Starting phenix.real_space_refine on Mon Jan 20 20:04:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xno_33321/01_2025/7xno_33321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xno_33321/01_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_33321/01_2025/7xno_33321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xno_33321/01_2025/7xno_33321.map" model { file = "/net/cci-nas-00/data/ceres_data/7xno_33321/01_2025/7xno_33321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xno_33321/01_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.32, per 1000 atoms: 0.59 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: 3.82 Conformation dependent library (CDL) restraints added in 2.0 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: 1.39 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: 4.69 Time building geometry restraints manager: 4.42 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: 0.06 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: 2.040 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.490 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.530 ------------------------------------------------------------------------------- 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 16209 Z= 0.157 Angle : 0.527 6.889 21993 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 *********************** 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 : 1.644 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: 1.6231 time to fit residues: 334.3622 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 : 2.027 ------------------------------------------------------------------------------- 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 = 0.070935 restraints weight = 28342.938| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.75 r_work: 0.3034 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- 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 16209 Z= 0.554 Angle : 0.729 8.001 21993 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 *********************** 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 : 1.796 Fit side-chains REVERT: A 13 LYS cc_start: 0.8415 (pptt) cc_final: 0.7740 (ptpp) REVERT: Z 169 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6594 (pp) REVERT: B 4 ASP cc_start: 0.6596 (p0) cc_final: 0.6198 (p0) REVERT: D 246 GLN cc_start: 0.7695 (pt0) cc_final: 0.6966 (pp30) REVERT: E 52 GLU cc_start: 0.7538 (mp0) cc_final: 0.6985 (mp0) REVERT: F 4 ASP cc_start: 0.6582 (p0) cc_final: 0.6326 (p0) REVERT: H 182 ASP cc_start: 0.8379 (m-30) cc_final: 0.8121 (m-30) REVERT: I 168 LYS cc_start: 0.6418 (ttpt) cc_final: 0.6072 (tttm) REVERT: J 4 ASP cc_start: 0.6744 (p0) cc_final: 0.6472 (p0) outliers start: 32 outliers final: 8 residues processed: 181 average time/residue: 1.5543 time to fit residues: 307.2868 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 : 1.915 ------------------------------------------------------------------------------- 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: 3.9990 chunk 50 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.094018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075155 restraints weight = 28143.635| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.73 r_work: 0.3124 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16209 Z= 0.174 Angle : 0.510 6.592 21993 Z= 0.276 Chirality : 0.040 0.140 2622 Planarity : 0.005 0.050 2691 Dihedral : 4.642 27.664 2250 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 1.21 % Allowed : 9.10 % Favored : 89.69 % 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: 1.64 (0.19), residues: 2061 helix: 1.94 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.40 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 26 HIS 0.002 0.000 HIS E 298 PHE 0.007 0.001 PHE I 219 TYR 0.018 0.001 TYR B 5 ARG 0.001 0.000 ARG E 86 *********************** 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 187 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.759 Fit side-chains REVERT: A 13 LYS cc_start: 0.8351 (pptt) cc_final: 0.7633 (ptpp) REVERT: Z 169 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6526 (pp) REVERT: D 182 ASP cc_start: 0.8204 (m-30) cc_final: 0.7973 (m-30) REVERT: D 246 GLN cc_start: 0.7691 (pt0) cc_final: 0.6987 (pp30) REVERT: E 50 THR cc_start: 0.8010 (t) cc_final: 0.7775 (t) REVERT: E 52 GLU cc_start: 0.7497 (mp0) cc_final: 0.7190 (mp0) REVERT: E 169 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6734 (pp) REVERT: F 1 MET cc_start: 0.6164 (mmm) cc_final: 0.5918 (mpt) REVERT: F 65 ASN cc_start: 0.7410 (t0) cc_final: 0.7160 (t0) REVERT: J 65 ASN cc_start: 0.7373 (t0) cc_final: 0.6933 (t0) outliers start: 20 outliers final: 5 residues processed: 179 average time/residue: 1.6555 time to fit residues: 323.3086 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 : 1.885 ------------------------------------------------------------------------------- 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 E residue 169 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 47 LEU 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: 10.0000 chunk 54 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN Y 246 GLN Z 98 GLN C 11 ASN D 246 GLN ** F -2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN I 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.091519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.072489 restraints weight = 28339.321| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.75 r_work: 0.3070 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16209 Z= 0.357 Angle : 0.606 7.170 21993 Z= 0.323 Chirality : 0.045 0.192 2622 Planarity : 0.006 0.057 2691 Dihedral : 4.893 26.661 2250 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.95 % Favored : 94.86 % Rotamer: Outliers : 2.17 % Allowed : 9.52 % Favored : 88.31 % 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: 1.33 (0.19), residues: 2061 helix: 1.65 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -1.38 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 26 HIS 0.004 0.001 HIS I 61 PHE 0.010 0.001 PHE Y 211 TYR 0.011 0.002 TYR E 157 ARG 0.002 0.000 ARG Z 86 *********************** 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: 36 poor density : 157 time to evaluate : 1.790 Fit side-chains REVERT: A 13 LYS cc_start: 0.8464 (pptt) cc_final: 0.7776 (ptpp) REVERT: Z 169 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6525 (pp) REVERT: D 182 ASP cc_start: 0.8348 (m-30) cc_final: 0.8101 (m-30) REVERT: D 206 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.5981 (tptp) REVERT: E 52 GLU cc_start: 0.7487 (mp0) cc_final: 0.7086 (mp0) REVERT: F 65 ASN cc_start: 0.7530 (t0) cc_final: 0.7276 (t0) REVERT: H 203 MET cc_start: 0.9004 (ptt) cc_final: 0.8798 (ptt) REVERT: J 65 ASN cc_start: 0.7431 (t0) cc_final: 0.7009 (t0) outliers start: 36 outliers final: 11 residues processed: 182 average time/residue: 1.5765 time to fit residues: 313.6264 Evaluate side-chains 165 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 96 THR 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 206 LYS Chi-restraints excluded: chain E residue 117 TRP 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 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: 2.9990 chunk 178 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.093517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.074606 restraints weight = 28455.148| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.74 r_work: 0.3114 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16209 Z= 0.205 Angle : 0.524 6.566 21993 Z= 0.281 Chirality : 0.041 0.154 2622 Planarity : 0.005 0.051 2691 Dihedral : 4.629 27.059 2250 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.63 % Allowed : 11.21 % Favored : 87.16 % 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: 1.67 (0.19), residues: 2061 helix: 1.96 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.38 (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 219 TYR 0.011 0.001 TYR B 5 ARG 0.001 0.000 ARG Z 86 *********************** 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 187 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.778 Fit side-chains REVERT: A 13 LYS cc_start: 0.8446 (pptt) cc_final: 0.7737 (ptpp) REVERT: Y 137 ARG cc_start: 0.7440 (mmp-170) cc_final: 0.7216 (mmp80) REVERT: Z 169 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6538 (pp) REVERT: D 182 ASP cc_start: 0.8209 (m-30) cc_final: 0.7988 (m-30) REVERT: D 206 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.5915 (tptp) REVERT: E 52 GLU cc_start: 0.7509 (mp0) cc_final: 0.7123 (mp0) REVERT: E 169 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6688 (pp) REVERT: F 65 ASN cc_start: 0.7454 (t0) cc_final: 0.7184 (t0) REVERT: H 137 ARG cc_start: 0.7442 (mmp-170) cc_final: 0.7214 (mmp80) REVERT: I 168 LYS cc_start: 0.6356 (ttpt) cc_final: 0.6044 (tmtp) REVERT: J 4 ASP cc_start: 0.6914 (p0) cc_final: 0.6580 (p0) REVERT: J 65 ASN cc_start: 0.7378 (t0) cc_final: 0.7003 (t0) REVERT: J 68 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8561 (mt-10) outliers start: 27 outliers final: 15 residues processed: 178 average time/residue: 1.5704 time to fit residues: 305.0758 Evaluate side-chains 175 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain D residue 152 VAL 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 152 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.9969 > 50: distance: 31 - 45: 5.921 distance: 35 - 53: 7.147 distance: 40 - 61: 6.494 distance: 43 - 45: 3.291 distance: 44 - 69: 5.805 distance: 46 - 49: 3.811 distance: 47 - 53: 5.034 distance: 48 - 76: 15.756 distance: 49 - 50: 3.791 distance: 50 - 51: 5.877 distance: 50 - 52: 5.812 distance: 54 - 57: 3.691 distance: 55 - 56: 3.737 distance: 56 - 84: 40.737 distance: 57 - 58: 6.635 distance: 58 - 59: 7.107 distance: 58 - 60: 13.134 distance: 63 - 64: 4.417 distance: 64 - 92: 5.321 distance: 65 - 66: 5.587 distance: 66 - 67: 3.153 distance: 66 - 68: 3.911 distance: 70 - 71: 6.105 distance: 70 - 73: 4.081 distance: 71 - 76: 6.476 distance: 72 - 99: 7.270 distance: 73 - 74: 4.972 distance: 73 - 75: 4.048 distance: 76 - 77: 7.299 distance: 77 - 78: 11.246 distance: 77 - 80: 4.878 distance: 78 - 79: 25.987 distance: 78 - 84: 32.116 distance: 79 - 110: 22.022 distance: 80 - 81: 7.555 distance: 80 - 82: 4.102 distance: 81 - 83: 5.876 distance: 84 - 85: 36.069 distance: 85 - 86: 3.542 distance: 85 - 88: 20.156 distance: 87 - 117: 5.449 distance: 88 - 89: 18.817 distance: 88 - 90: 14.952 distance: 89 - 91: 16.432 distance: 92 - 93: 3.861 distance: 93 - 94: 5.276 distance: 93 - 96: 6.331 distance: 94 - 95: 3.496 distance: 94 - 99: 3.722 distance: 95 - 125: 6.562 distance: 96 - 97: 4.432 distance: 96 - 98: 9.083 distance: 99 - 100: 5.393 distance: 100 - 101: 4.153 distance: 100 - 103: 3.475 distance: 101 - 102: 3.822 distance: 103 - 104: 8.590 distance: 104 - 105: 6.161 distance: 105 - 106: 6.295 distance: 106 - 107: 5.091 distance: 107 - 108: 5.118 distance: 107 - 109: 3.654 distance: 111 - 114: 3.390 distance: 114 - 116: 5.602 distance: 118 - 119: 3.303 distance: 118 - 121: 5.312 distance: 119 - 120: 3.552 distance: 121 - 122: 4.267 distance: 122 - 123: 12.037 distance: 122 - 124: 9.759