Starting phenix.real_space_refine on Thu Jul 31 05:43:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xi0_22189/07_2025/6xi0_22189.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xi0_22189/07_2025/6xi0_22189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xi0_22189/07_2025/6xi0_22189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xi0_22189/07_2025/6xi0_22189.map" model { file = "/net/cci-nas-00/data/ceres_data/6xi0_22189/07_2025/6xi0_22189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xi0_22189/07_2025/6xi0_22189.cif" } resolution = 3.3 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 10 7.16 5 S 78 5.16 5 C 8578 2.51 5 N 2155 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13079 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "C" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1801 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 3244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3244 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'HIS:plan': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "Q" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1794 Classifications: {'peptide': 235} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1365 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 933 SG CYS E 133 30.849 65.240 37.564 0.25105.87 S ATOM 1079 SG CYS E 153 29.828 61.763 37.104 0.25107.21 S ATOM 12381 SG CYS R 133 83.431 27.174 37.574 0.25105.87 S ATOM 12527 SG CYS R 153 84.451 30.652 37.124 0.25107.21 S Residues with excluded nonbonded symmetry interactions: 52 residue: pdb=" N MET E 129 " occ=0.25 ... (6 atoms not shown) pdb=" CE MET E 129 " occ=0.25 residue: pdb=" N GLY E 131 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 131 " occ=0.25 residue: pdb=" N VAL E 132 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 132 " occ=0.25 residue: pdb=" N CYS E 133 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 133 " occ=0.25 residue: pdb=" N THR E 134 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 THR E 134 " occ=0.25 residue: pdb=" N HIS E 135 " occ=0.25 ... (8 atoms not shown) pdb=" NE2 HIS E 135 " occ=0.25 residue: pdb=" N LEU E 136 " occ=0.25 ... (6 atoms not shown) pdb=" CD2 LEU E 136 " occ=0.25 residue: pdb=" N GLY E 137 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 137 " occ=0.25 residue: pdb=" N CYS E 138 " occ=0.25 ... (4 atoms not shown) pdb=" SG CYS E 138 " occ=0.25 residue: pdb=" N VAL E 139 " occ=0.25 ... (5 atoms not shown) pdb=" CG2 VAL E 139 " occ=0.25 residue: pdb=" N PRO E 140 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO E 140 " occ=0.25 residue: pdb=" N GLY E 142 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY E 142 " occ=0.25 ... (remaining 40 not shown) Time building chain proxies: 8.28, per 1000 atoms: 0.63 Number of scatterers: 13079 At special positions: 0 Unit cell: (115.6, 93.84, 106.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 10 26.01 S 78 16.00 O 2258 8.00 N 2155 7.00 C 8578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 138 " - pdb=" SG CYS R 155 " 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 501 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 135 " pdb="FE2 FES E 501 " - pdb=" ND1 HIS E 156 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 501 " - pdb=" SG CYS E 153 " pdb=" FES R 501 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 156 " pdb="FE2 FES R 501 " - pdb=" ND1 HIS R 135 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 133 " pdb="FE1 FES R 501 " - pdb=" SG CYS R 153 " Number of angles added : 6 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 51.5% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'E' and resid 11 through 37 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.563A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 87 Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.764A pdb=" N GLY C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 66 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.756A pdb=" N SER C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 148 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 169 removed outlier: 3.623A pdb=" N TRP C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE C 166 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 200 through 219 removed outlier: 3.960A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 270 Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 298 through 308 removed outlier: 4.405A pdb=" N PHE C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 327 through 346 removed outlier: 3.848A pdb=" N MET C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 360 through 381 Processing helix chain 'C' and resid 388 through 415 removed outlier: 5.576A pdb=" N LEU C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Proline residue: C 409 - end of helix Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.629A pdb=" N LEU D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 37 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 201 through 218 Processing helix chain 'D' and resid 220 through 250 Processing helix chain 'P' and resid 14 through 19 Processing helix chain 'P' and resid 23 through 33 removed outlier: 3.763A pdb=" N GLY P 27 " --> pdb=" O LEU P 23 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 66 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 90 through 118 removed outlier: 3.754A pdb=" N SER P 102 " --> pdb=" O ALA P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 148 removed outlier: 3.860A pdb=" N TRP P 129 " --> pdb=" O ARG P 125 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL P 148 " --> pdb=" O PHE P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 153 through 169 removed outlier: 3.623A pdb=" N TRP P 157 " --> pdb=" O GLN P 153 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE P 166 " --> pdb=" O ILE P 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY P 167 " --> pdb=" O THR P 163 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 182 removed outlier: 3.668A pdb=" N ILE P 176 " --> pdb=" O ILE P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 199 Processing helix chain 'P' and resid 200 through 219 removed outlier: 3.957A pdb=" N VAL P 204 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE P 216 " --> pdb=" O HIS P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 270 Processing helix chain 'P' and resid 276 through 281 Processing helix chain 'P' and resid 298 through 308 removed outlier: 4.405A pdb=" N PHE P 308 " --> pdb=" O ILE P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 316 through 321 Processing helix chain 'P' and resid 327 through 346 removed outlier: 3.847A pdb=" N MET P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 347 through 349 No H-bonds generated for 'chain 'P' and resid 347 through 349' Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 381 Processing helix chain 'P' and resid 388 through 415 removed outlier: 5.575A pdb=" N LEU P 408 " --> pdb=" O PHE P 404 " (cutoff:3.500A) Proline residue: P 409 - end of helix Processing helix chain 'Q' and resid 19 through 33 removed outlier: 3.628A pdb=" N LEU Q 23 " --> pdb=" O ASP Q 19 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU Q 32 " --> pdb=" O GLN Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 37 Processing helix chain 'Q' and resid 44 through 49 removed outlier: 3.567A pdb=" N THR Q 47 " --> pdb=" O PRO Q 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q 48 " --> pdb=" O ILE Q 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA Q 49 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 44 through 49' Processing helix chain 'Q' and resid 57 through 67 Processing helix chain 'Q' and resid 127 through 136 Processing helix chain 'Q' and resid 201 through 218 Processing helix chain 'Q' and resid 220 through 250 Processing helix chain 'R' and resid 12 through 37 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 41 through 46 removed outlier: 3.563A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 109 through 114 Processing sheet with id=AA1, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA E 181 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 64 through 67 Processing sheet with id=AA3, first strand: chain 'E' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP E 143 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY E 150 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP E 151 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 158 " --> pdb=" O CYS E 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'Q' and resid 153 through 155 Processing sheet with id=AA6, first strand: chain 'R' and resid 50 through 52 removed outlier: 3.607A pdb=" N ALA R 181 " --> pdb=" O LYS R 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'R' and resid 141 through 145 removed outlier: 4.683A pdb=" N ASP R 143 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY R 150 " --> pdb=" O ASP R 143 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP R 151 " --> pdb=" O TYR R 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER R 158 " --> pdb=" O CYS R 153 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1815 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: 3.42 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 5786 1.41 - 1.61: 7561 1.61 - 1.80: 103 1.80 - 2.00: 31 2.00 - 2.20: 28 Bond restraints: 13509 Sorted by residual: bond pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sigma weight residual 1.544 1.324 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" CAC HEC P 501 " pdb=" CBC HEC P 501 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC C 501 " pdb=" C3D HEC C 501 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C2D HEC P 501 " pdb=" C3D HEC P 501 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.08e+02 ... (remaining 13504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 18189 3.16 - 6.32: 279 6.32 - 9.49: 31 9.49 - 12.65: 5 12.65 - 15.81: 16 Bond angle restraints: 18520 Sorted by residual: angle pdb="FE1 FES R 501 " pdb=" S2 FES R 501 " pdb="FE2 FES R 501 " ideal model delta sigma weight residual 75.66 89.11 -13.45 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " pdb="FE2 FES E 501 " ideal model delta sigma weight residual 75.66 89.09 -13.43 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES R 501 " pdb="FE2 FES R 501 " pdb=" S2 FES R 501 " ideal model delta sigma weight residual 104.33 90.91 13.42 1.14e+00 7.69e-01 1.39e+02 angle pdb=" S1 FES E 501 " pdb="FE2 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.94 13.39 1.14e+00 7.69e-01 1.38e+02 angle pdb=" S1 FES E 501 " pdb="FE1 FES E 501 " pdb=" S2 FES E 501 " ideal model delta sigma weight residual 104.33 90.80 13.53 1.20e+00 6.94e-01 1.27e+02 ... (remaining 18515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6979 17.90 - 35.79: 535 35.79 - 53.69: 79 53.69 - 71.58: 10 71.58 - 89.48: 22 Dihedral angle restraints: 7625 sinusoidal: 2835 harmonic: 4790 Sorted by residual: dihedral pdb=" C2B HEC P 501 " pdb=" C3B HEC P 501 " pdb=" CAB HEC P 501 " pdb=" CBB HEC P 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.29 82.29 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC C 501 " pdb=" C3B HEC C 501 " pdb=" CAB HEC C 501 " pdb=" CBB HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -22.15 82.15 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2C HEC P 502 " pdb=" C3C HEC P 502 " pdb=" CAC HEC P 502 " pdb=" CBC HEC P 502 " ideal model delta sinusoidal sigma weight residual 60.00 -17.14 77.14 2 1.00e+01 1.00e-02 4.56e+01 ... (remaining 7622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1912 0.146 - 0.292: 45 0.292 - 0.439: 1 0.439 - 0.585: 10 0.585 - 0.731: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CG LEU Q 244 " pdb=" CB LEU Q 244 " pdb=" CD1 LEU Q 244 " pdb=" CD2 LEU Q 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU D 244 " pdb=" CB LEU D 244 " pdb=" CD1 LEU D 244 " pdb=" CD2 LEU D 244 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CB THR Q 198 " pdb=" CA THR Q 198 " pdb=" OG1 THR Q 198 " pdb=" CG2 THR Q 198 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.87e+00 ... (remaining 1967 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q 501 " 0.010 2.00e-02 2.50e+03 4.12e-02 3.82e+01 pdb=" C2C HEC Q 501 " -0.109 2.00e-02 2.50e+03 pdb=" C3C HEC Q 501 " 0.042 2.00e-02 2.50e+03 pdb=" C4C HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CAC HEC Q 501 " 0.007 2.00e-02 2.50e+03 pdb=" CHC HEC Q 501 " 0.018 2.00e-02 2.50e+03 pdb=" CHD HEC Q 501 " -0.007 2.00e-02 2.50e+03 pdb=" CMC HEC Q 501 " 0.031 2.00e-02 2.50e+03 pdb=" NC HEC Q 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 501 " -0.010 2.00e-02 2.50e+03 4.10e-02 3.78e+01 pdb=" C2C HEC D 501 " 0.109 2.00e-02 2.50e+03 pdb=" C3C HEC D 501 " -0.042 2.00e-02 2.50e+03 pdb=" C4C HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC D 501 " -0.007 2.00e-02 2.50e+03 pdb=" CHC HEC D 501 " -0.018 2.00e-02 2.50e+03 pdb=" CHD HEC D 501 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC D 501 " -0.031 2.00e-02 2.50e+03 pdb=" NC HEC D 501 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 222 " -0.021 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" C ASN C 222 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN C 222 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN C 223 " -0.025 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 160 2.57 - 3.15: 11764 3.15 - 3.73: 19511 3.73 - 4.32: 27440 4.32 - 4.90: 45711 Nonbonded interactions: 104586 Sorted by model distance: nonbonded pdb=" O THR E 186 " pdb=" OG1 THR E 187 " model vdw 1.987 3.040 nonbonded pdb=" O THR R 186 " pdb=" OG1 THR R 187 " model vdw 1.987 3.040 nonbonded pdb=" OG SER P 120 " pdb=" ND2 ASN P 222 " model vdw 1.988 3.120 nonbonded pdb=" NH2 ARG C 306 " pdb=" O MET C 383 " model vdw 2.007 3.120 nonbonded pdb=" NH2 ARG P 306 " pdb=" O MET P 383 " model vdw 2.007 3.120 ... (remaining 104581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = (chain 'D' and (resid 5 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 257 or resid 501)) selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.98 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: 0.690 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.280 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.010 0.220 13529 Z= 0.474 Angle : 1.046 23.217 18530 Z= 0.636 Chirality : 0.070 0.731 1970 Planarity : 0.007 0.082 2327 Dihedral : 13.757 89.475 4563 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.34 % Favored : 83.23 % Rotamer: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.56 % 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: -4.31 (0.17), residues: 1658 helix: -1.65 (0.16), residues: 784 sheet: -3.37 (0.48), residues: 64 loop : -4.22 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 296 HIS 0.010 0.001 HIS P 111 PHE 0.021 0.001 PHE P 104 TYR 0.010 0.001 TYR C 297 ARG 0.002 0.000 ARG P 85 Details of bonding type rmsd hydrogen bonds : bond 0.14334 ( 630) hydrogen bonds : angle 6.99174 ( 1815) metal coordination : bond 0.01153 ( 8) metal coordination : angle 14.22173 ( 6) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.58186 ( 4) covalent geometry : bond 0.00944 (13509) covalent geometry : angle 1.01486 (18520) Misc. bond : bond 0.14976 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 81 ASP cc_start: 0.1777 (t70) cc_final: 0.1459 (t70) REVERT: E 113 ARG cc_start: 0.7350 (tpt90) cc_final: 0.7095 (ttt90) REVERT: D 218 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8112 (tp30) REVERT: P 305 LEU cc_start: 0.8858 (tp) cc_final: 0.8566 (tt) REVERT: Q 74 LYS cc_start: 0.7557 (ttpt) cc_final: 0.7263 (tttt) REVERT: Q 218 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7916 (tp30) REVERT: Q 247 LYS cc_start: 0.7812 (tttt) cc_final: 0.7557 (tttt) REVERT: R 81 ASP cc_start: 0.1993 (t70) cc_final: 0.1623 (t70) REVERT: R 113 ARG cc_start: 0.7393 (tpt90) cc_final: 0.7086 (ttt90) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.3340 time to fit residues: 99.7378 Evaluate side-chains 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.6980 chunk 125 optimal weight: 0.0170 chunk 69 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 HIS E 100 ASN C 68 HIS C 82 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN D 177 HIS P 68 HIS P 82 HIS P 222 ASN Q 159 GLN Q 177 HIS R 17 HIS R 100 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136029 restraints weight = 15145.262| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.59 r_work: 0.3117 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.252 13529 Z= 0.158 Angle : 0.765 12.958 18530 Z= 0.357 Chirality : 0.045 0.196 1970 Planarity : 0.006 0.078 2327 Dihedral : 8.602 89.608 1861 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.10 % Favored : 88.78 % Rotamer: Outliers : 0.88 % Allowed : 8.81 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.19 (0.19), residues: 1658 helix: 0.21 (0.17), residues: 820 sheet: -1.82 (0.62), residues: 60 loop : -3.43 (0.19), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 157 HIS 0.003 0.001 HIS P 111 PHE 0.023 0.001 PHE C 216 TYR 0.025 0.001 TYR P 199 ARG 0.005 0.001 ARG Q 82 Details of bonding type rmsd hydrogen bonds : bond 0.05075 ( 630) hydrogen bonds : angle 4.77822 ( 1815) metal coordination : bond 0.00892 ( 8) metal coordination : angle 7.23576 ( 6) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.44474 ( 4) covalent geometry : bond 0.00346 (13509) covalent geometry : angle 0.75406 (18520) Misc. bond : bond 0.14830 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 1.959 Fit side-chains revert: symmetry clash REVERT: E 115 LEU cc_start: 0.6738 (pp) cc_final: 0.6449 (pt) REVERT: C 305 LEU cc_start: 0.9052 (tp) cc_final: 0.8830 (tt) REVERT: C 383 MET cc_start: 0.8351 (mmm) cc_final: 0.7826 (mmm) REVERT: D 80 ARG cc_start: 0.8611 (mtm110) cc_final: 0.8325 (mtm-85) REVERT: D 155 ASN cc_start: 0.8670 (t0) cc_final: 0.8438 (t0) REVERT: D 248 ARG cc_start: 0.8436 (ttm170) cc_final: 0.7292 (ttt-90) REVERT: P 305 LEU cc_start: 0.9066 (tp) cc_final: 0.8827 (tt) REVERT: P 383 MET cc_start: 0.8366 (mmm) cc_final: 0.7844 (mmm) REVERT: Q 74 LYS cc_start: 0.7677 (ttpt) cc_final: 0.7410 (tttt) REVERT: Q 247 LYS cc_start: 0.8352 (tttt) cc_final: 0.8098 (tttt) REVERT: Q 248 ARG cc_start: 0.8416 (ttm170) cc_final: 0.7260 (ttt180) REVERT: R 66 LYS cc_start: 0.8004 (tptm) cc_final: 0.7647 (tptp) REVERT: R 100 ASN cc_start: 0.7681 (p0) cc_final: 0.7158 (p0) REVERT: R 115 LEU cc_start: 0.7339 (pp) cc_final: 0.6854 (pt) outliers start: 11 outliers final: 9 residues processed: 187 average time/residue: 0.3697 time to fit residues: 100.0471 Evaluate side-chains 167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 ASN P 99 ASN P 272 ASN Q 155 ASN Q 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128483 restraints weight = 15772.973| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.95 r_work: 0.2905 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.308 13529 Z= 0.171 Angle : 0.745 15.707 18530 Z= 0.335 Chirality : 0.045 0.190 1970 Planarity : 0.006 0.067 2327 Dihedral : 8.252 81.898 1858 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.52 % Favored : 88.42 % Rotamer: Outliers : 1.76 % Allowed : 11.53 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.48 (0.20), residues: 1658 helix: 0.79 (0.18), residues: 826 sheet: -1.18 (0.78), residues: 44 loop : -3.10 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 126 HIS 0.006 0.001 HIS P 212 PHE 0.019 0.001 PHE C 113 TYR 0.012 0.001 TYR P 199 ARG 0.004 0.001 ARG Q 82 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 630) hydrogen bonds : angle 4.62342 ( 1815) metal coordination : bond 0.00830 ( 8) metal coordination : angle 7.10421 ( 6) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.33324 ( 4) covalent geometry : bond 0.00392 (13509) covalent geometry : angle 0.73372 (18520) Misc. bond : bond 0.14718 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 1.298 Fit side-chains REVERT: E 100 ASN cc_start: 0.7381 (p0) cc_final: 0.6972 (p0) REVERT: E 129 MET cc_start: 0.7117 (ptp) cc_final: 0.6842 (mtm) REVERT: C 162 ILE cc_start: 0.9131 (mt) cc_final: 0.8900 (mm) REVERT: C 252 ASP cc_start: 0.8422 (m-30) cc_final: 0.8204 (m-30) REVERT: D 80 ARG cc_start: 0.8691 (mtm110) cc_final: 0.8190 (mtm-85) REVERT: D 205 MET cc_start: 0.9147 (mtm) cc_final: 0.8894 (mtm) REVERT: D 218 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8801 (tp30) REVERT: D 248 ARG cc_start: 0.8625 (ttm170) cc_final: 0.7414 (ttt-90) REVERT: P 162 ILE cc_start: 0.9100 (mt) cc_final: 0.8884 (mm) REVERT: P 252 ASP cc_start: 0.8395 (m-30) cc_final: 0.8175 (m-30) REVERT: Q 74 LYS cc_start: 0.7701 (ttpt) cc_final: 0.7435 (tttt) REVERT: Q 79 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7334 (mm-30) REVERT: Q 143 GLU cc_start: 0.7195 (pp20) cc_final: 0.6974 (pp20) REVERT: Q 155 ASN cc_start: 0.9117 (t0) cc_final: 0.8904 (t0) REVERT: Q 174 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7846 (ptmm) REVERT: Q 205 MET cc_start: 0.9158 (mtm) cc_final: 0.8897 (mtm) REVERT: Q 218 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8782 (tp30) REVERT: Q 248 ARG cc_start: 0.8595 (ttm170) cc_final: 0.7434 (ttt180) REVERT: R 66 LYS cc_start: 0.7991 (tptm) cc_final: 0.7571 (tptp) REVERT: R 100 ASN cc_start: 0.7439 (p0) cc_final: 0.6973 (p0) REVERT: R 129 MET cc_start: 0.7139 (ptp) cc_final: 0.6836 (mtm) outliers start: 22 outliers final: 20 residues processed: 197 average time/residue: 0.2556 time to fit residues: 72.8693 Evaluate side-chains 178 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 234 MET Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 96 optimal weight: 0.7980 chunk 125 optimal weight: 0.0770 chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.0030 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN D 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.165998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128622 restraints weight = 15611.238| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.75 r_work: 0.2951 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 13529 Z= 0.132 Angle : 0.666 12.730 18530 Z= 0.310 Chirality : 0.043 0.184 1970 Planarity : 0.005 0.062 2327 Dihedral : 8.189 86.531 1858 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.07 % Favored : 89.87 % Rotamer: Outliers : 2.24 % Allowed : 12.65 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.05 (0.21), residues: 1658 helix: 1.20 (0.18), residues: 824 sheet: -0.96 (0.70), residues: 60 loop : -2.99 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 157 HIS 0.005 0.001 HIS P 212 PHE 0.014 0.001 PHE C 113 TYR 0.010 0.001 TYR D 134 ARG 0.003 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 630) hydrogen bonds : angle 4.40926 ( 1815) metal coordination : bond 0.00662 ( 8) metal coordination : angle 6.43188 ( 6) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.33833 ( 4) covalent geometry : bond 0.00300 (13509) covalent geometry : angle 0.65556 (18520) Misc. bond : bond 0.10236 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: E 100 ASN cc_start: 0.7415 (p0) cc_final: 0.6767 (p0) REVERT: C 18 TRP cc_start: 0.6107 (t-100) cc_final: 0.5603 (t-100) REVERT: C 252 ASP cc_start: 0.8407 (m-30) cc_final: 0.8145 (m-30) REVERT: D 205 MET cc_start: 0.9175 (mtm) cc_final: 0.8956 (mtm) REVERT: D 248 ARG cc_start: 0.8623 (ttm170) cc_final: 0.7287 (ttt-90) REVERT: P 252 ASP cc_start: 0.8373 (m-30) cc_final: 0.8103 (m-30) REVERT: Q 79 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7196 (mm-30) REVERT: Q 155 ASN cc_start: 0.9038 (t0) cc_final: 0.8808 (t0) REVERT: Q 174 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (ptmm) REVERT: Q 205 MET cc_start: 0.9184 (mtm) cc_final: 0.8969 (mtm) REVERT: Q 218 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8747 (tp30) REVERT: Q 248 ARG cc_start: 0.8637 (ttm170) cc_final: 0.7349 (ttt-90) REVERT: R 66 LYS cc_start: 0.7976 (tptm) cc_final: 0.7513 (tptp) REVERT: R 100 ASN cc_start: 0.7358 (p0) cc_final: 0.6874 (p0) outliers start: 28 outliers final: 17 residues processed: 187 average time/residue: 0.2392 time to fit residues: 65.8488 Evaluate side-chains 162 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 174 LYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 34 optimal weight: 0.0060 chunk 141 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 ASN D 159 GLN Q 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122285 restraints weight = 15719.735| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.88 r_work: 0.2930 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.252 13529 Z= 0.133 Angle : 0.668 13.259 18530 Z= 0.305 Chirality : 0.043 0.181 1970 Planarity : 0.005 0.059 2327 Dihedral : 8.120 89.018 1858 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.04 % Favored : 88.90 % Rotamer: Outliers : 2.08 % Allowed : 14.33 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.83 (0.21), residues: 1658 helix: 1.34 (0.18), residues: 822 sheet: -0.68 (0.72), residues: 60 loop : -2.84 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 400 HIS 0.005 0.001 HIS C 212 PHE 0.014 0.001 PHE C 113 TYR 0.011 0.001 TYR C 399 ARG 0.005 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 630) hydrogen bonds : angle 4.35688 ( 1815) metal coordination : bond 0.00595 ( 8) metal coordination : angle 6.23489 ( 6) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.32180 ( 4) covalent geometry : bond 0.00307 (13509) covalent geometry : angle 0.65897 (18520) Misc. bond : bond 0.12623 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 2.817 Fit side-chains REVERT: E 50 ILE cc_start: 0.3014 (OUTLIER) cc_final: 0.2491 (tt) REVERT: E 100 ASN cc_start: 0.7262 (p0) cc_final: 0.6521 (p0) REVERT: E 129 MET cc_start: 0.7256 (ptp) cc_final: 0.7056 (ptp) REVERT: C 18 TRP cc_start: 0.6332 (t-100) cc_final: 0.5892 (t-100) REVERT: C 252 ASP cc_start: 0.8425 (m-30) cc_final: 0.8150 (m-30) REVERT: D 205 MET cc_start: 0.9196 (mtm) cc_final: 0.8964 (mtm) REVERT: D 248 ARG cc_start: 0.8713 (ttm170) cc_final: 0.7373 (ttt-90) REVERT: P 252 ASP cc_start: 0.8389 (m-30) cc_final: 0.8090 (m-30) REVERT: Q 155 ASN cc_start: 0.9058 (t0) cc_final: 0.8814 (t0) REVERT: Q 174 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7946 (ptmm) REVERT: Q 191 GLN cc_start: 0.9033 (tt0) cc_final: 0.8699 (tt0) REVERT: Q 205 MET cc_start: 0.9209 (mtm) cc_final: 0.8853 (mtm) REVERT: Q 248 ARG cc_start: 0.8712 (ttm170) cc_final: 0.7382 (ttt-90) REVERT: R 50 ILE cc_start: 0.2593 (OUTLIER) cc_final: 0.2128 (tt) REVERT: R 66 LYS cc_start: 0.8067 (tptm) cc_final: 0.7621 (tptp) REVERT: R 100 ASN cc_start: 0.7294 (p0) cc_final: 0.6568 (p0) REVERT: R 115 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6083 (pt) outliers start: 26 outliers final: 15 residues processed: 172 average time/residue: 0.3837 time to fit residues: 98.3471 Evaluate side-chains 167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 174 LYS Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 chunk 119 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.158773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123971 restraints weight = 15848.670| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.87 r_work: 0.2936 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 13529 Z= 0.129 Angle : 0.645 13.131 18530 Z= 0.299 Chirality : 0.043 0.181 1970 Planarity : 0.005 0.059 2327 Dihedral : 8.031 86.536 1858 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.07 % Favored : 89.81 % Rotamer: Outliers : 2.32 % Allowed : 14.65 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.56 (0.21), residues: 1658 helix: 1.43 (0.18), residues: 828 sheet: -0.33 (0.75), residues: 60 loop : -2.58 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 400 HIS 0.005 0.001 HIS P 212 PHE 0.013 0.001 PHE C 113 TYR 0.011 0.001 TYR C 399 ARG 0.005 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 630) hydrogen bonds : angle 4.32629 ( 1815) metal coordination : bond 0.00556 ( 8) metal coordination : angle 5.81578 ( 6) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.39636 ( 4) covalent geometry : bond 0.00303 (13509) covalent geometry : angle 0.63646 (18520) Misc. bond : bond 0.08784 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 50 ILE cc_start: 0.3187 (OUTLIER) cc_final: 0.2648 (tt) REVERT: E 100 ASN cc_start: 0.7332 (p0) cc_final: 0.6545 (p0) REVERT: E 129 MET cc_start: 0.7380 (ptp) cc_final: 0.6985 (ptp) REVERT: E 175 LEU cc_start: 0.7263 (mt) cc_final: 0.7046 (mt) REVERT: C 154 MET cc_start: 0.8968 (tpp) cc_final: 0.8670 (mpp) REVERT: C 252 ASP cc_start: 0.8350 (m-30) cc_final: 0.8066 (m-30) REVERT: D 132 TYR cc_start: 0.9032 (t80) cc_final: 0.8500 (t80) REVERT: D 248 ARG cc_start: 0.8758 (ttm170) cc_final: 0.7513 (ttt-90) REVERT: P 18 TRP cc_start: 0.6843 (t-100) cc_final: 0.6612 (t-100) REVERT: P 154 MET cc_start: 0.8967 (tpp) cc_final: 0.8648 (mpp) REVERT: P 252 ASP cc_start: 0.8357 (m-30) cc_final: 0.8079 (m-30) REVERT: Q 73 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.5767 (t70) REVERT: Q 155 ASN cc_start: 0.8997 (t0) cc_final: 0.8769 (t0) REVERT: Q 191 GLN cc_start: 0.8966 (tt0) cc_final: 0.8602 (tt0) REVERT: Q 205 MET cc_start: 0.9191 (mtm) cc_final: 0.8840 (mtm) REVERT: Q 248 ARG cc_start: 0.8761 (ttm170) cc_final: 0.7533 (ttt-90) REVERT: R 50 ILE cc_start: 0.2912 (OUTLIER) cc_final: 0.2393 (tt) REVERT: R 66 LYS cc_start: 0.8131 (tptm) cc_final: 0.7704 (tptp) REVERT: R 100 ASN cc_start: 0.7424 (p0) cc_final: 0.6988 (p0) REVERT: R 115 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6213 (pt) outliers start: 29 outliers final: 20 residues processed: 187 average time/residue: 0.4659 time to fit residues: 131.5465 Evaluate side-chains 180 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 73 ASP Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 137 optimal weight: 0.0170 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN C 222 ASN P 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.151740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.112224 restraints weight = 15867.633| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.94 r_work: 0.2885 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.289 13529 Z= 0.161 Angle : 0.704 15.558 18530 Z= 0.314 Chirality : 0.044 0.185 1970 Planarity : 0.005 0.059 2327 Dihedral : 8.020 81.865 1858 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.92 % Favored : 88.96 % Rotamer: Outliers : 2.80 % Allowed : 14.73 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.58 (0.21), residues: 1658 helix: 1.39 (0.18), residues: 822 sheet: -0.19 (0.75), residues: 60 loop : -2.53 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 18 HIS 0.005 0.001 HIS P 212 PHE 0.015 0.001 PHE C 113 TYR 0.013 0.001 TYR P 399 ARG 0.008 0.000 ARG R 68 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 630) hydrogen bonds : angle 4.43832 ( 1815) metal coordination : bond 0.00857 ( 8) metal coordination : angle 6.14702 ( 6) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.33091 ( 4) covalent geometry : bond 0.00384 (13509) covalent geometry : angle 0.69536 (18520) Misc. bond : bond 0.14436 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.0954 (OUTLIER) cc_final: 0.0411 (tpm170) REVERT: E 45 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7883 (mtmt) REVERT: E 50 ILE cc_start: 0.2898 (OUTLIER) cc_final: 0.2403 (tt) REVERT: E 100 ASN cc_start: 0.7334 (p0) cc_final: 0.6496 (p0) REVERT: E 129 MET cc_start: 0.7291 (ptp) cc_final: 0.6894 (ptp) REVERT: C 252 ASP cc_start: 0.8401 (m-30) cc_final: 0.8110 (m-30) REVERT: C 351 THR cc_start: 0.8539 (p) cc_final: 0.8185 (p) REVERT: D 183 MET cc_start: 0.9101 (ttt) cc_final: 0.8146 (ttt) REVERT: D 205 MET cc_start: 0.9199 (mtm) cc_final: 0.8870 (mtm) REVERT: D 248 ARG cc_start: 0.8675 (ttm170) cc_final: 0.7317 (ttt-90) REVERT: P 18 TRP cc_start: 0.6673 (t-100) cc_final: 0.6467 (t-100) REVERT: P 252 ASP cc_start: 0.8369 (m-30) cc_final: 0.8077 (m-30) REVERT: P 351 THR cc_start: 0.8599 (p) cc_final: 0.8255 (p) REVERT: Q 191 GLN cc_start: 0.9113 (tt0) cc_final: 0.8738 (tt0) REVERT: Q 205 MET cc_start: 0.9199 (mtm) cc_final: 0.8878 (mtm) REVERT: R 66 LYS cc_start: 0.8086 (tptm) cc_final: 0.7588 (tptp) REVERT: R 100 ASN cc_start: 0.7297 (p0) cc_final: 0.6823 (p0) REVERT: R 115 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6351 (pt) REVERT: R 175 LEU cc_start: 0.7326 (mt) cc_final: 0.7114 (mt) outliers start: 35 outliers final: 26 residues processed: 187 average time/residue: 0.2678 time to fit residues: 71.6524 Evaluate side-chains 183 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 223 ASN Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 306 ARG Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain Q residue 237 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 4 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.157207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120578 restraints weight = 15840.532| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.98 r_work: 0.2898 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 13529 Z= 0.135 Angle : 0.664 13.839 18530 Z= 0.303 Chirality : 0.043 0.183 1970 Planarity : 0.005 0.080 2327 Dihedral : 7.993 79.991 1858 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.98 % Favored : 88.96 % Rotamer: Outliers : 2.80 % Allowed : 15.05 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.47 (0.21), residues: 1658 helix: 1.47 (0.18), residues: 826 sheet: -0.10 (0.75), residues: 60 loop : -2.49 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 18 HIS 0.005 0.001 HIS P 212 PHE 0.013 0.001 PHE C 113 TYR 0.013 0.001 TYR Q 134 ARG 0.011 0.000 ARG R 68 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 630) hydrogen bonds : angle 4.35020 ( 1815) metal coordination : bond 0.00676 ( 8) metal coordination : angle 5.97251 ( 6) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.32227 ( 4) covalent geometry : bond 0.00313 (13509) covalent geometry : angle 0.65551 (18520) Misc. bond : bond 0.11991 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.0737 (OUTLIER) cc_final: 0.0314 (tpm170) REVERT: E 50 ILE cc_start: 0.2899 (OUTLIER) cc_final: 0.2405 (tt) REVERT: E 100 ASN cc_start: 0.7360 (p0) cc_final: 0.6512 (p0) REVERT: E 129 MET cc_start: 0.7439 (ptp) cc_final: 0.7043 (ptp) REVERT: E 175 LEU cc_start: 0.6888 (mt) cc_final: 0.6663 (mt) REVERT: C 252 ASP cc_start: 0.8433 (m-30) cc_final: 0.8153 (m-30) REVERT: C 351 THR cc_start: 0.8564 (p) cc_final: 0.8214 (p) REVERT: D 183 MET cc_start: 0.8932 (ttt) cc_final: 0.8158 (ttt) REVERT: D 205 MET cc_start: 0.9198 (mtm) cc_final: 0.8864 (mtm) REVERT: D 248 ARG cc_start: 0.8682 (ttm170) cc_final: 0.7360 (ttt-90) REVERT: P 252 ASP cc_start: 0.8414 (m-30) cc_final: 0.8132 (m-30) REVERT: P 351 THR cc_start: 0.8566 (p) cc_final: 0.8253 (p) REVERT: Q 191 GLN cc_start: 0.9122 (tt0) cc_final: 0.8721 (tt0) REVERT: Q 205 MET cc_start: 0.9212 (mtm) cc_final: 0.8899 (mtm) REVERT: R 66 LYS cc_start: 0.8132 (tptm) cc_final: 0.7696 (tptp) REVERT: R 100 ASN cc_start: 0.7535 (p0) cc_final: 0.6717 (p0) REVERT: R 115 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6661 (pt) outliers start: 35 outliers final: 26 residues processed: 184 average time/residue: 0.2512 time to fit residues: 67.2224 Evaluate side-chains 184 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 306 ARG Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 49 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.156140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120337 restraints weight = 15771.714| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.93 r_work: 0.2892 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.256 13529 Z= 0.148 Angle : 0.696 16.545 18530 Z= 0.312 Chirality : 0.043 0.183 1970 Planarity : 0.005 0.058 2327 Dihedral : 7.949 77.638 1858 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.86 % Favored : 89.08 % Rotamer: Outliers : 2.64 % Allowed : 15.29 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.47 (0.21), residues: 1658 helix: 1.45 (0.18), residues: 826 sheet: -0.02 (0.75), residues: 60 loop : -2.47 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 18 HIS 0.005 0.001 HIS P 212 PHE 0.014 0.001 PHE C 113 TYR 0.013 0.001 TYR C 399 ARG 0.013 0.000 ARG R 68 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 630) hydrogen bonds : angle 4.37523 ( 1815) metal coordination : bond 0.00732 ( 8) metal coordination : angle 5.95668 ( 6) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.35700 ( 4) covalent geometry : bond 0.00350 (13509) covalent geometry : angle 0.68776 (18520) Misc. bond : bond 0.13045 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.0824 (OUTLIER) cc_final: 0.0558 (tpm170) REVERT: E 50 ILE cc_start: 0.3191 (OUTLIER) cc_final: 0.2701 (tt) REVERT: E 100 ASN cc_start: 0.7381 (p0) cc_final: 0.6527 (p0) REVERT: C 351 THR cc_start: 0.8568 (p) cc_final: 0.8260 (p) REVERT: D 183 MET cc_start: 0.8944 (ttt) cc_final: 0.8177 (ttt) REVERT: D 205 MET cc_start: 0.9105 (mtm) cc_final: 0.8793 (mtm) REVERT: D 248 ARG cc_start: 0.8652 (ttm170) cc_final: 0.7402 (ttt-90) REVERT: P 351 THR cc_start: 0.8645 (p) cc_final: 0.8352 (p) REVERT: Q 191 GLN cc_start: 0.9035 (tt0) cc_final: 0.8631 (tt0) REVERT: Q 205 MET cc_start: 0.9115 (mtm) cc_final: 0.8814 (mtm) REVERT: R 45 LYS cc_start: 0.8225 (mttt) cc_final: 0.8019 (mtmt) REVERT: R 50 ILE cc_start: 0.3030 (OUTLIER) cc_final: 0.2612 (tt) REVERT: R 66 LYS cc_start: 0.8042 (tptm) cc_final: 0.7654 (tptp) REVERT: R 100 ASN cc_start: 0.7497 (p0) cc_final: 0.6647 (p0) REVERT: R 115 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6705 (pt) outliers start: 33 outliers final: 27 residues processed: 183 average time/residue: 0.2494 time to fit residues: 66.5129 Evaluate side-chains 186 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 234 MET Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 105 optimal weight: 0.0370 chunk 149 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.160166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123930 restraints weight = 15677.129| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.86 r_work: 0.2949 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 13529 Z= 0.115 Angle : 0.623 10.639 18530 Z= 0.291 Chirality : 0.042 0.176 1970 Planarity : 0.005 0.057 2327 Dihedral : 7.879 78.447 1858 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.01 % Favored : 89.93 % Rotamer: Outliers : 1.92 % Allowed : 16.33 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.25 (0.21), residues: 1658 helix: 1.64 (0.18), residues: 826 sheet: 0.11 (0.74), residues: 60 loop : -2.37 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 18 HIS 0.004 0.001 HIS P 212 PHE 0.013 0.001 PHE C 216 TYR 0.010 0.001 TYR C 399 ARG 0.006 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 630) hydrogen bonds : angle 4.19511 ( 1815) metal coordination : bond 0.00523 ( 8) metal coordination : angle 5.24173 ( 6) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.27332 ( 4) covalent geometry : bond 0.00254 (13509) covalent geometry : angle 0.61592 (18520) Misc. bond : bond 0.09844 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3316 Ramachandran restraints generated. 1658 Oldfield, 0 Emsley, 1658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: E 12 ARG cc_start: 0.0530 (OUTLIER) cc_final: -0.0045 (tpp-160) REVERT: E 50 ILE cc_start: 0.3191 (OUTLIER) cc_final: 0.2649 (tt) REVERT: E 100 ASN cc_start: 0.7301 (p0) cc_final: 0.6447 (p0) REVERT: C 252 ASP cc_start: 0.8358 (m-30) cc_final: 0.8055 (m-30) REVERT: C 351 THR cc_start: 0.8577 (p) cc_final: 0.8304 (p) REVERT: D 205 MET cc_start: 0.9163 (mtm) cc_final: 0.8817 (mtm) REVERT: D 248 ARG cc_start: 0.8677 (ttm170) cc_final: 0.7482 (tmm160) REVERT: P 252 ASP cc_start: 0.8368 (m-30) cc_final: 0.8067 (m-30) REVERT: P 351 THR cc_start: 0.8550 (p) cc_final: 0.8279 (p) REVERT: P 406 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7995 (m) REVERT: Q 191 GLN cc_start: 0.9061 (tt0) cc_final: 0.8480 (tt0) REVERT: Q 205 MET cc_start: 0.9182 (mtm) cc_final: 0.8845 (mtm) REVERT: R 66 LYS cc_start: 0.8021 (tptm) cc_final: 0.7714 (tptp) REVERT: R 100 ASN cc_start: 0.7297 (p0) cc_final: 0.6811 (p0) REVERT: R 115 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6692 (pt) REVERT: R 188 ILE cc_start: 0.4590 (pt) cc_final: 0.4167 (mm) outliers start: 24 outliers final: 17 residues processed: 180 average time/residue: 0.2596 time to fit residues: 67.9792 Evaluate side-chains 173 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ARG Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 306 ARG Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 227 VAL Chi-restraints excluded: chain P residue 270 MET Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain P residue 306 ARG Chi-restraints excluded: chain P residue 406 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 41 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 156 optimal weight: 0.0270 chunk 115 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.157932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121115 restraints weight = 15878.053| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.98 r_work: 0.2926 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.222 13529 Z= 0.130 Angle : 0.652 13.635 18530 Z= 0.299 Chirality : 0.043 0.178 1970 Planarity : 0.005 0.056 2327 Dihedral : 7.818 77.538 1858 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.74 % Favored : 89.20 % Rotamer: Outliers : 1.92 % Allowed : 16.57 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.27 (0.21), residues: 1658 helix: 1.59 (0.18), residues: 828 sheet: 0.05 (0.73), residues: 60 loop : -2.34 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 18 HIS 0.004 0.001 HIS C 212 PHE 0.013 0.001 PHE P 113 TYR 0.011 0.001 TYR P 399 ARG 0.007 0.000 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 630) hydrogen bonds : angle 4.24579 ( 1815) metal coordination : bond 0.00495 ( 8) metal coordination : angle 5.25334 ( 6) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.36369 ( 4) covalent geometry : bond 0.00306 (13509) covalent geometry : angle 0.64513 (18520) Misc. bond : bond 0.11121 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7543.17 seconds wall clock time: 135 minutes 34.92 seconds (8134.92 seconds total)