Starting phenix.real_space_refine on Thu Jul 2 03:45:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcn_44431/07_2026/9bcn_44431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcn_44431/07_2026/9bcn_44431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bcn_44431/07_2026/9bcn_44431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcn_44431/07_2026/9bcn_44431.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bcn_44431/07_2026/9bcn_44431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcn_44431/07_2026/9bcn_44431.map" } resolution = 2.9 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= 0.005 sd= 0.262 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 S 26 5.16 5 Cl 2 4.86 5 C 4248 2.51 5 N 1128 2.21 5 O 1202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6606 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3212 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3208 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.73, per 1000 atoms: 0.26 Number of scatterers: 6606 At special positions: 0 Unit cell: (98.5166, 84.4428, 86.608, 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) Cl 2 17.00 S 26 16.00 O 1202 8.00 N 1128 7.00 C 4248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 213 " 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 Links applied ALPHA1-3 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1102 " - " ASN A 354 " " NAG B1102 " - " ASN B 354 " " NAG C 1 " - " ASN A 13 " " NAG D 1 " - " ASN A 395 " " NAG E 1 " - " ASN B 13 " " NAG F 1 " - " ASN B 395 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 337.7 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 42.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 19 through 37 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.913A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.638A pdb=" N PHE A 114 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.938A pdb=" N LEU A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.678A pdb=" N PHE A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 203 removed outlier: 3.760A pdb=" N TYR A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 245 through 249 removed outlier: 4.133A pdb=" N GLN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 3.557A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.562A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 336 removed outlier: 3.513A pdb=" N ALA A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 326 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'B' and resid 19 through 37 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.902A pdb=" N ALA B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.746A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.775A pdb=" N GLY B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 removed outlier: 3.767A pdb=" N PHE B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 removed outlier: 3.674A pdb=" N ARG B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 removed outlier: 3.718A pdb=" N LYS B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 207 " --> pdb=" O MET B 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 207' Processing helix chain 'B' and resid 215 through 229 Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.983A pdb=" N GLN B 249 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.543A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 338 Processing helix chain 'B' and resid 344 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 52 removed outlier: 9.226A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE A 81 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 189 removed outlier: 5.029A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 210 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU A 241 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 212 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 389 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 400 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 359 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 52 removed outlier: 9.152A pdb=" N VAL B 80 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B 4 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU B 82 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA B 6 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.159A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.668A pdb=" N ILE B 210 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 241 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 212 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE B 376 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN B 393 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 378 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 355 through 359 275 hydrogen bonds defined for protein. 798 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: 0.97 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1035 1.32 - 1.44: 1982 1.44 - 1.57: 3733 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 6790 Sorted by residual: bond pdb=" C5 MAN F 3 " pdb=" O5 MAN F 3 " ideal model delta sigma weight residual 1.418 1.496 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sigma weight residual 1.418 1.494 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 MAN E 3 " pdb=" O5 MAN E 3 " ideal model delta sigma weight residual 1.418 1.492 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 6785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8994 2.02 - 4.03: 220 4.03 - 6.05: 53 6.05 - 8.06: 13 8.06 - 10.08: 3 Bond angle restraints: 9283 Sorted by residual: angle pdb=" C GLU A 373 " pdb=" CA GLU A 373 " pdb=" CB GLU A 373 " ideal model delta sigma weight residual 110.77 100.69 10.08 1.67e+00 3.59e-01 3.64e+01 angle pdb=" C GLU B 373 " pdb=" CA GLU B 373 " pdb=" CB GLU B 373 " ideal model delta sigma weight residual 110.22 100.52 9.70 1.67e+00 3.59e-01 3.37e+01 angle pdb=" CA GLY B 207 " pdb=" C GLY B 207 " pdb=" N ARG B 208 " ideal model delta sigma weight residual 114.58 119.56 -4.98 8.60e-01 1.35e+00 3.35e+01 angle pdb=" O GLY B 207 " pdb=" C GLY B 207 " pdb=" N ARG B 208 " ideal model delta sigma weight residual 123.87 118.54 5.33 1.01e+00 9.80e-01 2.78e+01 angle pdb=" N THR B 197 " pdb=" CA THR B 197 " pdb=" C THR B 197 " ideal model delta sigma weight residual 111.14 105.84 5.30 1.08e+00 8.57e-01 2.41e+01 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 3878 24.16 - 48.31: 198 48.31 - 72.47: 26 72.47 - 96.63: 13 96.63 - 120.79: 4 Dihedral angle restraints: 4119 sinusoidal: 1691 harmonic: 2428 Sorted by residual: dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 86 " pdb=" CB CYS B 86 " ideal model delta sinusoidal sigma weight residual 93.00 137.58 -44.58 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" C GLU A 373 " pdb=" N GLU A 373 " pdb=" CA GLU A 373 " pdb=" CB GLU A 373 " ideal model delta harmonic sigma weight residual -122.60 -109.81 -12.79 0 2.50e+00 1.60e-01 2.62e+01 dihedral pdb=" C GLU B 373 " pdb=" N GLU B 373 " pdb=" CA GLU B 373 " pdb=" CB GLU B 373 " ideal model delta harmonic sigma weight residual -122.60 -109.94 -12.66 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 4116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1011 0.107 - 0.214: 49 0.214 - 0.321: 2 0.321 - 0.427: 2 0.427 - 0.534: 2 Chirality restraints: 1066 Sorted by residual: chirality pdb=" C1 NAG A1102 " pdb=" ND2 ASN A 354 " pdb=" C2 NAG A1102 " pdb=" O5 NAG A1102 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" C1 NAG B1102 " pdb=" ND2 ASN B 354 " pdb=" C2 NAG B1102 " pdb=" O5 NAG B1102 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1063 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1102 " 0.049 2.00e-02 2.50e+03 3.97e-02 1.97e+01 pdb=" C7 NAG B1102 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG B1102 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG B1102 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B1102 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 200 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C LEU B 200 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU B 200 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG B 201 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 236 " -0.016 2.00e-02 2.50e+03 2.12e-02 8.99e+00 pdb=" CG TYR A 236 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 236 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 236 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 236 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR A 236 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 236 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 236 " 0.020 2.00e-02 2.50e+03 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 181 2.71 - 3.25: 6365 3.25 - 3.80: 10206 3.80 - 4.35: 13912 4.35 - 4.90: 23450 Nonbonded interactions: 54114 Sorted by model distance: nonbonded pdb=" O PRO B 204 " pdb=" NH2 ARG B 208 " model vdw 2.156 3.120 nonbonded pdb=" O3 NAG C 2 " pdb=" O7 NAG C 2 " model vdw 2.159 3.040 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.198 3.040 nonbonded pdb=" O THR B 14 " pdb=" OG1 THR B 14 " model vdw 2.217 3.040 nonbonded pdb=" O GLU A 190 " pdb=" OH TYR A 196 " model vdw 2.319 3.040 ... (remaining 54109 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 1 through 310 or (resid 311 and (name N or name CA or name \ C or name O or name CB )) or resid 312 through 345 or (resid 346 and (name N or \ name CA or name C or name O or name CB )) or resid 347 through 1102)) selection = (chain 'B' and (resid 1 through 234 or (resid 235 and (name N or name CA or name \ C or name O or name CB )) or resid 236 through 1102)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.240 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.850 Find NCS groups from input model: 0.120 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.006 0.078 6808 Z= 0.323 Angle : 0.952 18.299 9333 Z= 0.468 Chirality : 0.056 0.534 1066 Planarity : 0.006 0.046 1183 Dihedral : 15.344 120.785 2559 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.96 % Allowed : 0.96 % Favored : 98.07 % Cbeta Deviations : 0.26 % 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: -0.99 (0.28), residues: 846 helix: 0.22 (0.30), residues: 314 sheet: -0.28 (0.41), residues: 162 loop : -1.56 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 389 TYR 0.036 0.002 TYR A 236 PHE 0.016 0.001 PHE A 172 TRP 0.012 0.001 TRP A 379 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.32 ( 6790) covalent geometry : angle 0.80524 / 0.44 ( 9283) SS BOND : bond 0.00464 / 0.30 ( 4) SS BOND : angle 1.41998 / 0.84 ( 8) hydrogen bonds : bond 0.16691 / 11.20 ( 275) hydrogen bonds : angle 7.32340 / 5.52 ( 798) link_ALPHA1-3 : bond 0.01025 / 0.61 ( 4) link_ALPHA1-3 : angle 5.46209 / 3.50 ( 12) link_BETA1-4 : bond 0.01410 / 0.80 ( 4) link_BETA1-4 : angle 12.25995 / 7.36 ( 12) link_NAG-ASN : bond 0.01978 / 1.26 ( 6) link_NAG-ASN : angle 3.76899 / 2.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.260 Fit side-chains REVERT: A 119 GLU cc_start: 0.7097 (tt0) cc_final: 0.6842 (tt0) REVERT: A 298 LYS cc_start: 0.8116 (mttt) cc_final: 0.7581 (mmtp) REVERT: A 389 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8053 (pmt170) outliers start: 6 outliers final: 2 residues processed: 111 average time/residue: 0.4421 time to fit residues: 52.1779 Evaluate side-chains 80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 208 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.094674 restraints weight = 7767.905| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.87 r_work: 0.2881 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6808 Z= 0.151 Angle : 0.794 14.730 9333 Z= 0.341 Chirality : 0.047 0.341 1066 Planarity : 0.005 0.039 1183 Dihedral : 13.249 108.820 1224 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.44 % Allowed : 8.51 % Favored : 90.05 % 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: -0.25 (0.29), residues: 846 helix: 1.14 (0.31), residues: 314 sheet: -0.45 (0.37), residues: 178 loop : -1.16 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 262 TYR 0.014 0.001 TYR B 154 PHE 0.016 0.001 PHE A 172 TRP 0.010 0.001 TRP A 100 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 6790) covalent geometry : angle 0.69186 / 0.32 ( 9283) SS BOND : bond 0.00349 / 0.24 ( 4) SS BOND : angle 0.89895 / 0.55 ( 8) hydrogen bonds : bond 0.04161 / 2.89 ( 275) hydrogen bonds : angle 5.00580 / 3.80 ( 798) link_ALPHA1-3 : bond 0.02061 / 1.26 ( 4) link_ALPHA1-3 : angle 5.02954 / 2.78 ( 12) link_BETA1-4 : bond 0.01655 / 0.93 ( 4) link_BETA1-4 : angle 9.30279 / 5.48 ( 12) link_NAG-ASN : bond 0.00653 / 0.46 ( 6) link_NAG-ASN : angle 2.27905 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.252 Fit side-chains REVERT: A 173 MET cc_start: 0.8686 (mmm) cc_final: 0.8426 (mmt) REVERT: A 192 ASP cc_start: 0.7438 (t70) cc_final: 0.6889 (t0) REVERT: A 298 LYS cc_start: 0.7703 (mttt) cc_final: 0.7114 (mmtp) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.4499 time to fit residues: 40.3073 Evaluate side-chains 74 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 80 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.125293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.093402 restraints weight = 7723.545| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.03 r_work: 0.2873 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6808 Z= 0.153 Angle : 0.754 13.621 9333 Z= 0.322 Chirality : 0.046 0.336 1066 Planarity : 0.005 0.036 1183 Dihedral : 12.883 111.014 1220 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.57 % Allowed : 10.43 % Favored : 87.00 % 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: 0.15 (0.29), residues: 846 helix: 1.42 (0.31), residues: 316 sheet: -0.11 (0.39), residues: 160 loop : -0.94 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 47 TYR 0.013 0.001 TYR B 154 PHE 0.014 0.001 PHE A 172 TRP 0.008 0.001 TRP A 18 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 6790) covalent geometry : angle 0.66113 / 0.30 ( 9283) SS BOND : bond 0.00326 / 0.21 ( 4) SS BOND : angle 0.90905 / 0.58 ( 8) hydrogen bonds : bond 0.04028 / 2.80 ( 275) hydrogen bonds : angle 4.74872 / 3.62 ( 798) link_ALPHA1-3 : bond 0.01628 / 0.99 ( 4) link_ALPHA1-3 : angle 4.49953 / 2.51 ( 12) link_BETA1-4 : bond 0.01811 / 1.03 ( 4) link_BETA1-4 : angle 8.65306 / 4.93 ( 12) link_NAG-ASN : bond 0.00648 / 0.39 ( 6) link_NAG-ASN : angle 2.40114 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.252 Fit side-chains REVERT: A 192 ASP cc_start: 0.7437 (t70) cc_final: 0.6884 (t0) REVERT: A 298 LYS cc_start: 0.7783 (mttt) cc_final: 0.7179 (mmtp) REVERT: B 344 ASP cc_start: 0.7616 (m-30) cc_final: 0.7388 (m-30) outliers start: 16 outliers final: 11 residues processed: 83 average time/residue: 0.4200 time to fit residues: 37.3625 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.124177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.092346 restraints weight = 7760.910| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.00 r_work: 0.2843 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6808 Z= 0.180 Angle : 0.768 13.732 9333 Z= 0.327 Chirality : 0.047 0.336 1066 Planarity : 0.005 0.035 1183 Dihedral : 12.768 110.818 1220 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.89 % Allowed : 11.72 % Favored : 85.39 % 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: 0.16 (0.29), residues: 846 helix: 1.50 (0.31), residues: 314 sheet: -0.09 (0.39), residues: 160 loop : -1.00 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 47 TYR 0.011 0.001 TYR A 154 PHE 0.015 0.001 PHE A 172 TRP 0.008 0.001 TRP A 18 HIS 0.007 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 ( 6790) covalent geometry : angle 0.67816 / 0.30 ( 9283) SS BOND : bond 0.00338 / 0.22 ( 4) SS BOND : angle 0.99329 / 0.64 ( 8) hydrogen bonds : bond 0.04160 / 2.89 ( 275) hydrogen bonds : angle 4.69645 / 3.58 ( 798) link_ALPHA1-3 : bond 0.01587 / 0.97 ( 4) link_ALPHA1-3 : angle 4.42921 / 2.45 ( 12) link_BETA1-4 : bond 0.01666 / 0.94 ( 4) link_BETA1-4 : angle 8.50269 / 4.77 ( 12) link_NAG-ASN : bond 0.00473 / 0.30 ( 6) link_NAG-ASN : angle 2.59111 / 1.98 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.245 Fit side-chains REVERT: A 192 ASP cc_start: 0.7382 (t70) cc_final: 0.6655 (t70) REVERT: A 298 LYS cc_start: 0.7632 (mttt) cc_final: 0.7031 (mmtp) REVERT: B 344 ASP cc_start: 0.7586 (m-30) cc_final: 0.7310 (m-30) outliers start: 18 outliers final: 11 residues processed: 85 average time/residue: 0.3858 time to fit residues: 35.3927 Evaluate side-chains 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 352 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.095516 restraints weight = 7828.803| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.98 r_work: 0.2865 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6808 Z= 0.124 Angle : 0.720 13.493 9333 Z= 0.305 Chirality : 0.045 0.320 1066 Planarity : 0.004 0.036 1183 Dihedral : 12.536 109.705 1220 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.41 % Allowed : 14.77 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.29), residues: 846 helix: 1.61 (0.31), residues: 316 sheet: -0.06 (0.39), residues: 160 loop : -0.87 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 47 TYR 0.008 0.001 TYR A 154 PHE 0.009 0.001 PHE A 188 TRP 0.008 0.001 TRP B 379 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 6790) covalent geometry : angle 0.63102 / 0.28 ( 9283) SS BOND : bond 0.00244 / 0.16 ( 4) SS BOND : angle 0.69310 / 0.45 ( 8) hydrogen bonds : bond 0.03493 / 2.43 ( 275) hydrogen bonds : angle 4.56260 / 3.48 ( 798) link_ALPHA1-3 : bond 0.01649 / 1.01 ( 4) link_ALPHA1-3 : angle 4.30130 / 2.40 ( 12) link_BETA1-4 : bond 0.01592 / 0.90 ( 4) link_BETA1-4 : angle 8.08362 / 4.48 ( 12) link_NAG-ASN : bond 0.00639 / 0.39 ( 6) link_NAG-ASN : angle 2.73578 / 2.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.254 Fit side-chains REVERT: A 192 ASP cc_start: 0.7315 (t70) cc_final: 0.6657 (t0) REVERT: A 298 LYS cc_start: 0.7624 (mttt) cc_final: 0.7009 (mmtp) REVERT: B 344 ASP cc_start: 0.7578 (m-30) cc_final: 0.7296 (m-30) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 0.3770 time to fit residues: 34.2695 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.091753 restraints weight = 7822.348| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.04 r_work: 0.2992 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6808 Z= 0.181 Angle : 0.765 13.916 9333 Z= 0.326 Chirality : 0.047 0.333 1066 Planarity : 0.005 0.036 1183 Dihedral : 12.522 109.249 1220 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.73 % Allowed : 14.93 % Favored : 82.34 % 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 (0.29), residues: 846 helix: 1.57 (0.31), residues: 316 sheet: -0.08 (0.39), residues: 160 loop : -0.96 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.010 0.001 TYR A 154 PHE 0.012 0.001 PHE B 188 TRP 0.009 0.001 TRP B 74 HIS 0.007 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 ( 6790) covalent geometry : angle 0.67760 / 0.30 ( 9283) SS BOND : bond 0.00315 / 0.20 ( 4) SS BOND : angle 1.03251 / 0.68 ( 8) hydrogen bonds : bond 0.04117 / 2.86 ( 275) hydrogen bonds : angle 4.61709 / 3.52 ( 798) link_ALPHA1-3 : bond 0.01550 / 0.94 ( 4) link_ALPHA1-3 : angle 4.38062 / 2.44 ( 12) link_BETA1-4 : bond 0.01573 / 0.90 ( 4) link_BETA1-4 : angle 8.28646 / 4.59 ( 12) link_NAG-ASN : bond 0.00518 / 0.31 ( 6) link_NAG-ASN : angle 2.82625 / 2.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.252 Fit side-chains REVERT: A 298 LYS cc_start: 0.7859 (mttt) cc_final: 0.7254 (mmtp) REVERT: B 344 ASP cc_start: 0.7730 (m-30) cc_final: 0.7462 (m-30) outliers start: 17 outliers final: 10 residues processed: 79 average time/residue: 0.3679 time to fit residues: 31.4739 Evaluate side-chains 80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.092572 restraints weight = 7760.333| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.05 r_work: 0.2841 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6808 Z= 0.134 Angle : 0.724 13.233 9333 Z= 0.306 Chirality : 0.045 0.321 1066 Planarity : 0.004 0.036 1183 Dihedral : 12.378 108.741 1220 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.73 % Allowed : 15.25 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.29), residues: 846 helix: 1.68 (0.31), residues: 316 sheet: -0.02 (0.39), residues: 160 loop : -0.89 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.009 0.001 TYR A 154 PHE 0.014 0.001 PHE A 172 TRP 0.008 0.001 TRP B 74 HIS 0.007 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 6790) covalent geometry : angle 0.64017 / 0.29 ( 9283) SS BOND : bond 0.00274 / 0.17 ( 4) SS BOND : angle 0.77691 / 0.51 ( 8) hydrogen bonds : bond 0.03586 / 2.50 ( 275) hydrogen bonds : angle 4.53896 / 3.46 ( 798) link_ALPHA1-3 : bond 0.01624 / 0.99 ( 4) link_ALPHA1-3 : angle 4.23756 / 2.36 ( 12) link_BETA1-4 : bond 0.01565 / 0.89 ( 4) link_BETA1-4 : angle 7.93189 / 4.38 ( 12) link_NAG-ASN : bond 0.00417 / 0.28 ( 6) link_NAG-ASN : angle 2.50315 / 1.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.295 Fit side-chains REVERT: A 135 ASP cc_start: 0.8226 (m-30) cc_final: 0.7940 (m-30) REVERT: A 192 ASP cc_start: 0.7330 (t70) cc_final: 0.6595 (t70) REVERT: A 298 LYS cc_start: 0.7541 (mttt) cc_final: 0.6920 (mmtp) REVERT: B 344 ASP cc_start: 0.7524 (m-30) cc_final: 0.7205 (m-30) outliers start: 17 outliers final: 12 residues processed: 83 average time/residue: 0.3877 time to fit residues: 34.8325 Evaluate side-chains 82 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 352 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.126755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095191 restraints weight = 7811.251| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.97 r_work: 0.2870 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6808 Z= 0.125 Angle : 0.720 13.553 9333 Z= 0.304 Chirality : 0.044 0.306 1066 Planarity : 0.004 0.036 1183 Dihedral : 12.258 108.352 1220 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.77 % Allowed : 17.01 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.45 (0.30), residues: 846 helix: 1.75 (0.31), residues: 316 sheet: -0.15 (0.37), residues: 180 loop : -0.76 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.009 0.001 TYR B 154 PHE 0.009 0.001 PHE A 188 TRP 0.010 0.001 TRP B 74 HIS 0.007 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6790) covalent geometry : angle 0.63499 / 0.28 ( 9283) SS BOND : bond 0.00241 / 0.15 ( 4) SS BOND : angle 0.75145 / 0.48 ( 8) hydrogen bonds : bond 0.03380 / 2.36 ( 275) hydrogen bonds : angle 4.47888 / 3.41 ( 798) link_ALPHA1-3 : bond 0.01636 / 1.00 ( 4) link_ALPHA1-3 : angle 4.19456 / 2.37 ( 12) link_BETA1-4 : bond 0.01522 / 0.86 ( 4) link_BETA1-4 : angle 7.79594 / 4.27 ( 12) link_NAG-ASN : bond 0.00496 / 0.31 ( 6) link_NAG-ASN : angle 2.87564 / 2.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.252 Fit side-chains REVERT: A 192 ASP cc_start: 0.7232 (t70) cc_final: 0.6593 (t70) REVERT: A 298 LYS cc_start: 0.7581 (mttt) cc_final: 0.6951 (mmtp) REVERT: B 344 ASP cc_start: 0.7560 (m-30) cc_final: 0.7246 (m-30) outliers start: 11 outliers final: 10 residues processed: 78 average time/residue: 0.3746 time to fit residues: 31.6237 Evaluate side-chains 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 83 optimal weight: 0.4980 chunk 67 optimal weight: 0.0980 chunk 42 optimal weight: 7.9990 chunk 57 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.097633 restraints weight = 7884.887| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.00 r_work: 0.2923 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6808 Z= 0.104 Angle : 0.690 12.536 9333 Z= 0.290 Chirality : 0.043 0.280 1066 Planarity : 0.004 0.036 1183 Dihedral : 12.032 108.177 1220 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 17.82 % Favored : 80.26 % 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: 0.59 (0.30), residues: 846 helix: 1.86 (0.31), residues: 316 sheet: -0.15 (0.37), residues: 180 loop : -0.62 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.010 0.001 TYR B 154 PHE 0.014 0.001 PHE A 172 TRP 0.008 0.001 TRP B 379 HIS 0.008 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6790) covalent geometry : angle 0.61242 / 0.27 ( 9283) SS BOND : bond 0.00192 / 0.12 ( 4) SS BOND : angle 0.55695 / 0.37 ( 8) hydrogen bonds : bond 0.02918 / 2.04 ( 275) hydrogen bonds : angle 4.36210 / 3.32 ( 798) link_ALPHA1-3 : bond 0.01677 / 1.03 ( 4) link_ALPHA1-3 : angle 4.04773 / 2.31 ( 12) link_BETA1-4 : bond 0.01463 / 0.83 ( 4) link_BETA1-4 : angle 7.28262 / 3.98 ( 12) link_NAG-ASN : bond 0.00475 / 0.32 ( 6) link_NAG-ASN : angle 2.68836 / 2.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.245 Fit side-chains REVERT: A 173 MET cc_start: 0.8811 (mmm) cc_final: 0.8492 (mmp) REVERT: A 192 ASP cc_start: 0.7104 (t70) cc_final: 0.6640 (t0) REVERT: A 298 LYS cc_start: 0.7592 (mttt) cc_final: 0.6961 (mmtp) REVERT: B 344 ASP cc_start: 0.7589 (m-30) cc_final: 0.7302 (m-30) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.3791 time to fit residues: 34.0418 Evaluate side-chains 78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 341 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.124550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.092268 restraints weight = 7828.729| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.04 r_work: 0.2842 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6808 Z= 0.193 Angle : 0.768 13.401 9333 Z= 0.327 Chirality : 0.047 0.319 1066 Planarity : 0.004 0.036 1183 Dihedral : 12.185 107.998 1220 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.61 % Allowed : 17.98 % Favored : 80.42 % 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: 0.52 (0.30), residues: 846 helix: 1.76 (0.31), residues: 316 sheet: -0.06 (0.37), residues: 180 loop : -0.71 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.011 0.001 TYR B 154 PHE 0.011 0.001 PHE B 188 TRP 0.012 0.001 TRP B 74 HIS 0.008 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.19 ( 6790) covalent geometry : angle 0.68864 / 0.31 ( 9283) SS BOND : bond 0.00352 / 0.22 ( 4) SS BOND : angle 1.07706 / 0.70 ( 8) hydrogen bonds : bond 0.04058 / 2.81 ( 275) hydrogen bonds : angle 4.55773 / 3.47 ( 798) link_ALPHA1-3 : bond 0.01473 / 0.90 ( 4) link_ALPHA1-3 : angle 4.20679 / 2.37 ( 12) link_BETA1-4 : bond 0.01498 / 0.85 ( 4) link_BETA1-4 : angle 7.87174 / 4.35 ( 12) link_NAG-ASN : bond 0.00314 / 0.20 ( 6) link_NAG-ASN : angle 2.74462 / 2.18 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.307 Fit side-chains REVERT: A 192 ASP cc_start: 0.7264 (t70) cc_final: 0.6627 (t70) REVERT: A 298 LYS cc_start: 0.7804 (mttt) cc_final: 0.7187 (mmtp) REVERT: B 182 THR cc_start: 0.8447 (m) cc_final: 0.8097 (t) REVERT: B 344 ASP cc_start: 0.7672 (m-30) cc_final: 0.7175 (m-30) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.3487 time to fit residues: 30.3719 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 341 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN A 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.095846 restraints weight = 7699.553| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.97 r_work: 0.2875 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6808 Z= 0.114 Angle : 0.718 13.266 9333 Z= 0.302 Chirality : 0.044 0.296 1066 Planarity : 0.004 0.036 1183 Dihedral : 12.072 107.958 1220 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.44 % Allowed : 18.14 % Favored : 80.42 % 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: 0.66 (0.30), residues: 846 helix: 1.88 (0.31), residues: 316 sheet: -0.01 (0.37), residues: 180 loop : -0.61 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.011 0.001 TYR B 154 PHE 0.012 0.001 PHE B 172 TRP 0.010 0.001 TRP B 74 HIS 0.007 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 6790) covalent geometry : angle 0.63438 / 0.28 ( 9283) SS BOND : bond 0.00215 / 0.13 ( 4) SS BOND : angle 0.64973 / 0.43 ( 8) hydrogen bonds : bond 0.03274 / 2.30 ( 275) hydrogen bonds : angle 4.45741 / 3.41 ( 798) link_ALPHA1-3 : bond 0.01619 / 0.99 ( 4) link_ALPHA1-3 : angle 4.09125 / 2.32 ( 12) link_BETA1-4 : bond 0.01478 / 0.84 ( 4) link_BETA1-4 : angle 7.59916 / 4.15 ( 12) link_NAG-ASN : bond 0.00528 / 0.33 ( 6) link_NAG-ASN : angle 3.20127 / 2.59 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.48 seconds wall clock time: 38 minutes 49.24 seconds (2329.24 seconds total)