Starting phenix.real_space_refine on Sun May 3 04:00:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nyf_49933/05_2026/9nyf_49933_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nyf_49933/05_2026/9nyf_49933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nyf_49933/05_2026/9nyf_49933_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nyf_49933/05_2026/9nyf_49933_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nyf_49933/05_2026/9nyf_49933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nyf_49933/05_2026/9nyf_49933.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 32 5.16 5 C 6720 2.51 5 N 1656 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10288 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2512 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 2 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, '5TR': 1, 'UPG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'5TR:plan-4': 1, '5TR:plan-5': 1, '5TR:plan-6': 1, '5TR:plan-7': 1, '5TR:plan-8': 1, '5TR:plan-9': 1, '5TR:plan-10': 1, '5TR:plan-11': 1} Unresolved non-hydrogen planarities: 37 Restraints were copied for chains: A, C, D Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10288 At special positions: 0 Unit cell: (108.73, 108.73, 105.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 32 16.00 P 12 15.00 Mg 4 11.99 O 1864 8.00 N 1656 7.00 C 6720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 411.2 milliseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 55.5% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 17 through 30 Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 73 through 84 Processing helix chain 'B' and resid 102 through 113 removed outlier: 4.256A pdb=" N GLU B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.928A pdb=" N PHE B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 255 removed outlier: 5.244A pdb=" N TRP B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 296 Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 73 through 84 Processing helix chain 'A' and resid 102 through 113 removed outlier: 4.256A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 147 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.928A pdb=" N PHE A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 255 removed outlier: 5.243A pdb=" N TRP A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 296 Processing helix chain 'C' and resid 17 through 30 Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 102 through 113 removed outlier: 4.256A pdb=" N GLU C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 147 Processing helix chain 'C' and resid 163 through 171 Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 208 through 224 removed outlier: 3.927A pdb=" N PHE C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 255 removed outlier: 5.243A pdb=" N TRP C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N THR C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 296 Processing helix chain 'D' and resid 17 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 73 through 84 Processing helix chain 'D' and resid 102 through 113 removed outlier: 4.257A pdb=" N GLU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 147 Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'D' and resid 178 through 186 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.929A pdb=" N PHE D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 255 removed outlier: 5.244A pdb=" N TRP D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 296 Processing sheet with id=AA1, first strand: chain 'B' and resid 190 through 195 removed outlier: 5.647A pdb=" N PHE B 158 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ARG B 122 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLY B 156 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG B 159 " --> pdb=" O PRO B 92 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 5 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE B 39 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 7 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL B 41 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 9 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS B 64 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 38 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B 66 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS B 40 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU B 68 " --> pdb=" O CYS B 40 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B 42 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 65 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU A 306 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN B 67 " --> pdb=" O SER A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 303 through 307 removed outlier: 7.029A pdb=" N ASN C 67 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 306 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 65 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS C 64 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 38 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 66 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS C 40 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU C 68 " --> pdb=" O CYS C 40 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C 42 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 5 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE C 39 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 7 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 41 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 9 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG C 159 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLY C 156 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ARG C 122 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE C 158 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 195 removed outlier: 5.647A pdb=" N PHE A 158 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ARG A 122 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLY A 156 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG A 159 " --> pdb=" O PRO A 92 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 5 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 39 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 7 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 41 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A 9 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS A 64 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE A 38 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 66 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS A 40 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU A 68 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A 42 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 65 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU D 306 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN A 67 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 303 through 307 removed outlier: 7.024A pdb=" N ASN D 67 " --> pdb=" O SER C 304 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU C 306 " --> pdb=" O ILE D 65 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 65 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LYS D 64 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE D 38 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL D 66 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS D 40 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU D 68 " --> pdb=" O CYS D 40 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN D 42 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU D 5 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE D 39 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE D 7 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL D 41 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 9 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG D 159 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N GLY D 156 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ARG D 122 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE D 158 " --> pdb=" O ALA D 120 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1680 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: 1.44 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1608 1.29 - 1.42: 2740 1.42 - 1.55: 6092 1.55 - 1.68: 24 1.68 - 1.81: 60 Bond restraints: 10524 Sorted by residual: bond pdb=" C4C UPG C 401 " pdb=" O4C UPG C 401 " ideal model delta sigma weight residual 1.431 1.671 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C4C UPG B 401 " pdb=" O4C UPG B 401 " ideal model delta sigma weight residual 1.431 1.671 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C4C UPG D 401 " pdb=" O4C UPG D 401 " ideal model delta sigma weight residual 1.431 1.671 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C4C UPG A 401 " pdb=" O4C UPG A 401 " ideal model delta sigma weight residual 1.431 1.671 -0.240 2.00e-02 2.50e+03 1.43e+02 bond pdb=" O02 5TR C 402 " pdb=" P01 5TR C 402 " ideal model delta sigma weight residual 1.824 1.620 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 10519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 14108 3.28 - 6.57: 136 6.57 - 9.85: 16 9.85 - 13.13: 20 13.13 - 16.41: 4 Bond angle restraints: 14284 Sorted by residual: angle pdb=" O04 5TR D 402 " pdb=" P01 5TR D 402 " pdb=" O05 5TR D 402 " ideal model delta sigma weight residual 129.39 112.98 16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" O04 5TR A 402 " pdb=" P01 5TR A 402 " pdb=" O05 5TR A 402 " ideal model delta sigma weight residual 129.39 113.02 16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O04 5TR C 402 " pdb=" P01 5TR C 402 " pdb=" O05 5TR C 402 " ideal model delta sigma weight residual 129.39 113.02 16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O04 5TR B 402 " pdb=" P01 5TR B 402 " pdb=" O05 5TR B 402 " ideal model delta sigma weight residual 129.39 113.03 16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" O1B UPG D 401 " pdb=" PB UPG D 401 " pdb=" O2B UPG D 401 " ideal model delta sigma weight residual 122.19 109.19 13.00 3.00e+00 1.11e-01 1.88e+01 ... (remaining 14279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.91: 5620 23.91 - 47.81: 580 47.81 - 71.72: 132 71.72 - 95.62: 36 95.62 - 119.53: 16 Dihedral angle restraints: 6384 sinusoidal: 2788 harmonic: 3596 Sorted by residual: dihedral pdb=" CD ARG B 197 " pdb=" NE ARG B 197 " pdb=" CZ ARG B 197 " pdb=" NH1 ARG B 197 " ideal model delta sinusoidal sigma weight residual 0.00 -72.85 72.85 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CD ARG A 197 " pdb=" NE ARG A 197 " pdb=" CZ ARG A 197 " pdb=" NH1 ARG A 197 " ideal model delta sinusoidal sigma weight residual 0.00 -72.79 72.79 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CD ARG C 197 " pdb=" NE ARG C 197 " pdb=" CZ ARG C 197 " pdb=" NH1 ARG C 197 " ideal model delta sinusoidal sigma weight residual 0.00 -72.79 72.79 1 1.00e+01 1.00e-02 6.76e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1340 0.060 - 0.120: 226 0.120 - 0.179: 18 0.179 - 0.239: 8 0.239 - 0.299: 8 Chirality restraints: 1600 Sorted by residual: chirality pdb=" CG LEU D 243 " pdb=" CB LEU D 243 " pdb=" CD1 LEU D 243 " pdb=" CD2 LEU D 243 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CG LEU A 243 " pdb=" CB LEU A 243 " pdb=" CD1 LEU A 243 " pdb=" CD2 LEU A 243 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU C 243 " pdb=" CB LEU C 243 " pdb=" CD1 LEU C 243 " pdb=" CD2 LEU C 243 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1597 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " -1.053 9.50e-02 1.11e+02 4.72e-01 1.35e+02 pdb=" NE ARG B 197 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 197 " 1.053 9.50e-02 1.11e+02 4.72e-01 1.34e+02 pdb=" NE ARG C 197 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 197 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 197 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 197 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 197 " -1.052 9.50e-02 1.11e+02 4.72e-01 1.34e+02 pdb=" NE ARG A 197 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 197 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 197 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 197 " -0.022 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 68 2.41 - 3.03: 6245 3.03 - 3.65: 15723 3.65 - 4.28: 23403 4.28 - 4.90: 39912 Nonbonded interactions: 85351 Sorted by model distance: nonbonded pdb=" OD2 ASP A 96 " pdb="MG MG A 403 " model vdw 1.781 2.170 nonbonded pdb=" OD2 ASP B 96 " pdb="MG MG B 403 " model vdw 1.782 2.170 nonbonded pdb=" OD2 ASP D 96 " pdb="MG MG D 403 " model vdw 1.782 2.170 nonbonded pdb=" OD2 ASP C 96 " pdb="MG MG C 403 " model vdw 1.782 2.170 nonbonded pdb=" O2B UPG B 401 " pdb="MG MG B 403 " model vdw 1.830 2.170 ... (remaining 85346 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 : 0.012 0.240 10524 Z= 0.593 Angle : 0.913 16.413 14284 Z= 0.407 Chirality : 0.049 0.299 1600 Planarity : 0.025 0.472 1748 Dihedral : 21.056 119.527 4072 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.84 % Allowed : 23.53 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.25), residues: 1208 helix: 2.00 (0.20), residues: 676 sheet: -0.66 (0.39), residues: 164 loop : -0.82 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 159 TYR 0.011 0.001 TYR D 292 PHE 0.007 0.001 PHE B 223 TRP 0.017 0.002 TRP C 231 HIS 0.004 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.01172 (10524) covalent geometry : angle 0.91257 (14284) hydrogen bonds : bond 0.11977 ( 560) hydrogen bonds : angle 5.57646 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.332 Fit side-chains REVERT: B 98 GLN cc_start: 0.7100 (tt0) cc_final: 0.6758 (tt0) REVERT: A 98 GLN cc_start: 0.7100 (tt0) cc_final: 0.6758 (tt0) REVERT: C 98 GLN cc_start: 0.7224 (tt0) cc_final: 0.6799 (tt0) REVERT: D 98 GLN cc_start: 0.7120 (tt0) cc_final: 0.6758 (tt0) outliers start: 20 outliers final: 0 residues processed: 173 average time/residue: 0.0918 time to fit residues: 23.1778 Evaluate side-chains 139 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.183566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151747 restraints weight = 14218.417| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.05 r_work: 0.3748 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10524 Z= 0.132 Angle : 0.567 6.896 14284 Z= 0.276 Chirality : 0.046 0.239 1600 Planarity : 0.004 0.037 1748 Dihedral : 16.291 90.175 1636 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.56 % Allowed : 18.01 % 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: 1.42 (0.25), residues: 1208 helix: 2.31 (0.20), residues: 656 sheet: -0.60 (0.39), residues: 164 loop : -0.75 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 197 TYR 0.007 0.001 TYR C 209 PHE 0.008 0.001 PHE C 223 TRP 0.022 0.001 TRP C 307 HIS 0.001 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00291 (10524) covalent geometry : angle 0.56709 (14284) hydrogen bonds : bond 0.03905 ( 560) hydrogen bonds : angle 4.10429 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.392 Fit side-chains REVERT: B 197 ARG cc_start: 0.5671 (ttm110) cc_final: 0.5428 (ttm110) REVERT: A 197 ARG cc_start: 0.5676 (ttm110) cc_final: 0.5429 (ttm110) REVERT: C 197 ARG cc_start: 0.5686 (ttm110) cc_final: 0.5455 (ttm110) REVERT: D 197 ARG cc_start: 0.5668 (ttm110) cc_final: 0.5424 (ttm110) outliers start: 17 outliers final: 12 residues processed: 166 average time/residue: 0.0920 time to fit residues: 22.5641 Evaluate side-chains 159 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 271 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN A 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.181349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149774 restraints weight = 14364.170| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.05 r_work: 0.3725 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10524 Z= 0.134 Angle : 0.549 8.626 14284 Z= 0.262 Chirality : 0.046 0.292 1600 Planarity : 0.004 0.036 1748 Dihedral : 14.340 82.689 1636 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.30 % Allowed : 21.05 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.25), residues: 1208 helix: 2.41 (0.20), residues: 660 sheet: -0.87 (0.37), residues: 164 loop : -0.52 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 125 TYR 0.008 0.001 TYR D 263 PHE 0.005 0.001 PHE C 223 TRP 0.010 0.001 TRP B 307 HIS 0.001 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00304 (10524) covalent geometry : angle 0.54913 (14284) hydrogen bonds : bond 0.03712 ( 560) hydrogen bonds : angle 3.87742 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.292 Fit side-chains REVERT: B 98 GLN cc_start: 0.7734 (tt0) cc_final: 0.7407 (tt0) REVERT: B 163 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7536 (tpt170) REVERT: B 197 ARG cc_start: 0.6023 (ttm110) cc_final: 0.5761 (ttm110) REVERT: B 294 GLU cc_start: 0.7423 (tp30) cc_final: 0.7127 (mm-30) REVERT: A 98 GLN cc_start: 0.7723 (tt0) cc_final: 0.7398 (tt0) REVERT: A 163 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7466 (tpt170) REVERT: A 197 ARG cc_start: 0.6032 (ttm110) cc_final: 0.5774 (ttm110) REVERT: A 294 GLU cc_start: 0.7403 (tp30) cc_final: 0.7096 (mm-30) REVERT: C 98 GLN cc_start: 0.7671 (tt0) cc_final: 0.7398 (tt0) REVERT: C 163 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7540 (tpt170) REVERT: C 197 ARG cc_start: 0.5980 (ttm110) cc_final: 0.5767 (ttm110) REVERT: C 294 GLU cc_start: 0.7426 (tp30) cc_final: 0.7079 (mm-30) REVERT: D 163 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7591 (tpt170) REVERT: D 197 ARG cc_start: 0.6056 (ttm110) cc_final: 0.5852 (ttm110) REVERT: D 294 GLU cc_start: 0.7406 (tp30) cc_final: 0.7100 (mm-30) outliers start: 25 outliers final: 13 residues processed: 182 average time/residue: 0.0879 time to fit residues: 23.4729 Evaluate side-chains 157 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 163 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN D 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.172796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142108 restraints weight = 14420.345| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.90 r_work: 0.3653 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10524 Z= 0.217 Angle : 0.614 8.038 14284 Z= 0.297 Chirality : 0.049 0.341 1600 Planarity : 0.004 0.037 1748 Dihedral : 12.805 88.068 1636 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 3.58 % Allowed : 20.04 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1208 helix: 2.15 (0.20), residues: 660 sheet: -1.17 (0.37), residues: 164 loop : -0.65 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 125 TYR 0.009 0.001 TYR C 287 PHE 0.010 0.001 PHE B 178 TRP 0.027 0.002 TRP B 307 HIS 0.002 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00521 (10524) covalent geometry : angle 0.61363 (14284) hydrogen bonds : bond 0.03922 ( 560) hydrogen bonds : angle 3.92357 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.423 Fit side-chains REVERT: B 98 GLN cc_start: 0.7860 (tt0) cc_final: 0.7625 (tt0) REVERT: B 129 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7028 (p) REVERT: B 163 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7489 (tpt170) REVERT: A 98 GLN cc_start: 0.7879 (tt0) cc_final: 0.7640 (tt0) REVERT: A 129 THR cc_start: 0.7453 (OUTLIER) cc_final: 0.7065 (p) REVERT: A 163 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7471 (tpt170) REVERT: C 60 ASN cc_start: 0.8282 (t0) cc_final: 0.8076 (t0) REVERT: C 98 GLN cc_start: 0.7824 (tt0) cc_final: 0.7621 (tt0) REVERT: C 163 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7468 (tpt170) REVERT: D 129 THR cc_start: 0.7411 (OUTLIER) cc_final: 0.7035 (p) REVERT: D 163 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8320 (tpp-160) REVERT: D 197 ARG cc_start: 0.6331 (ttm110) cc_final: 0.6083 (ttm110) outliers start: 39 outliers final: 21 residues processed: 189 average time/residue: 0.0985 time to fit residues: 26.8852 Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN A 126 GLN C 126 GLN D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.176563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.149853 restraints weight = 14153.847| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.63 r_work: 0.3735 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10524 Z= 0.114 Angle : 0.533 10.742 14284 Z= 0.254 Chirality : 0.046 0.305 1600 Planarity : 0.005 0.064 1748 Dihedral : 11.771 85.450 1636 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.82 % Favored : 98.01 % Rotamer: Outliers : 2.94 % Allowed : 20.96 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.25), residues: 1208 helix: 2.35 (0.19), residues: 660 sheet: -1.03 (0.37), residues: 164 loop : -0.55 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 125 TYR 0.008 0.001 TYR A 263 PHE 0.005 0.001 PHE C 223 TRP 0.018 0.001 TRP D 307 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00252 (10524) covalent geometry : angle 0.53315 (14284) hydrogen bonds : bond 0.03549 ( 560) hydrogen bonds : angle 3.75484 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.379 Fit side-chains REVERT: B 98 GLN cc_start: 0.7836 (tt0) cc_final: 0.7621 (tt0) REVERT: B 129 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7202 (p) REVERT: B 197 ARG cc_start: 0.6044 (ttm110) cc_final: 0.5787 (ttm110) REVERT: A 98 GLN cc_start: 0.7832 (tt0) cc_final: 0.7624 (tt0) REVERT: A 129 THR cc_start: 0.7526 (OUTLIER) cc_final: 0.7241 (p) REVERT: A 197 ARG cc_start: 0.6016 (ttm110) cc_final: 0.5763 (ttm110) REVERT: A 294 GLU cc_start: 0.7381 (tp30) cc_final: 0.7170 (mm-30) REVERT: C 197 ARG cc_start: 0.5997 (ttm110) cc_final: 0.5746 (ttm110) REVERT: C 294 GLU cc_start: 0.7380 (tp30) cc_final: 0.7172 (mm-30) REVERT: D 129 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7203 (p) REVERT: D 197 ARG cc_start: 0.6216 (ttm110) cc_final: 0.5998 (ttm110) REVERT: D 278 LEU cc_start: 0.8709 (mt) cc_final: 0.8307 (mt) REVERT: D 294 GLU cc_start: 0.7395 (tp30) cc_final: 0.7187 (mm-30) outliers start: 32 outliers final: 15 residues processed: 181 average time/residue: 0.0871 time to fit residues: 23.8212 Evaluate side-chains 167 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 149 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN A 126 GLN C 126 GLN D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.176297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147140 restraints weight = 14507.521| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.79 r_work: 0.3724 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10524 Z= 0.116 Angle : 0.522 10.943 14284 Z= 0.249 Chirality : 0.044 0.301 1600 Planarity : 0.004 0.052 1748 Dihedral : 10.937 80.686 1636 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.82 % Favored : 97.85 % Rotamer: Outliers : 2.76 % Allowed : 22.33 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1208 helix: 2.41 (0.19), residues: 660 sheet: -0.87 (0.37), residues: 164 loop : -0.57 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 125 TYR 0.006 0.001 TYR D 263 PHE 0.015 0.001 PHE B 223 TRP 0.012 0.001 TRP B 307 HIS 0.001 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00262 (10524) covalent geometry : angle 0.52233 (14284) hydrogen bonds : bond 0.03420 ( 560) hydrogen bonds : angle 3.67125 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.424 Fit side-chains REVERT: B 98 GLN cc_start: 0.7822 (tt0) cc_final: 0.7615 (tt0) REVERT: B 129 THR cc_start: 0.7472 (OUTLIER) cc_final: 0.7183 (p) REVERT: B 197 ARG cc_start: 0.6044 (ttm110) cc_final: 0.5779 (ttm110) REVERT: B 294 GLU cc_start: 0.7378 (tp30) cc_final: 0.7174 (mm-30) REVERT: A 129 THR cc_start: 0.7441 (OUTLIER) cc_final: 0.7175 (p) REVERT: A 197 ARG cc_start: 0.6014 (ttm110) cc_final: 0.5762 (ttm110) REVERT: A 294 GLU cc_start: 0.7374 (tp30) cc_final: 0.7164 (mm-30) REVERT: C 197 ARG cc_start: 0.6076 (ttm110) cc_final: 0.5850 (ttm110) REVERT: C 294 GLU cc_start: 0.7378 (tp30) cc_final: 0.7175 (mm-30) REVERT: D 129 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7226 (p) REVERT: D 294 GLU cc_start: 0.7387 (tp30) cc_final: 0.7177 (mm-30) outliers start: 30 outliers final: 22 residues processed: 192 average time/residue: 0.0902 time to fit residues: 25.8094 Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN A 126 GLN C 126 GLN D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.169389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140314 restraints weight = 14785.691| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.71 r_work: 0.3660 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 10524 Z= 0.322 Angle : 0.684 10.243 14284 Z= 0.339 Chirality : 0.050 0.293 1600 Planarity : 0.006 0.055 1748 Dihedral : 10.990 83.011 1636 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.31 % Favored : 96.36 % Rotamer: Outliers : 4.04 % Allowed : 22.79 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.25), residues: 1208 helix: 1.87 (0.20), residues: 660 sheet: -1.54 (0.38), residues: 152 loop : -1.07 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 197 TYR 0.010 0.002 TYR C 301 PHE 0.013 0.002 PHE C 178 TRP 0.026 0.002 TRP C 307 HIS 0.002 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00775 (10524) covalent geometry : angle 0.68408 (14284) hydrogen bonds : bond 0.04136 ( 560) hydrogen bonds : angle 4.06288 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.435 Fit side-chains REVERT: B 129 THR cc_start: 0.7624 (OUTLIER) cc_final: 0.7396 (p) REVERT: B 163 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7335 (tpt170) REVERT: A 129 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.7382 (p) REVERT: A 163 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7344 (tpt170) REVERT: A 197 ARG cc_start: 0.6399 (ttm110) cc_final: 0.6167 (ttm110) REVERT: C 163 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7333 (tpt170) REVERT: D 129 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.7385 (p) REVERT: D 163 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7321 (tpt170) outliers start: 44 outliers final: 32 residues processed: 176 average time/residue: 0.0930 time to fit residues: 23.8268 Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 163 ARG Chi-restraints excluded: chain D residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.177117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.149246 restraints weight = 14606.282| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.65 r_work: 0.3730 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10524 Z= 0.123 Angle : 0.533 11.814 14284 Z= 0.259 Chirality : 0.044 0.314 1600 Planarity : 0.005 0.063 1748 Dihedral : 10.472 78.360 1636 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.15 % Favored : 97.52 % Rotamer: Outliers : 2.76 % Allowed : 24.17 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.25), residues: 1208 helix: 2.19 (0.20), residues: 660 sheet: -1.26 (0.38), residues: 152 loop : -0.94 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 197 TYR 0.010 0.001 TYR D 292 PHE 0.009 0.001 PHE C 223 TRP 0.028 0.001 TRP C 307 HIS 0.001 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00282 (10524) covalent geometry : angle 0.53330 (14284) hydrogen bonds : bond 0.03568 ( 560) hydrogen bonds : angle 3.78971 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.423 Fit side-chains outliers start: 30 outliers final: 19 residues processed: 162 average time/residue: 0.0812 time to fit residues: 20.5816 Evaluate side-chains 164 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 149 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN A 126 GLN C 42 ASN C 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.177606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.149116 restraints weight = 14578.509| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.69 r_work: 0.3753 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10524 Z= 0.113 Angle : 0.525 11.844 14284 Z= 0.253 Chirality : 0.043 0.328 1600 Planarity : 0.005 0.053 1748 Dihedral : 10.030 75.442 1636 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.90 % Favored : 97.76 % Rotamer: Outliers : 2.39 % Allowed : 24.72 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1208 helix: 2.32 (0.19), residues: 660 sheet: -0.96 (0.39), residues: 152 loop : -0.87 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 197 TYR 0.012 0.001 TYR D 292 PHE 0.011 0.001 PHE C 223 TRP 0.026 0.002 TRP C 307 HIS 0.001 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00258 (10524) covalent geometry : angle 0.52487 (14284) hydrogen bonds : bond 0.03386 ( 560) hydrogen bonds : angle 3.70900 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.450 Fit side-chains outliers start: 26 outliers final: 23 residues processed: 165 average time/residue: 0.0773 time to fit residues: 20.3246 Evaluate side-chains 174 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 149 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 11 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 ASN C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.173022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.144404 restraints weight = 14620.310| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.68 r_work: 0.3705 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10524 Z= 0.197 Angle : 0.594 11.523 14284 Z= 0.291 Chirality : 0.046 0.329 1600 Planarity : 0.005 0.056 1748 Dihedral : 10.088 76.778 1636 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.99 % Favored : 97.68 % Rotamer: Outliers : 2.76 % Allowed : 24.63 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.25), residues: 1208 helix: 2.13 (0.19), residues: 660 sheet: -0.98 (0.40), residues: 152 loop : -1.08 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 197 TYR 0.017 0.002 TYR D 292 PHE 0.010 0.001 PHE D 178 TRP 0.020 0.001 TRP C 307 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00474 (10524) covalent geometry : angle 0.59393 (14284) hydrogen bonds : bond 0.03665 ( 560) hydrogen bonds : angle 3.85376 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.397 Fit side-chains REVERT: B 179 MET cc_start: 0.7921 (mmm) cc_final: 0.7479 (mmp) REVERT: A 179 MET cc_start: 0.7921 (mmm) cc_final: 0.7489 (mmp) REVERT: A 197 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5926 (mtm110) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.0818 time to fit residues: 20.1936 Evaluate side-chains 165 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 149 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 GLN A 126 GLN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.176875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148478 restraints weight = 14584.961| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.69 r_work: 0.3750 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10524 Z= 0.124 Angle : 0.564 11.519 14284 Z= 0.275 Chirality : 0.044 0.318 1600 Planarity : 0.004 0.049 1748 Dihedral : 9.839 75.538 1636 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.48 % Favored : 97.19 % Rotamer: Outliers : 2.67 % Allowed : 25.00 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1208 helix: 2.25 (0.19), residues: 660 sheet: -0.82 (0.40), residues: 152 loop : -0.94 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 197 TYR 0.018 0.001 TYR B 292 PHE 0.009 0.001 PHE C 223 TRP 0.025 0.001 TRP C 307 HIS 0.001 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00290 (10524) covalent geometry : angle 0.56410 (14284) hydrogen bonds : bond 0.03441 ( 560) hydrogen bonds : angle 3.78132 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.55 seconds wall clock time: 38 minutes 29.11 seconds (2309.11 seconds total)