 2.20091 ( 6) covalent geometry : bond 0.00867 (16209) covalent geometry : angle 0.72937 (21993) *********************** 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 196 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 2.293 Fit side-chains REVERT: A 13 LYS cc_start: 0.8415 (pptt) cc_final: 0.7740 (ptpp) REVERT: Z 169 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6594 (pp) REVERT: B 4 ASP cc_start: 0.6591 (p0) cc_final: 0.6193 (p0) REVERT: D 246 GLN cc_start: 0.7696 (pt0) cc_final: 0.6968 (pp30) REVERT: E 52 GLU cc_start: 0.7538 (mp0) cc_final: 0.6984 (mp0) REVERT: F 4 ASP cc_start: 0.6578 (p0) cc_final: 0.6321 (p0) REVERT: H 182 ASP cc_start: 0.8379 (m-30) cc_final: 0.8122 (m-30) REVERT: I 168 LYS cc_start: 0.6416 (ttpt) cc_final: 0.6070 (tttm) REVERT: J 4 ASP cc_start: 0.6740 (p0) cc_final: 0.6469 (p0) outliers start: 32 outliers final: 8 residues processed: 181 average time/residue: 1.6429 time to fit residues: 324.3853 Evaluate side-chains 158 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 13 LYS Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 117 TRP Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 198 MET 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 132 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.093322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074384 restraints weight = 28180.989| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.74 r_work: 0.3109 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1270 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= 0.145 Angle : 0.527 6.319 21999 Z= 0.284 Chirality : 0.041 0.152 2622 Planarity : 0.005 0.050 2691 Dihedral : 4.703 27.363 2250 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 1.39 % Allowed : 9.04 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 2061 helix: 1.85 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.42 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 26 HIS 0.002 0.001 HIS E 298 PHE 0.007 0.001 PHE I 219 TYR 0.018 0.001 TYR B 5 ARG 0.002 0.000 ARG Z 86 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 1129) hydrogen bonds : angle 4.09732 ( 3360) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.93290 ( 6) covalent geometry : bond 0.00323 (16209) covalent geometry : angle 0.52691 (21993) *********************** 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 189 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.891 Fit side-chains REVERT: A 13 LYS cc_start: 0.8370 (pptt) cc_final: 0.7649 (ptpp) REVERT: Z 169 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6443 (pp) REVERT: D 182 ASP cc_start: 0.8210 (m-30) cc_final: 0.7979 (m-30) REVERT: E 52 GLU cc_start: 0.7511 (mp0) cc_final: 0.7211 (mp0) REVERT: F 1 MET cc_start: 0.6174 (mmm) cc_final: 0.5922 (mpt) REVERT: F 65 ASN cc_start: 0.7440 (t0) cc_final: 0.7161 (t0) REVERT: J 65 ASN cc_start: 0.7374 (t0) cc_final: 0.6963 (t0) outliers start: 23 outliers final: 6 residues processed: 180 average time/residue: 1.6986 time to fit residues: 335.6018 Evaluate side-chains 161 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 117 TRP Chi-restraints excluded: chain H residue 33 VAL 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 139 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.090505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071467 restraints weight = 28431.316| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.74 r_work: 0.3053 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16212 Z= 0.293 Angle : 0.664 7.741 21999 Z= 0.353 Chirality : 0.049 0.221 2622 Planarity : 0.006 0.060 2691 Dihedral : 5.122 27.003 2250 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.80 % Favored : 94.91 % Rotamer: Outliers : 2.35 % Allowed : 10.07 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2061 helix: 1.37 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.47 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 26 HIS 0.005 0.001 HIS I 61 PHE 0.011 0.002 PHE I 65 TYR 0.015 0.002 TYR E 157 ARG 0.003 0.001 ARG Z 86 Details of bonding type rmsd hydrogen bonds : bond 0.06199 ( 1129) hydrogen bonds : angle 4.35523 ( 3360) SS BOND : bond 0.00269 ( 3) SS BOND : angle 1.92746 ( 6) covalent geometry : bond 0.00721 (16209) covalent geometry : angle 0.66291 (21993) *********************** 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: 39 poor density : 154 time to evaluate : 1.713 Fit side-chains REVERT: A 13 LYS cc_start: 0.8455 (pptt) cc_final: 0.7779 (ptpp) REVERT: Z 169 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6646 (pp) REVERT: D 182 ASP cc_start: 0.8390 (m-30) cc_final: 0.8149 (m-30) REVERT: D 206 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6097 (tptp) REVERT: E 52 GLU cc_start: 0.7514 (mp0) cc_final: 0.7156 (mp0) REVERT: E 169 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6984 (pp) REVERT: F 65 ASN cc_start: 0.7561 (t0) cc_final: 0.7285 (t0) REVERT: I 168 LYS cc_start: 0.6475 (ttpt) cc_final: 0.6137 (tttm) REVERT: J -7 GLU cc_start: 0.6922 (tt0) cc_final: 0.6714 (tt0) REVERT: J 4 ASP cc_start: 0.6889 (p0) cc_final: 0.6536 (p0) REVERT: J 65 ASN cc_start: 0.7463 (t0) cc_final: 0.7084 (t0) outliers start: 39 outliers final: 12 residues processed: 182 average time/residue: 1.4765 time to fit residues: 294.2479 Evaluate side-chains 167 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 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 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 117 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 1 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075158 restraints weight = 28319.818| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.74 r_work: 0.3122 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1343 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= 0.130 Angle : 0.508 6.559 21999 Z= 0.274 Chirality : 0.040 0.140 2622 Planarity : 0.005 0.051 2691 Dihedral : 4.575 27.353 2250 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.75 % Favored : 95.10 % Rotamer: Outliers : 1.39 % Allowed : 11.39 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2061 helix: 1.95 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.39 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 142 HIS 0.002 0.000 HIS I 61 PHE 0.006 0.001 PHE E 219 TYR 0.012 0.001 TYR B 5 ARG 0.001 0.000 ARG Z 30 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 1129) hydrogen bonds : angle 3.98637 ( 3360) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.81670 ( 6) covalent geometry : bond 0.00281 (16209) covalent geometry : angle 0.50838 (21993) *********************** 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: 23 poor density : 166 time to evaluate : 3.010 Fit side-chains REVERT: A 13 LYS cc_start: 0.8364 (pptt) cc_final: 0.7652 (ptpp) REVERT: Y 137 ARG cc_start: 0.7379 (mmp-170) cc_final: 0.7153 (mmp80) REVERT: Z 169 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6528 (pp) REVERT: D 21 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8029 (mm-30) REVERT: D 206 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.5967 (tptp) REVERT: E 52 GLU cc_start: 0.7487 (mp0) cc_final: 0.6799 (mp0) REVERT: E 169 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6664 (pp) REVERT: F 4 ASP cc_start: 0.6759 (p0) cc_final: 0.6477 (p0) REVERT: F 65 ASN cc_start: 0.7500 (t0) cc_final: 0.7240 (t0) REVERT: I 168 LYS cc_start: 0.6375 (ttpt) cc_final: 0.6068 (tmtp) REVERT: J 1 MET cc_start: 0.5894 (mmm) cc_final: 0.5586 (mmt) REVERT: J 65 ASN cc_start: 0.7421 (t0) cc_final: 0.7014 (t0) outliers start: 23 outliers final: 13 residues processed: 183 average time/residue: 2.2481 time to fit residues: 447.5935 Evaluate side-chains 173 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 96 THR 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 33 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 H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue -6 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ** 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 = 0.3545 r_free = 0.3545 target = 0.093406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074534 restraints weight = 28233.841| |-----------------------------------------------------------------------------| r_work (start): 0.3203 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: 3.80 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1374 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= 0.150 Angle : 0.530 6.794 21999 Z= 0.283 Chirality : 0.042 0.156 2622 Planarity : 0.005 0.053 2691 Dihedral : 4.569 25.730 2250 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 1.81 % Allowed : 12.06 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 2061 helix: 1.94 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.25 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 26 HIS 0.003 0.001 HIS I 61 PHE 0.007 0.001 PHE I 65 TYR 0.010 0.001 TYR B 5 ARG 0.002 0.000 ARG Z 86 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 1129) hydrogen bonds : angle 3.99571 ( 3360) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.98970 ( 6) covalent geometry : bond 0.00343 (16209) covalent geometry : angle 0.52941 (21993) *********************** 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 187 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 1.696 Fit side-chains REVERT: A 13 LYS cc_start: 0.8431 (pptt) cc_final: 0.7712 (ptpp) REVERT: Y 137 ARG cc_start: 0.7458 (mmp-170) cc_final: 0.7209 (mmp80) REVERT: Z 169 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6572 (pp) REVERT: D 206 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.5927 (tptp) REVERT: E 52 GLU cc_start: 0.7457 (mp0) cc_final: 0.6756 (mp0) REVERT: E 169 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6682 (pp) REVERT: F 65 ASN cc_start: 0.7462 (t0) cc_final: 0.7205 (t0) REVERT: J 4 ASP cc_start: 0.6884 (p0) cc_final: 0.6544 (p0) REVERT: J 65 ASN cc_start: 0.7387 (t0) cc_final: 0.7021 (t0) REVERT: J 68 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8546 (mt-10) outliers start: 30 outliers final: 17 residues processed: 177 average time/residue: 1.7806 time to fit residues: 344.2249 Evaluate side-chains 176 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain Y residue 113 THR 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 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 47 LEU Chi-restraints excluded: chain H residue 113 THR 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 26 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.073335 restraints weight = 28064.851| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.76 r_work: 0.3086 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16212 Z= 0.182 Angle : 0.559 6.376 21999 Z= 0.300 Chirality : 0.043 0.174 2622 Planarity : 0.005 0.055 2691 Dihedral : 4.714 26.269 2250 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 1.99 % Allowed : 12.00 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 2061 helix: 1.82 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.30 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 26 HIS 0.004 0.001 HIS Z 61 PHE 0.009 0.001 PHE I 65 TYR 0.009 0.001 TYR E 157 ARG 0.002 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 1129) hydrogen bonds : angle 4.08865 ( 3360) SS BOND : bond 0.00224 ( 3) SS BOND : angle 1.26684 ( 6) covalent geometry : bond 0.00432 (16209) covalent geometry : angle 0.55917 (21993) *********************** 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: 33 poor density : 159 time to evaluate : 1.641 Fit side-chains REVERT: A 13 LYS cc_start: 0.8458 (pptt) cc_final: 0.7741 (ptpp) REVERT: Y 137 ARG cc_start: 0.7476 (mmp-170) cc_final: 0.7208 (mmp80) REVERT: Z 169 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6643 (pp) REVERT: B 4 ASP cc_start: 0.6587 (p0) cc_final: 0.6265 (p0) REVERT: D 206 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6047 (tptp) REVERT: E 52 GLU cc_start: 0.7495 (mp0) cc_final: 0.6706 (mp0) REVERT: E 169 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6727 (pp) REVERT: F 4 ASP cc_start: 0.6713 (p0) cc_final: 0.6382 (p0) REVERT: F 65 ASN cc_start: 0.7551 (t0) cc_final: 0.7292 (t0) REVERT: I 168 LYS cc_start: 0.6406 (ttpt) cc_final: 0.6136 (mptt) REVERT: J 65 ASN cc_start: 0.7440 (t0) cc_final: 0.7065 (t0) REVERT: J 68 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8592 (mt-10) outliers start: 33 outliers final: 18 residues processed: 182 average time/residue: 1.4871 time to fit residues: 296.3281 Evaluate side-chains 179 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 2.024 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain Y residue 113 THR 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 C residue 41 MET Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 94 ASP 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 113 THR Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue -6 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 128 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 193 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.093793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.074367 restraints weight = 27693.153| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.74 r_work: 0.3105 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1417 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= 0.150 Angle : 0.530 6.038 21999 Z= 0.285 Chirality : 0.042 0.165 2622 Planarity : 0.005 0.052 2691 Dihedral : 4.600 26.446 2250 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.43 % Favored : 94.42 % Rotamer: Outliers : 1.99 % Allowed : 12.30 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 2061 helix: 1.96 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 26 HIS 0.003 0.001 HIS I 61 PHE 0.007 0.001 PHE I 65 TYR 0.009 0.001 TYR B 5 ARG 0.002 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 1129) hydrogen bonds : angle 4.00954 ( 3360) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.99881 ( 6) covalent geometry : bond 0.00340 (16209) covalent geometry : angle 0.53022 (21993) *********************** 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 191 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.807 Fit side-chains REVERT: A 13 LYS cc_start: 0.8439 (pptt) cc_final: 0.7722 (ptpp) REVERT: Y 137 ARG cc_start: 0.7427 (mmp-170) cc_final: 0.7160 (mmp80) REVERT: Z 169 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6572 (pp) REVERT: D 206 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.5971 (tptp) REVERT: E 52 GLU cc_start: 0.7446 (mp0) cc_final: 0.6666 (mp0) REVERT: E 169 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6579 (pp) REVERT: F 65 ASN cc_start: 0.7507 (t0) cc_final: 0.7250 (t0) REVERT: I 168 LYS cc_start: 0.6411 (ttpt) cc_final: 0.6043 (ttpt) REVERT: J 4 ASP cc_start: 0.6906 (p0) cc_final: 0.6604 (p0) REVERT: J 65 ASN cc_start: 0.7426 (t0) cc_final: 0.7049 (t0) REVERT: J 68 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8581 (mt-10) outliers start: 33 outliers final: 21 residues processed: 182 average time/residue: 1.4829 time to fit residues: 295.4981 Evaluate side-chains 181 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.958 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain Y residue 113 THR 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 96 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain E residue 94 ASP 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 47 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain I residue 117 TRP Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue -6 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 182 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 157 optimal weight: 0.0970 chunk 58 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 E 248 HIS F -2 GLN F 66 ASN I 98 GLN I 248 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078153 restraints weight = 27809.710| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.74 r_work: 0.3184 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1448 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= 0.109 Angle : 0.478 5.970 21999 Z= 0.256 Chirality : 0.039 0.154 2622 Planarity : 0.005 0.048 2691 Dihedral : 4.272 25.780 2250 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.80 % Favored : 95.05 % Rotamer: Outliers : 1.02 % Allowed : 13.08 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.19), residues: 2061 helix: 2.27 (0.13), residues: 1497 sheet: None (None), residues: 0 loop : -1.32 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 142 HIS 0.002 0.000 HIS Z 298 PHE 0.006 0.001 PHE Z 219 TYR 0.008 0.001 TYR B 5 ARG 0.001 0.000 ARG H 153 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 1129) hydrogen bonds : angle 3.79445 ( 3360) SS BOND : bond 0.00180 ( 3) SS BOND : angle 0.43640 ( 6) covalent geometry : bond 0.00218 (16209) covalent geometry : angle 0.47833 (21993) *********************** 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 182 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.612 Fit side-chains REVERT: A 13 LYS cc_start: 0.8378 (pptt) cc_final: 0.7662 (ptpp) REVERT: Y 137 ARG cc_start: 0.7361 (mmp-170) cc_final: 0.7093 (mmp80) REVERT: Z 169 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6588 (pp) REVERT: B 4 ASP cc_start: 0.6650 (p0) cc_final: 0.6324 (p0) REVERT: D 128 ASP cc_start: 0.7557 (m-30) cc_final: 0.7216 (m-30) REVERT: D 133 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7777 (mt-10) REVERT: D 137 ARG cc_start: 0.7528 (mmp-170) cc_final: 0.7215 (mmp80) REVERT: D 246 GLN cc_start: 0.7445 (pt0) cc_final: 0.6797 (pp30) REVERT: E 169 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6209 (pp) REVERT: F 4 ASP cc_start: 0.6688 (p0) cc_final: 0.6389 (p0) REVERT: F 65 ASN cc_start: 0.7413 (t0) cc_final: 0.7162 (t0) REVERT: H 137 ARG cc_start: 0.7353 (mmp-170) cc_final: 0.7109 (mmp80) REVERT: J 4 ASP cc_start: 0.6854 (p0) cc_final: 0.6537 (p0) REVERT: J 65 ASN cc_start: 0.7354 (t0) cc_final: 0.6966 (t0) REVERT: J 68 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8526 (mt-10) outliers start: 17 outliers final: 9 residues processed: 178 average time/residue: 1.4647 time to fit residues: 285.0585 Evaluate side-chains 165 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain D residue 33 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 I residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 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 = 0.093479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074499 restraints weight = 28377.247| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.74 r_work: 0.3112 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1464 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= 0.163 Angle : 0.543 5.915 21999 Z= 0.289 Chirality : 0.042 0.154 2622 Planarity : 0.005 0.051 2691 Dihedral : 4.538 24.898 2250 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.19 % Favored : 94.66 % Rotamer: Outliers : 1.21 % Allowed : 12.96 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 2061 helix: 2.01 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.20 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 142 HIS 0.004 0.001 HIS I 61 PHE 0.008 0.001 PHE I 65 TYR 0.008 0.001 TYR B 5 ARG 0.002 0.000 ARG I 86 Details of bonding type rmsd hydrogen bonds : bond 0.04764 ( 1129) hydrogen bonds : angle 3.96249 ( 3360) SS BOND : bond 0.00176 ( 3) SS BOND : angle 1.02795 ( 6) covalent geometry : bond 0.00382 (16209) covalent geometry : angle 0.54234 (21993) ********************** 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 178 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.693 Fit side-chains REVERT: A 13 LYS cc_start: 0.8472 (pptt) cc_final: 0.7754 (ptpp) REVERT: Y 137 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.7213 (mmp80) REVERT: Z 169 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6510 (pp) REVERT: E 169 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6458 (pp) REVERT: F 4 ASP cc_start: 0.6643 (p0) cc_final: 0.6362 (p0) REVERT: F 65 ASN cc_start: 0.7431 (t0) cc_final: 0.7184 (t0) REVERT: I 168 LYS cc_start: 0.6434 (ttpt) cc_final: 0.6082 (tttm) REVERT: J 4 ASP cc_start: 0.6923 (p0) cc_final: 0.6573 (p0) REVERT: J 65 ASN cc_start: 0.7437 (t0) cc_final: 0.7042 (t0) REVERT: J 68 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8577 (mt-10) outliers start: 20 outliers final: 11 residues processed: 174 average time/residue: 1.5059 time to fit residues: 286.1550 Evaluate side-chains 168 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 113 THR 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 113 THR 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 43 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 I 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.071717 restraints weight = 28213.786| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.73 r_work: 0.3056 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16212 Z= 0.295 Angle : 0.668 6.423 21999 Z= 0.354 Chirality : 0.049 0.196 2622 Planarity : 0.006 0.057 2691 Dihedral : 5.121 27.504 2250 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.09 % Favored : 94.61 % Rotamer: Outliers : 1.33 % Allowed : 13.02 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2061 helix: 1.44 (0.13), residues: 1527 sheet: None (None), residues: 0 loop : -1.41 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 26 HIS 0.005 0.001 HIS Z 61 PHE 0.011 0.002 PHE Z 65 TYR 0.015 0.002 TYR E 157 ARG 0.003 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.06144 ( 1129) hydrogen bonds : angle 4.31229 ( 3360) SS BOND : bond 0.00203 ( 3) SS BOND : angle 1.95773 ( 6) covalent geometry : bond 0.00729 (16209) covalent geometry : angle 0.66690 (21993) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11415.31 seconds wall clock time: 200 minutes 10.56 seconds (12010.56 seconds total)