Starting phenix.real_space_refine on Tue Jan 14 09:52:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcn_44431/01_2025/9bcn_44431.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLU:plan': 9, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 8} 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: {'GLU:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 3, 'ASP:plan': 8} 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, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4.38, per 1000 atoms: 0.66 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: 1.75 Conformation dependent library (CDL) restraints added in 898.5 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: 0.65 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: 1.78 Time building geometry restraints manager: 2.02 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 425 or resid 110 \ 1 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 425 or resid 1101 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: 0.300 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.100 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 6790 Z= 0.429 Angle : 0.805 10.078 9283 Z= 0.437 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (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 TRP 0.012 0.001 TRP A 379 HIS 0.006 0.001 HIS B 322 PHE 0.016 0.001 PHE A 172 TYR 0.036 0.002 TYR A 236 ARG 0.015 0.001 ARG B 389 *********************** 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 : 0.721 Fit side-chains REVERT: A 119 GLU cc_start: 0.7097 (tt0) cc_final: 0.6841 (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: 0.8054 (pmt170) outliers start: 6 outliers final: 2 residues processed: 111 average time/residue: 0.9470 time to fit residues: 112.0028 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3330 r_free = 0.3330 target = 0.124854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.093587 restraints weight = 7651.843| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.96 r_work: 0.2868 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.003 0.029 6790 Z= 0.223 Angle : 0.689 11.510 9283 Z= 0.314 Chirality : 0.047 0.340 1066 Planarity : 0.005 0.039 1183 Dihedral : 13.238 108.777 1224 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.44 % Allowed : 8.35 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 846 helix: 1.13 (0.31), residues: 316 sheet: -0.46 (0.37), residues: 178 loop : -1.13 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 100 HIS 0.006 0.001 HIS B 322 PHE 0.015 0.001 PHE A 172 TYR 0.011 0.001 TYR B 154 ARG 0.003 0.000 ARG B 262 *********************** 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 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.658 Fit side-chains REVERT: A 173 MET cc_start: 0.8584 (mmm) cc_final: 0.8323 (mmt) REVERT: A 192 ASP cc_start: 0.7400 (t70) cc_final: 0.6671 (t70) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.9837 time to fit residues: 87.1269 Evaluate side-chains 73 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 24 optimal weight: 0.0060 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.0370 chunk 53 optimal weight: 0.0770 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3363 r_free = 0.3363 target = 0.127475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.096306 restraints weight = 7763.732| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.00 r_work: 0.2906 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6790 Z= 0.156 Angle : 0.621 9.939 9283 Z= 0.281 Chirality : 0.045 0.319 1066 Planarity : 0.004 0.034 1183 Dihedral : 12.775 110.601 1218 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.77 % Allowed : 10.43 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 846 helix: 1.42 (0.30), residues: 320 sheet: -0.29 (0.36), residues: 184 loop : -0.80 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 100 HIS 0.005 0.001 HIS B 322 PHE 0.015 0.001 PHE A 172 TYR 0.011 0.001 TYR B 154 ARG 0.004 0.000 ARG A 47 *********************** 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 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.698 Fit side-chains REVERT: A 192 ASP cc_start: 0.7335 (t70) cc_final: 0.6623 (t70) REVERT: A 298 LYS cc_start: 0.7515 (mttt) cc_final: 0.6962 (mmtp) REVERT: B 344 ASP cc_start: 0.7517 (m-30) cc_final: 0.7283 (m-30) outliers start: 11 outliers final: 4 residues processed: 89 average time/residue: 0.9115 time to fit residues: 86.9478 Evaluate side-chains 80 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 208 ARG Chi-restraints excluded: chain B residue 341 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 80 optimal weight: 0.0370 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.127111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.094933 restraints weight = 7800.086| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.05 r_work: 0.2896 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6790 Z= 0.209 Angle : 0.638 10.285 9283 Z= 0.286 Chirality : 0.045 0.314 1066 Planarity : 0.004 0.036 1183 Dihedral : 12.558 111.154 1218 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.57 % Allowed : 12.52 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 846 helix: 1.72 (0.31), residues: 314 sheet: -0.24 (0.36), residues: 184 loop : -0.82 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.007 0.001 HIS B 299 PHE 0.011 0.001 PHE B 188 TYR 0.011 0.001 TYR B 154 ARG 0.003 0.000 ARG A 47 *********************** 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 96 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.716 Fit side-chains REVERT: A 192 ASP cc_start: 0.7407 (t70) cc_final: 0.6736 (t70) REVERT: A 298 LYS cc_start: 0.7746 (mttt) cc_final: 0.7179 (mmtp) REVERT: B 344 ASP cc_start: 0.7672 (m-30) cc_final: 0.7452 (m-30) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.8620 time to fit residues: 83.4991 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 : 0.777 ------------------------------------------------------------------------------- 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 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 347 ASN Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 77 optimal weight: 0.0070 chunk 47 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099320 restraints weight = 7743.647| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.91 r_work: 0.2925 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6790 Z= 0.149 Angle : 0.604 9.878 9283 Z= 0.269 Chirality : 0.044 0.292 1066 Planarity : 0.004 0.037 1183 Dihedral : 12.293 110.421 1218 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.25 % Allowed : 14.77 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.29), residues: 846 helix: 1.81 (0.30), residues: 316 sheet: -0.19 (0.36), residues: 184 loop : -0.70 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 379 HIS 0.007 0.001 HIS B 299 PHE 0.014 0.001 PHE A 172 TYR 0.009 0.001 TYR B 154 ARG 0.005 0.000 ARG A 47 *********************** 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 91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.566 Fit side-chains REVERT: A 192 ASP cc_start: 0.7295 (t70) cc_final: 0.6620 (t70) REVERT: A 298 LYS cc_start: 0.7537 (mttt) cc_final: 0.6940 (mmtp) REVERT: B 344 ASP cc_start: 0.7539 (m-30) cc_final: 0.7302 (m-30) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 0.7818 time to fit residues: 72.9983 Evaluate side-chains 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 83 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 195 HIS A 338 HIS B 299 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097760 restraints weight = 7718.574| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.97 r_work: 0.2899 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6790 Z= 0.181 Angle : 0.615 9.734 9283 Z= 0.272 Chirality : 0.044 0.292 1066 Planarity : 0.004 0.037 1183 Dihedral : 12.202 109.962 1218 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.09 % Allowed : 15.25 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 846 helix: 1.91 (0.31), residues: 316 sheet: -0.14 (0.36), residues: 184 loop : -0.70 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 379 HIS 0.007 0.001 HIS B 299 PHE 0.009 0.001 PHE B 188 TYR 0.010 0.001 TYR B 154 ARG 0.004 0.000 ARG A 47 *********************** 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 89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.735 Fit side-chains REVERT: A 192 ASP cc_start: 0.7269 (t70) cc_final: 0.6533 (t0) REVERT: A 195 HIS cc_start: 0.7300 (m-70) cc_final: 0.7020 (m-70) REVERT: A 298 LYS cc_start: 0.7499 (mttt) cc_final: 0.6915 (mmtp) REVERT: B 344 ASP cc_start: 0.7522 (m-30) cc_final: 0.7260 (m-30) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 0.9771 time to fit residues: 88.9926 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 185 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 338 HIS B 299 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.093489 restraints weight = 7680.477| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.04 r_work: 0.2840 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6790 Z= 0.234 Angle : 0.642 10.141 9283 Z= 0.285 Chirality : 0.045 0.305 1066 Planarity : 0.004 0.037 1183 Dihedral : 12.160 109.340 1218 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.93 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 846 helix: 1.88 (0.31), residues: 316 sheet: -0.10 (0.37), residues: 180 loop : -0.68 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.007 0.001 HIS B 299 PHE 0.013 0.001 PHE A 172 TYR 0.010 0.001 TYR A 154 ARG 0.004 0.000 ARG A 47 *********************** 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 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.732 Fit side-chains REVERT: A 192 ASP cc_start: 0.7055 (t70) cc_final: 0.6332 (t0) REVERT: A 298 LYS cc_start: 0.7328 (mttt) cc_final: 0.6724 (mmtp) REVERT: B 344 ASP cc_start: 0.7415 (m-30) cc_final: 0.7070 (m-30) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.8306 time to fit residues: 70.1629 Evaluate side-chains 76 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 208 ARG Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3358 r_free = 0.3358 target = 0.127168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.095061 restraints weight = 7722.232| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.04 r_work: 0.2900 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6790 Z= 0.192 Angle : 0.623 9.970 9283 Z= 0.276 Chirality : 0.044 0.299 1066 Planarity : 0.004 0.037 1183 Dihedral : 12.056 108.797 1218 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.77 % Allowed : 17.17 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 846 helix: 1.89 (0.31), residues: 316 sheet: -0.07 (0.37), residues: 180 loop : -0.63 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 74 HIS 0.006 0.001 HIS B 322 PHE 0.010 0.001 PHE A 188 TYR 0.010 0.001 TYR B 154 ARG 0.004 0.000 ARG A 47 *********************** 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 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.739 Fit side-chains REVERT: A 192 ASP cc_start: 0.7237 (t70) cc_final: 0.6517 (t70) REVERT: A 298 LYS cc_start: 0.7696 (mttt) cc_final: 0.7104 (mmtp) REVERT: B 344 ASP cc_start: 0.7674 (m-30) cc_final: 0.7402 (m-30) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 0.8167 time to fit residues: 69.9225 Evaluate side-chains 75 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3386 r_free = 0.3386 target = 0.129262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.097595 restraints weight = 7811.214| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.99 r_work: 0.2936 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6790 Z= 0.158 Angle : 0.610 10.159 9283 Z= 0.269 Chirality : 0.043 0.283 1066 Planarity : 0.004 0.037 1183 Dihedral : 11.917 108.443 1218 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.61 % Allowed : 17.66 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.30), residues: 846 helix: 1.96 (0.31), residues: 316 sheet: -0.07 (0.37), residues: 180 loop : -0.57 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.005 0.001 HIS B 322 PHE 0.012 0.001 PHE A 172 TYR 0.010 0.001 TYR B 154 ARG 0.004 0.000 ARG A 47 *********************** 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 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.727 Fit side-chains REVERT: A 192 ASP cc_start: 0.7165 (t70) cc_final: 0.6459 (t70) REVERT: A 298 LYS cc_start: 0.7714 (mttt) cc_final: 0.7113 (mmtp) REVERT: B 344 ASP cc_start: 0.7628 (m-30) cc_final: 0.7370 (m-30) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.8672 time to fit residues: 72.5174 Evaluate side-chains 77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3385 r_free = 0.3385 target = 0.129148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.097300 restraints weight = 7830.111| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.00 r_work: 0.2910 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6790 Z= 0.171 Angle : 0.616 9.737 9283 Z= 0.270 Chirality : 0.043 0.276 1066 Planarity : 0.004 0.037 1183 Dihedral : 11.749 108.031 1214 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.44 % Allowed : 17.82 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 846 helix: 1.97 (0.31), residues: 316 sheet: -0.05 (0.37), residues: 180 loop : -0.58 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 74 HIS 0.005 0.001 HIS B 322 PHE 0.009 0.001 PHE A 188 TYR 0.010 0.001 TYR B 154 ARG 0.004 0.000 ARG A 47 ********************** 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 81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.997 Fit side-chains REVERT: A 192 ASP cc_start: 0.7123 (t70) cc_final: 0.6358 (t70) REVERT: A 298 LYS cc_start: 0.7573 (mttt) cc_final: 0.6965 (mmtp) REVERT: B 344 ASP cc_start: 0.7555 (m-30) cc_final: 0.7282 (m-30) outliers start: 9 outliers final: 7 residues processed: 77 average time/residue: 0.8928 time to fit residues: 74.3519 Evaluate side-chains 78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 341 THR Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 77 ASN A 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099727 restraints weight = 7824.893| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.92 r_work: 0.2943 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6790 Z= 0.151 Angle : 0.602 9.386 9283 Z= 0.263 Chirality : 0.043 0.265 1066 Planarity : 0.004 0.037 1183 Dihedral : 11.633 108.008 1214 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.28 % Allowed : 18.14 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.30), residues: 846 helix: 1.96 (0.31), residues: 318 sheet: -0.06 (0.37), residues: 184 loop : -0.51 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.005 0.001 HIS B 322 PHE 0.013 0.001 PHE A 172 TYR 0.010 0.001 TYR B 154 ARG 0.004 0.000 ARG A 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4247.68 seconds wall clock time: 76 minutes 36.83 seconds (4596.83 seconds total)