Starting phenix.real_space_refine on Fri Sep 11 17:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xeu_22150/09_2026/6xeu_22150.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians K 8 8.98 5 P 12 5.49 5 S 56 5.16 5 Na 4 4.78 5 C 6792 2.51 5 N 1716 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10544 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "J" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2602 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 39 Unusual residues: {' K': 7, ' NA': 1, 'PIO': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' NA': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.86, per 1000 atoms: 0.27 Number of scatterers: 10544 At special positions: 0 Unit cell: (89.25, 89.25, 131.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 8 19.00 S 56 16.00 P 12 15.00 Na 4 11.00 O 1956 8.00 N 1716 7.00 C 6792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 166 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 166 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 513.8 milliseconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 20 sheets defined 35.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.727A pdb=" N ASP A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.705A pdb=" N THR A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 121 removed outlier: 3.816A pdb=" N LEU A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.812A pdb=" N SER A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 196 removed outlier: 3.619A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 removed outlier: 4.017A pdb=" N LYS A 200 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 202 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.727A pdb=" N ASP D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.705A pdb=" N THR D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 121 removed outlier: 3.816A pdb=" N LEU D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 109 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 153 removed outlier: 3.812A pdb=" N SER D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 149 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 196 removed outlier: 3.619A pdb=" N ILE D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 4.017A pdb=" N LYS D 200 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA D 202 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 368 through 380 Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.727A pdb=" N ASP G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 89 removed outlier: 3.705A pdb=" N THR G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 121 removed outlier: 3.816A pdb=" N LEU G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE G 109 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 153 removed outlier: 3.812A pdb=" N SER G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE G 149 " --> pdb=" O PHE G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 196 removed outlier: 3.619A pdb=" N ILE G 175 " --> pdb=" O ILE G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 203 removed outlier: 4.017A pdb=" N LYS G 200 " --> pdb=" O GLN G 197 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 368 through 380 Processing helix chain 'J' and resid 76 through 81 removed outlier: 3.728A pdb=" N ASP J 81 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 89 removed outlier: 3.705A pdb=" N THR J 85 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 121 removed outlier: 3.816A pdb=" N LEU J 96 " --> pdb=" O ARG J 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE J 109 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 153 removed outlier: 3.812A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE J 149 " --> pdb=" O PHE J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 196 removed outlier: 3.619A pdb=" N ILE J 175 " --> pdb=" O ILE J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 203 removed outlier: 4.017A pdb=" N LYS J 200 " --> pdb=" O GLN J 197 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA J 202 " --> pdb=" O LYS J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 302 Processing helix chain 'J' and resid 368 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 206 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 206 removed outlier: 6.893A pdb=" N ALA A 211 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 254 through 262 removed outlier: 4.855A pdb=" N LYS A 247 " --> pdb=" O PRO A 256 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 262 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA A 241 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU A 236 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET A 313 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.818A pdb=" N TYR A 349 " --> pdb=" O HIS J 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AA8, first strand: chain 'D' and resid 205 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 205 through 206 removed outlier: 6.893A pdb=" N ALA D 211 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 254 through 262 removed outlier: 4.855A pdb=" N LYS D 247 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 262 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA D 241 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU D 236 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET D 313 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 336 through 338 Processing sheet with id=AB3, first strand: chain 'G' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'G' and resid 205 through 206 Processing sheet with id=AB5, first strand: chain 'G' and resid 205 through 206 removed outlier: 6.893A pdb=" N ALA G 211 " --> pdb=" O LEU G 333 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 262 removed outlier: 4.855A pdb=" N LYS G 247 " --> pdb=" O PRO G 256 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 262 " --> pdb=" O ALA G 241 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA G 241 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU G 236 " --> pdb=" O MET G 313 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET G 313 " --> pdb=" O GLU G 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 336 through 338 Processing sheet with id=AB8, first strand: chain 'J' and resid 205 through 206 Processing sheet with id=AB9, first strand: chain 'J' and resid 205 through 206 removed outlier: 6.893A pdb=" N ALA J 211 " --> pdb=" O LEU J 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 254 through 262 removed outlier: 4.855A pdb=" N LYS J 247 " --> pdb=" O PRO J 256 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J 262 " --> pdb=" O ALA J 241 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA J 241 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU J 236 " --> pdb=" O MET J 313 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N MET J 313 " --> pdb=" O GLU J 236 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 336 through 338 463 hydrogen bonds defined for protein. 1293 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: 1.65 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3260 1.34 - 1.46: 2144 1.46 - 1.57: 5272 1.57 - 1.69: 16 1.69 - 1.81: 88 Bond restraints: 10780 Sorted by residual: bond pdb=" C1B PIO J 401 " pdb=" O3C PIO J 401 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1B PIO A 401 " pdb=" O3C PIO A 401 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1B PIO G 401 " pdb=" O3C PIO G 401 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1B PIO D 401 " pdb=" O3C PIO D 401 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1A PIO J 401 " pdb=" O2C PIO J 401 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 10775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 14252 2.36 - 4.73: 308 4.73 - 7.09: 96 7.09 - 9.45: 8 9.45 - 11.82: 8 Bond angle restraints: 14672 Sorted by residual: angle pdb=" N ASN G 354 " pdb=" CA ASN G 354 " pdb=" C ASN G 354 " ideal model delta sigma weight residual 114.04 108.25 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" N ASN D 354 " pdb=" CA ASN D 354 " pdb=" C ASN D 354 " ideal model delta sigma weight residual 114.04 108.25 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" N ASN A 354 " pdb=" CA ASN A 354 " pdb=" C ASN A 354 " ideal model delta sigma weight residual 114.04 108.25 5.79 1.24e+00 6.50e-01 2.18e+01 angle pdb=" N ASN J 354 " pdb=" CA ASN J 354 " pdb=" C ASN J 354 " ideal model delta sigma weight residual 114.04 108.26 5.78 1.24e+00 6.50e-01 2.17e+01 angle pdb=" N ASN A 263 " pdb=" CA ASN A 263 " pdb=" C ASN A 263 " ideal model delta sigma weight residual 109.76 116.88 -7.12 1.59e+00 3.96e-01 2.00e+01 ... (remaining 14667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5564 17.72 - 35.44: 548 35.44 - 53.17: 132 53.17 - 70.89: 32 70.89 - 88.61: 8 Dihedral angle restraints: 6284 sinusoidal: 2448 harmonic: 3836 Sorted by residual: dihedral pdb=" C ILE D 126 " pdb=" N ILE D 126 " pdb=" CA ILE D 126 " pdb=" CB ILE D 126 " ideal model delta harmonic sigma weight residual -122.00 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C ILE G 126 " pdb=" N ILE G 126 " pdb=" CA ILE G 126 " pdb=" CB ILE G 126 " ideal model delta harmonic sigma weight residual -122.00 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C ILE J 126 " pdb=" N ILE J 126 " pdb=" CA ILE J 126 " pdb=" CB ILE J 126 " ideal model delta harmonic sigma weight residual -122.00 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 6281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1475 0.072 - 0.144: 197 0.144 - 0.217: 20 0.217 - 0.289: 4 0.289 - 0.361: 4 Chirality restraints: 1700 Sorted by residual: chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ILE J 126 " pdb=" N ILE J 126 " pdb=" C ILE J 126 " pdb=" CB ILE J 126 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ILE G 126 " pdb=" N ILE G 126 " pdb=" C ILE G 126 " pdb=" CB ILE G 126 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 1697 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 128 " -0.062 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO A 129 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 128 " 0.062 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO D 129 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 129 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 129 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 128 " 0.062 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO G 129 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO G 129 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO G 129 " 0.051 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.94: 5099 2.94 - 3.49: 10464 3.49 - 4.04: 16308 4.04 - 4.59: 23351 4.59 - 5.14: 36328 Nonbonded interactions: 91550 Sorted by model distance: nonbonded pdb=" N ASP D 62 " pdb=" OD1 ASP D 62 " model vdw 2.387 3.120 nonbonded pdb=" N ASP J 62 " pdb=" OD1 ASP J 62 " model vdw 2.387 3.120 nonbonded pdb=" N ASP G 62 " pdb=" OD1 ASP G 62 " model vdw 2.387 3.120 nonbonded pdb=" N ASP A 62 " pdb=" OD1 ASP A 62 " model vdw 2.387 3.120 nonbonded pdb=" O THR G 154 " pdb=" K K A 404 " model vdw 2.426 2.850 ... (remaining 91545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 401) selection = (chain 'D' and resid 55 through 401) selection = (chain 'G' and resid 55 through 401) selection = (chain 'J' and resid 55 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.110 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 : 0.009 0.067 10784 Z= 0.373 Angle : 0.940 11.818 14680 Z= 0.513 Chirality : 0.056 0.361 1700 Planarity : 0.006 0.096 1796 Dihedral : 15.433 88.609 3800 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 2.83 % Allowed : 10.16 % Favored : 87.01 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.22), residues: 1304 helix: -0.38 (0.24), residues: 424 sheet: -0.75 (0.31), residues: 288 loop : -3.82 (0.21), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 225 TYR 0.010 0.001 TYR J 360 PHE 0.014 0.002 PHE J 224 TRP 0.005 0.001 TRP A 113 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00853 / 0.37 (10780) covalent geometry : angle 0.94045 / 0.51 (14672) SS BOND : bond 0.00532 / 0.25 ( 4) SS BOND : angle 0.70841 / 0.35 ( 8) hydrogen bonds : bond 0.18273 / 11.88 ( 455) hydrogen bonds : angle 6.50574 / 4.54 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.447 Fit side-chains REVERT: A 88 ASP cc_start: 0.8695 (t0) cc_final: 0.8465 (t0) REVERT: A 298 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8686 (tm-30) REVERT: D 88 ASP cc_start: 0.8699 (t0) cc_final: 0.8466 (t0) REVERT: D 298 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8687 (tm-30) REVERT: G 88 ASP cc_start: 0.8696 (t0) cc_final: 0.8462 (t0) REVERT: G 298 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8687 (tm-30) REVERT: J 88 ASP cc_start: 0.8696 (t0) cc_final: 0.8466 (t0) REVERT: J 298 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8686 (tm-30) outliers start: 32 outliers final: 8 residues processed: 110 average time/residue: 0.1442 time to fit residues: 21.1312 Evaluate side-chains 72 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 199 LYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 199 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN G 322 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.074072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.055545 restraints weight = 24171.171| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.41 r_work: 0.2519 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10784 Z= 0.139 Angle : 0.535 4.603 14680 Z= 0.294 Chirality : 0.044 0.142 1700 Planarity : 0.004 0.044 1796 Dihedral : 6.770 54.086 1468 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.06 % Allowed : 16.25 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.23), residues: 1304 helix: 0.75 (0.25), residues: 440 sheet: -0.21 (0.31), residues: 288 loop : -3.23 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 378 TYR 0.008 0.001 TYR J 360 PHE 0.009 0.001 PHE J 186 TRP 0.007 0.001 TRP G 113 HIS 0.002 0.001 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (10780) covalent geometry : angle 0.53520 / 0.29 (14672) SS BOND : bond 0.00321 / 0.15 ( 4) SS BOND : angle 0.75990 / 0.34 ( 8) hydrogen bonds : bond 0.05981 / 3.95 ( 455) hydrogen bonds : angle 4.49152 / 3.11 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.460 Fit side-chains REVERT: A 88 ASP cc_start: 0.8823 (t0) cc_final: 0.8618 (t0) REVERT: A 288 GLN cc_start: 0.9565 (mp10) cc_final: 0.9189 (mp10) REVERT: A 298 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8108 (tm-30) REVERT: D 88 ASP cc_start: 0.8825 (t0) cc_final: 0.8618 (t0) REVERT: D 288 GLN cc_start: 0.9566 (mp10) cc_final: 0.9190 (mp10) REVERT: D 298 GLN cc_start: 0.8850 (tp-100) cc_final: 0.8100 (tm-30) REVERT: G 88 ASP cc_start: 0.8821 (t0) cc_final: 0.8617 (t0) REVERT: G 288 GLN cc_start: 0.9566 (mp10) cc_final: 0.9188 (mp10) REVERT: G 298 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8108 (tm-30) REVERT: J 88 ASP cc_start: 0.8825 (t0) cc_final: 0.8620 (t0) REVERT: J 288 GLN cc_start: 0.9563 (mp10) cc_final: 0.9187 (mp10) REVERT: J 298 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8105 (tm-30) outliers start: 12 outliers final: 12 residues processed: 98 average time/residue: 0.1037 time to fit residues: 15.0059 Evaluate side-chains 88 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 273 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 110 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 0.0870 chunk 127 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.072341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.054272 restraints weight = 24407.315| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.37 r_work: 0.2500 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 10784 Z= 0.226 Angle : 0.586 5.524 14680 Z= 0.317 Chirality : 0.044 0.146 1700 Planarity : 0.004 0.037 1796 Dihedral : 6.561 58.598 1452 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.77 % Allowed : 18.82 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1304 helix: 0.96 (0.25), residues: 440 sheet: -0.04 (0.32), residues: 288 loop : -2.85 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 378 TYR 0.011 0.001 TYR J 360 PHE 0.011 0.001 PHE J 274 TRP 0.005 0.001 TRP G 113 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (10780) covalent geometry : angle 0.58591 / 0.32 (14672) SS BOND : bond 0.00329 / 0.16 ( 4) SS BOND : angle 0.85679 / 0.42 ( 8) hydrogen bonds : bond 0.07062 / 4.64 ( 455) hydrogen bonds : angle 4.51397 / 3.14 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.435 Fit side-chains REVERT: A 96 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8047 (mp) REVERT: A 111 MET cc_start: 0.8709 (tpp) cc_final: 0.8433 (tpt) REVERT: A 288 GLN cc_start: 0.9588 (mp10) cc_final: 0.9333 (mp10) REVERT: A 298 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8128 (tm-30) REVERT: D 96 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8052 (mp) REVERT: D 111 MET cc_start: 0.8709 (tpp) cc_final: 0.8432 (tpt) REVERT: D 288 GLN cc_start: 0.9585 (mp10) cc_final: 0.9330 (mp10) REVERT: D 298 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8127 (tm-30) REVERT: G 96 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8051 (mp) REVERT: G 111 MET cc_start: 0.8710 (tpp) cc_final: 0.8433 (tpt) REVERT: G 288 GLN cc_start: 0.9586 (mp10) cc_final: 0.9331 (mp10) REVERT: G 298 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8131 (tm-30) REVERT: J 96 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8048 (mp) REVERT: J 111 MET cc_start: 0.8714 (tpp) cc_final: 0.8437 (tpt) REVERT: J 288 GLN cc_start: 0.9586 (mp10) cc_final: 0.9327 (mp10) REVERT: J 298 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8133 (tm-30) outliers start: 20 outliers final: 4 residues processed: 100 average time/residue: 0.0910 time to fit residues: 13.8596 Evaluate side-chains 84 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 210 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 66 optimal weight: 0.0570 chunk 108 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 322 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.057354 restraints weight = 24240.839| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.37 r_work: 0.2542 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10784 Z= 0.115 Angle : 0.529 8.053 14680 Z= 0.277 Chirality : 0.043 0.158 1700 Planarity : 0.004 0.035 1796 Dihedral : 6.025 57.853 1452 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.12 % Allowed : 18.46 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.24), residues: 1304 helix: 1.57 (0.26), residues: 440 sheet: 0.20 (0.32), residues: 288 loop : -2.62 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 378 TYR 0.007 0.001 TYR J 360 PHE 0.024 0.001 PHE G 186 TRP 0.006 0.001 TRP G 113 HIS 0.002 0.001 HIS J 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10780) covalent geometry : angle 0.52934 / 0.28 (14672) SS BOND : bond 0.00206 / 0.10 ( 4) SS BOND : angle 0.69121 / 0.32 ( 8) hydrogen bonds : bond 0.05019 / 3.33 ( 455) hydrogen bonds : angle 4.23650 / 2.94 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.412 Fit side-chains REVERT: A 288 GLN cc_start: 0.9584 (mp10) cc_final: 0.9353 (mp10) REVERT: A 298 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8022 (tm-30) REVERT: A 378 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8269 (ttp80) REVERT: D 288 GLN cc_start: 0.9582 (mp10) cc_final: 0.9350 (mp10) REVERT: D 298 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8015 (tm-30) REVERT: D 378 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8266 (ttp80) REVERT: G 288 GLN cc_start: 0.9585 (mp10) cc_final: 0.9354 (mp10) REVERT: G 298 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8022 (tm-30) REVERT: G 378 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8265 (ttp80) REVERT: J 288 GLN cc_start: 0.9586 (mp10) cc_final: 0.9354 (mp10) REVERT: J 298 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8015 (tm-30) REVERT: J 378 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8271 (ttp80) outliers start: 24 outliers final: 12 residues processed: 100 average time/residue: 0.0911 time to fit residues: 13.9308 Evaluate side-chains 84 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.056446 restraints weight = 24190.896| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.36 r_work: 0.2528 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10784 Z= 0.139 Angle : 0.536 7.714 14680 Z= 0.281 Chirality : 0.043 0.138 1700 Planarity : 0.004 0.035 1796 Dihedral : 4.998 50.266 1444 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.77 % Allowed : 18.82 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1304 helix: 1.76 (0.26), residues: 440 sheet: 0.36 (0.32), residues: 288 loop : -2.45 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 378 TYR 0.009 0.001 TYR J 360 PHE 0.020 0.001 PHE A 186 TRP 0.005 0.001 TRP G 113 HIS 0.002 0.001 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10780) covalent geometry : angle 0.53561 / 0.28 (14672) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 0.80121 / 0.38 ( 8) hydrogen bonds : bond 0.05403 / 3.56 ( 455) hydrogen bonds : angle 4.17010 / 2.89 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.437 Fit side-chains REVERT: A 111 MET cc_start: 0.8654 (tpp) cc_final: 0.8347 (tpt) REVERT: A 288 GLN cc_start: 0.9590 (mp10) cc_final: 0.9370 (mp10) REVERT: A 298 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8012 (tm-30) REVERT: A 378 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8301 (ttp80) REVERT: D 111 MET cc_start: 0.8646 (tpp) cc_final: 0.8341 (tpt) REVERT: D 288 GLN cc_start: 0.9589 (mp10) cc_final: 0.9369 (mp10) REVERT: D 298 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8015 (tm-30) REVERT: D 378 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8299 (ttp80) REVERT: G 111 MET cc_start: 0.8646 (tpp) cc_final: 0.8339 (tpt) REVERT: G 288 GLN cc_start: 0.9591 (mp10) cc_final: 0.9371 (mp10) REVERT: G 298 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8016 (tm-30) REVERT: G 378 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8296 (ttp80) REVERT: J 111 MET cc_start: 0.8650 (tpp) cc_final: 0.8344 (tpt) REVERT: J 288 GLN cc_start: 0.9591 (mp10) cc_final: 0.9370 (mp10) REVERT: J 298 GLN cc_start: 0.8758 (tp-100) cc_final: 0.8009 (tm-30) REVERT: J 378 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8303 (ttp80) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.0953 time to fit residues: 13.8949 Evaluate side-chains 88 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.055234 restraints weight = 24370.315| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.36 r_work: 0.2520 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 10784 Z= 0.184 Angle : 0.553 5.314 14680 Z= 0.295 Chirality : 0.044 0.137 1700 Planarity : 0.004 0.036 1796 Dihedral : 5.094 47.802 1444 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.86 % Allowed : 19.79 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1304 helix: 1.77 (0.25), residues: 440 sheet: 0.30 (0.32), residues: 288 loop : -2.29 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 378 TYR 0.010 0.001 TYR J 360 PHE 0.023 0.001 PHE J 186 TRP 0.005 0.001 TRP J 113 HIS 0.003 0.001 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (10780) covalent geometry : angle 0.55265 / 0.30 (14672) SS BOND : bond 0.00271 / 0.13 ( 4) SS BOND : angle 0.72065 / 0.34 ( 8) hydrogen bonds : bond 0.06146 / 4.04 ( 455) hydrogen bonds : angle 4.24204 / 2.95 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.437 Fit side-chains REVERT: A 288 GLN cc_start: 0.9603 (mp10) cc_final: 0.9383 (mp10) REVERT: A 298 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8039 (tm-30) REVERT: D 288 GLN cc_start: 0.9602 (mp10) cc_final: 0.9382 (mp10) REVERT: D 298 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8041 (tm-30) REVERT: G 288 GLN cc_start: 0.9602 (mp10) cc_final: 0.9382 (mp10) REVERT: G 298 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8043 (tm-30) REVERT: J 288 GLN cc_start: 0.9602 (mp10) cc_final: 0.9381 (mp10) REVERT: J 298 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8049 (tm-30) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 0.0910 time to fit residues: 13.5092 Evaluate side-chains 85 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 86 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.057347 restraints weight = 24309.511| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.36 r_work: 0.2539 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10784 Z= 0.126 Angle : 0.528 8.508 14680 Z= 0.277 Chirality : 0.042 0.136 1700 Planarity : 0.004 0.035 1796 Dihedral : 4.801 45.303 1444 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.83 % Allowed : 19.17 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1304 helix: 1.99 (0.25), residues: 444 sheet: 0.47 (0.32), residues: 288 loop : -2.14 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 378 TYR 0.008 0.001 TYR J 360 PHE 0.022 0.001 PHE A 186 TRP 0.005 0.001 TRP D 113 HIS 0.002 0.001 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10780) covalent geometry : angle 0.52825 / 0.28 (14672) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 0.52422 / 0.25 ( 8) hydrogen bonds : bond 0.05089 / 3.36 ( 455) hydrogen bonds : angle 4.02762 / 2.79 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.492 Fit side-chains REVERT: A 288 GLN cc_start: 0.9607 (mp10) cc_final: 0.9401 (mp10) REVERT: A 298 GLN cc_start: 0.8749 (tp-100) cc_final: 0.7977 (tm-30) REVERT: A 378 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8371 (ttp80) REVERT: D 255 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8937 (mm) REVERT: D 288 GLN cc_start: 0.9605 (mp10) cc_final: 0.9400 (mp10) REVERT: D 298 GLN cc_start: 0.8750 (tp-100) cc_final: 0.7975 (tm-30) REVERT: D 378 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8371 (ttp80) REVERT: G 187 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8337 (mmt) REVERT: G 288 GLN cc_start: 0.9607 (mp10) cc_final: 0.9400 (mp10) REVERT: G 298 GLN cc_start: 0.8753 (tp-100) cc_final: 0.7979 (tm-30) REVERT: G 378 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8368 (ttp80) REVERT: J 187 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8337 (mmt) REVERT: J 288 GLN cc_start: 0.9608 (mp10) cc_final: 0.9401 (mp10) REVERT: J 298 GLN cc_start: 0.8757 (tp-100) cc_final: 0.7985 (tm-30) REVERT: J 378 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8383 (ttp80) outliers start: 32 outliers final: 19 residues processed: 100 average time/residue: 0.0908 time to fit residues: 14.0073 Evaluate side-chains 98 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 187 MET Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 187 MET Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 11 optimal weight: 0.0270 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.056292 restraints weight = 24331.190| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.35 r_work: 0.2545 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10784 Z= 0.158 Angle : 0.558 8.877 14680 Z= 0.294 Chirality : 0.043 0.137 1700 Planarity : 0.004 0.036 1796 Dihedral : 4.858 44.866 1444 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.56 % Allowed : 19.26 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1304 helix: 2.11 (0.25), residues: 440 sheet: 0.48 (0.32), residues: 288 loop : -2.08 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 378 TYR 0.009 0.001 TYR J 360 PHE 0.021 0.001 PHE G 186 TRP 0.005 0.001 TRP A 113 HIS 0.002 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10780) covalent geometry : angle 0.55788 / 0.29 (14672) SS BOND : bond 0.00177 / 0.08 ( 4) SS BOND : angle 0.61065 / 0.29 ( 8) hydrogen bonds : bond 0.05624 / 3.70 ( 455) hydrogen bonds : angle 4.07014 / 2.82 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.481 Fit side-chains REVERT: A 255 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 288 GLN cc_start: 0.9613 (mp10) cc_final: 0.9408 (mp10) REVERT: A 298 GLN cc_start: 0.8783 (tp-100) cc_final: 0.7987 (tm-30) REVERT: A 378 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8291 (ttp80) REVERT: D 255 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8944 (mm) REVERT: D 288 GLN cc_start: 0.9609 (mp10) cc_final: 0.9405 (mp10) REVERT: D 298 GLN cc_start: 0.8785 (tp-100) cc_final: 0.7987 (tm-30) REVERT: D 378 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8289 (ttp80) REVERT: G 255 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8945 (mm) REVERT: G 288 GLN cc_start: 0.9614 (mp10) cc_final: 0.9408 (mp10) REVERT: G 298 GLN cc_start: 0.8782 (tp-100) cc_final: 0.7984 (tm-30) REVERT: G 378 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8288 (ttp80) REVERT: J 255 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8940 (mm) REVERT: J 288 GLN cc_start: 0.9612 (mp10) cc_final: 0.9406 (mp10) REVERT: J 298 GLN cc_start: 0.8789 (tp-100) cc_final: 0.7994 (tm-30) REVERT: J 378 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8292 (ttp80) outliers start: 29 outliers final: 19 residues processed: 98 average time/residue: 0.0921 time to fit residues: 13.8756 Evaluate side-chains 94 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 255 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.058340 restraints weight = 24340.223| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.36 r_work: 0.2564 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10784 Z= 0.116 Angle : 0.529 9.357 14680 Z= 0.277 Chirality : 0.042 0.135 1700 Planarity : 0.004 0.035 1796 Dihedral : 4.597 42.568 1444 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.03 % Allowed : 19.43 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1304 helix: 2.30 (0.26), residues: 444 sheet: 0.56 (0.32), residues: 288 loop : -1.96 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 378 TYR 0.008 0.001 TYR D 360 PHE 0.021 0.001 PHE A 186 TRP 0.006 0.001 TRP J 113 HIS 0.002 0.001 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10780) covalent geometry : angle 0.52903 / 0.28 (14672) SS BOND : bond 0.00115 / 0.05 ( 4) SS BOND : angle 0.59462 / 0.26 ( 8) hydrogen bonds : bond 0.04622 / 3.05 ( 455) hydrogen bonds : angle 3.90597 / 2.70 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.429 Fit side-chains REVERT: A 255 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8927 (mm) REVERT: A 298 GLN cc_start: 0.8740 (tp-100) cc_final: 0.7938 (tm-30) REVERT: A 378 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8293 (ttp80) REVERT: D 298 GLN cc_start: 0.8743 (tp-100) cc_final: 0.7940 (tm-30) REVERT: D 378 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8295 (ttp80) REVERT: G 255 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8931 (mm) REVERT: G 298 GLN cc_start: 0.8744 (tp-100) cc_final: 0.7943 (tm-30) REVERT: G 378 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8294 (ttp80) REVERT: J 255 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8930 (mm) REVERT: J 298 GLN cc_start: 0.8748 (tp-100) cc_final: 0.7948 (tm-30) REVERT: J 378 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8295 (ttp80) outliers start: 23 outliers final: 20 residues processed: 95 average time/residue: 0.0915 time to fit residues: 13.3022 Evaluate side-chains 91 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 255 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 273 LEU Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 288 GLN D 288 GLN G 288 GLN J 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.056399 restraints weight = 24108.102| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.34 r_work: 0.2548 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10784 Z= 0.163 Angle : 0.562 9.355 14680 Z= 0.296 Chirality : 0.043 0.137 1700 Planarity : 0.004 0.036 1796 Dihedral : 4.780 43.304 1444 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.03 % Allowed : 19.26 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1304 helix: 2.26 (0.25), residues: 440 sheet: 0.52 (0.32), residues: 288 loop : -2.01 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 378 TYR 0.009 0.001 TYR J 360 PHE 0.021 0.001 PHE G 186 TRP 0.005 0.001 TRP J 113 HIS 0.002 0.001 HIS J 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (10780) covalent geometry : angle 0.56165 / 0.30 (14672) SS BOND : bond 0.00170 / 0.08 ( 4) SS BOND : angle 0.59340 / 0.29 ( 8) hydrogen bonds : bond 0.05621 / 3.69 ( 455) hydrogen bonds : angle 4.03031 / 2.80 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.442 Fit side-chains REVERT: A 255 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 298 GLN cc_start: 0.8781 (tp-100) cc_final: 0.7968 (tm-30) REVERT: D 298 GLN cc_start: 0.8781 (tp-100) cc_final: 0.7967 (tm-30) REVERT: G 255 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8940 (mm) REVERT: G 298 GLN cc_start: 0.8783 (tp-100) cc_final: 0.7969 (tm-30) REVERT: J 255 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8927 (mm) REVERT: J 298 GLN cc_start: 0.8788 (tp-100) cc_final: 0.7976 (tm-30) outliers start: 23 outliers final: 16 residues processed: 87 average time/residue: 0.0951 time to fit residues: 12.6096 Evaluate side-chains 83 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain G residue 255 ILE Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 210 HIS Chi-restraints excluded: chain J residue 255 ILE Chi-restraints excluded: chain J residue 268 THR Chi-restraints excluded: chain J residue 351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.075548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.057638 restraints weight = 24263.480| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.36 r_work: 0.2543 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10784 Z= 0.129 Angle : 0.542 9.374 14680 Z= 0.284 Chirality : 0.042 0.136 1700 Planarity : 0.004 0.045 1796 Dihedral : 4.666 42.285 1444 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.21 % Allowed : 19.43 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1304 helix: 2.31 (0.25), residues: 444 sheet: 0.61 (0.32), residues: 288 loop : -1.95 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 378 TYR 0.008 0.001 TYR J 360 PHE 0.021 0.001 PHE A 186 TRP 0.005 0.001 TRP J 113 HIS 0.002 0.001 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (10780) covalent geometry : angle 0.54195 / 0.28 (14672) SS BOND : bond 0.00154 / 0.07 ( 4) SS BOND : angle 0.58743 / 0.26 ( 8) hydrogen bonds : bond 0.05008 / 3.30 ( 455) hydrogen bonds : angle 3.93268 / 2.72 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.28 seconds wall clock time: 36 minutes 48.84 seconds (2208.84 seconds total)