Starting phenix.real_space_refine on Mon Jul 28 05:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s5t_24839/07_2025/7s5t_24839.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5t_24839/07_2025/7s5t_24839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s5t_24839/07_2025/7s5t_24839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5t_24839/07_2025/7s5t_24839.map" model { file = "/net/cci-nas-00/data/ceres_data/7s5t_24839/07_2025/7s5t_24839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5t_24839/07_2025/7s5t_24839.cif" } resolution = 3.1 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= 0.065 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 K 2 8.98 5 S 64 5.16 5 C 6488 2.51 5 N 1720 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10078 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.42, per 1000 atoms: 0.54 Number of scatterers: 10078 At special positions: 0 Unit cell: (91, 89.7, 122.2, 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) K 2 19.00 S 64 16.00 O 1804 8.00 N 1720 7.00 C 6488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 34.8% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG A 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.670A pdb=" N THR A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG A 176 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 178 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.809A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG B 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.670A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG B 176 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 178 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.809A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 333 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.784A pdb=" N ARG C 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 65 removed outlier: 3.668A pdb=" N THR C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 142 through 172 removed outlier: 3.558A pdb=" N ILE C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG C 176 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA C 178 " --> pdb=" O HIS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'D' and resid 51 through 57 removed outlier: 3.783A pdb=" N ARG D 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.669A pdb=" N THR D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 142 through 172 removed outlier: 3.557A pdb=" N ILE D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.042A pdb=" N ARG D 176 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 178 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.810A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 346 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR A 223 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR B 223 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 213 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU B 288 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE B 215 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 286 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET B 217 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 284 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 219 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU B 282 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AB2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.774A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR C 223 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 213 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU C 288 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE C 215 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 286 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET C 217 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 284 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL C 219 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU C 282 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB7, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.773A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 230 through 238 removed outlier: 5.064A pdb=" N THR D 223 " --> pdb=" O PRO D 232 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA D 213 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU D 288 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D 215 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 286 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N MET D 217 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 284 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL D 219 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU D 282 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'D' and resid 319 through 322 447 hydrogen bonds defined for protein. 1224 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: 2.73 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3272 1.34 - 1.46: 2071 1.46 - 1.57: 4857 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 10304 Sorted by residual: bond pdb=" CB GLU D 104 " pdb=" CG GLU D 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.03e+00 bond pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.98e+00 bond pdb=" CG GLU A 104 " pdb=" CD GLU A 104 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 13302 1.29 - 2.58: 580 2.58 - 3.88: 62 3.88 - 5.17: 41 5.17 - 6.46: 23 Bond angle restraints: 14008 Sorted by residual: angle pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " pdb=" CD GLU B 104 " ideal model delta sigma weight residual 112.60 118.72 -6.12 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " pdb=" CD GLU C 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " pdb=" CD GLU A 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CB GLU D 104 " pdb=" CG GLU D 104 " pdb=" CD GLU D 104 " ideal model delta sigma weight residual 112.60 118.71 -6.11 1.70e+00 3.46e-01 1.29e+01 angle pdb=" CA GLU C 104 " pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 5494 16.98 - 33.95: 446 33.95 - 50.93: 120 50.93 - 67.91: 52 67.91 - 84.88: 16 Dihedral angle restraints: 6128 sinusoidal: 2412 harmonic: 3716 Sorted by residual: dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.06 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS D 110 " pdb=" SG CYS D 110 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.07 -73.93 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C 110 " pdb=" SG CYS C 110 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual -86.00 -12.08 -73.92 1 1.00e+01 1.00e-02 6.94e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 834 0.029 - 0.058: 487 0.058 - 0.086: 148 0.086 - 0.115: 145 0.115 - 0.144: 38 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB ILE B 210 " pdb=" CA ILE B 210 " pdb=" CG1 ILE B 210 " pdb=" CG2 ILE B 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CB ILE D 210 " pdb=" CA ILE D 210 " pdb=" CG1 ILE D 210 " pdb=" CG2 ILE D 210 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1649 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 68 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 69 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 69 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 69 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 68 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B 69 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 68 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 69 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 69 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 69 " -0.022 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 3141 2.83 - 3.41: 10274 3.41 - 3.98: 19076 3.98 - 4.56: 26741 4.56 - 5.14: 40974 Nonbonded interactions: 100206 Sorted by model distance: nonbonded pdb=" O PRO C 109 " pdb=" OG1 THR C 139 " model vdw 2.252 3.040 nonbonded pdb=" O PRO B 109 " pdb=" OG1 THR B 139 " model vdw 2.252 3.040 nonbonded pdb=" O PRO D 109 " pdb=" OG1 THR D 139 " model vdw 2.252 3.040 nonbonded pdb=" O PRO A 109 " pdb=" OG1 THR A 139 " model vdw 2.253 3.040 nonbonded pdb=" OE2 GLU C 140 " pdb=" OG SER D 119 " model vdw 2.263 3.040 ... (remaining 100201 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 32 through 352) selection = chain 'B' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 23.410 Find NCS groups from input model: 0.370 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.005 0.043 10308 Z= 0.235 Angle : 0.679 6.459 14016 Z= 0.398 Chirality : 0.048 0.144 1652 Planarity : 0.005 0.039 1764 Dihedral : 15.459 84.882 3700 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.68 % Allowed : 16.19 % Favored : 79.14 % 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: -2.41 (0.19), residues: 1276 helix: -1.26 (0.21), residues: 396 sheet: -1.35 (0.31), residues: 256 loop : -1.87 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 311 HIS 0.003 0.001 HIS D 175 PHE 0.015 0.002 PHE B 75 TYR 0.007 0.001 TYR A 258 ARG 0.002 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.15100 ( 439) hydrogen bonds : angle 5.16719 ( 1224) SS BOND : bond 0.00228 ( 4) SS BOND : angle 1.78093 ( 8) covalent geometry : bond 0.00514 (10304) covalent geometry : angle 0.67748 (14008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8742 (mtmm) REVERT: A 47 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8228 (mtpp) REVERT: A 332 LYS cc_start: 0.9210 (mttt) cc_final: 0.8944 (mtpp) REVERT: B 110 CYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6448 (m) REVERT: B 137 MET cc_start: 0.9032 (ptt) cc_final: 0.8364 (ptm) REVERT: B 169 MET cc_start: 0.8866 (ttm) cc_final: 0.8451 (ttm) REVERT: B 185 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8659 (ttpt) REVERT: B 222 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8628 (ttpp) REVERT: B 225 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7555 (p) REVERT: C 67 LYS cc_start: 0.7945 (mttp) cc_final: 0.7208 (mmmt) REVERT: C 88 MET cc_start: 0.7668 (mtt) cc_final: 0.7462 (mtt) REVERT: C 102 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7666 (Cg_exo) REVERT: C 185 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8477 (tptt) REVERT: C 240 MET cc_start: 0.9007 (ttp) cc_final: 0.8788 (ttp) REVERT: C 304 TYR cc_start: 0.9174 (m-80) cc_final: 0.8871 (m-80) REVERT: D 47 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7880 (mmtt) REVERT: D 67 LYS cc_start: 0.7763 (mttp) cc_final: 0.7460 (mtmt) REVERT: D 102 PRO cc_start: 0.7467 (Cg_endo) cc_final: 0.7149 (Cg_exo) REVERT: D 199 MET cc_start: 0.9054 (mtm) cc_final: 0.8827 (mtp) REVERT: D 217 MET cc_start: 0.8874 (mtm) cc_final: 0.8635 (mtm) outliers start: 52 outliers final: 27 residues processed: 215 average time/residue: 0.2453 time to fit residues: 72.4877 Evaluate side-chains 161 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 110 CYS Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 160 ASN A 218 GLN A 276 HIS A 277 HIS B 48 ASN B 218 GLN B 276 HIS B 348 GLN C 41 ASN C 218 GLN C 276 HIS C 348 GLN D 48 ASN D 218 GLN D 264 ASN D 276 HIS D 277 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.090501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.079597 restraints weight = 16117.564| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.18 r_work: 0.2860 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10308 Z= 0.122 Angle : 0.484 7.339 14016 Z= 0.262 Chirality : 0.044 0.130 1652 Planarity : 0.003 0.031 1764 Dihedral : 6.430 75.646 1403 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.24 % Allowed : 15.92 % Favored : 80.85 % 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 (0.23), residues: 1276 helix: 0.74 (0.26), residues: 400 sheet: -1.06 (0.31), residues: 252 loop : -1.04 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 68 HIS 0.002 0.000 HIS B 276 PHE 0.014 0.001 PHE C 75 TYR 0.007 0.001 TYR A 330 ARG 0.003 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 439) hydrogen bonds : angle 4.16775 ( 1224) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.49952 ( 8) covalent geometry : bond 0.00268 (10304) covalent geometry : angle 0.48331 (14008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.041 Fit side-chains REVERT: A 67 LYS cc_start: 0.8537 (mttp) cc_final: 0.7855 (mmmt) REVERT: A 77 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8510 (mpp) REVERT: A 140 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: A 247 ASN cc_start: 0.8683 (p0) cc_final: 0.8472 (p0) REVERT: A 258 TYR cc_start: 0.9150 (p90) cc_final: 0.8653 (p90) REVERT: A 268 TYR cc_start: 0.9260 (t80) cc_final: 0.8908 (t80) REVERT: B 47 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8033 (mmmt) REVERT: B 50 ARG cc_start: 0.6733 (mmt-90) cc_final: 0.6427 (mmp80) REVERT: B 137 MET cc_start: 0.9368 (ptt) cc_final: 0.8902 (ptm) REVERT: B 160 ASN cc_start: 0.8860 (m-40) cc_final: 0.8614 (m-40) REVERT: B 169 MET cc_start: 0.9076 (ttm) cc_final: 0.8687 (ttm) REVERT: B 185 LYS cc_start: 0.9145 (ttpp) cc_final: 0.8628 (ttpt) REVERT: B 222 LYS cc_start: 0.9319 (ttmt) cc_final: 0.9019 (ttpp) REVERT: B 258 TYR cc_start: 0.9157 (p90) cc_final: 0.8883 (p90) REVERT: B 334 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8919 (m-30) REVERT: C 67 LYS cc_start: 0.8438 (mttp) cc_final: 0.7718 (mmmt) REVERT: C 185 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8672 (tptt) REVERT: C 207 LYS cc_start: 0.8970 (tptm) cc_final: 0.8753 (tptt) REVERT: C 304 TYR cc_start: 0.9397 (m-80) cc_final: 0.9169 (m-80) REVERT: C 334 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: D 47 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8251 (mmtm) REVERT: D 67 LYS cc_start: 0.8399 (mttp) cc_final: 0.8034 (mtmt) REVERT: D 93 ILE cc_start: 0.9403 (mm) cc_final: 0.9187 (mt) REVERT: D 199 MET cc_start: 0.9331 (mtm) cc_final: 0.9123 (mtp) REVERT: D 338 LYS cc_start: 0.8612 (mtpp) cc_final: 0.7843 (tptt) outliers start: 36 outliers final: 15 residues processed: 175 average time/residue: 0.2450 time to fit residues: 57.8667 Evaluate side-chains 151 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 0.7980 chunk 113 optimal weight: 0.2980 chunk 106 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 234 HIS A 235 GLN B 277 HIS C 41 ASN D 235 GLN D 277 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.090209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.079662 restraints weight = 16280.752| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.05 r_work: 0.2846 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10308 Z= 0.142 Angle : 0.472 5.737 14016 Z= 0.254 Chirality : 0.044 0.133 1652 Planarity : 0.003 0.031 1764 Dihedral : 5.586 50.454 1384 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.69 % Allowed : 16.19 % Favored : 80.13 % 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: -0.07 (0.24), residues: 1276 helix: 1.55 (0.27), residues: 400 sheet: -0.88 (0.31), residues: 252 loop : -0.69 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.002 0.001 HIS C 276 PHE 0.014 0.001 PHE C 75 TYR 0.005 0.001 TYR B 330 ARG 0.002 0.000 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 439) hydrogen bonds : angle 3.94924 ( 1224) SS BOND : bond 0.00236 ( 4) SS BOND : angle 1.47740 ( 8) covalent geometry : bond 0.00325 (10304) covalent geometry : angle 0.47035 (14008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.125 Fit side-chains REVERT: A 67 LYS cc_start: 0.8534 (mttp) cc_final: 0.7869 (mmmt) REVERT: A 77 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8476 (mpp) REVERT: A 160 ASN cc_start: 0.8700 (m-40) cc_final: 0.8212 (m110) REVERT: A 268 TYR cc_start: 0.9262 (t80) cc_final: 0.8900 (t80) REVERT: B 47 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8037 (mmmt) REVERT: B 137 MET cc_start: 0.9344 (ptt) cc_final: 0.8861 (ptm) REVERT: B 169 MET cc_start: 0.9066 (ttm) cc_final: 0.8839 (ttm) REVERT: B 185 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8582 (ttpt) REVERT: B 222 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9027 (ttpp) REVERT: B 258 TYR cc_start: 0.9109 (p90) cc_final: 0.8502 (p90) REVERT: B 277 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7372 (t70) REVERT: B 334 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8912 (m-30) REVERT: C 67 LYS cc_start: 0.8489 (mttp) cc_final: 0.7743 (mmmt) REVERT: C 185 LYS cc_start: 0.9058 (ttpp) cc_final: 0.8651 (tptt) REVERT: C 207 LYS cc_start: 0.8976 (tptm) cc_final: 0.8647 (tptt) REVERT: C 304 TYR cc_start: 0.9390 (m-80) cc_final: 0.9098 (m-80) REVERT: C 334 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8533 (m-30) REVERT: D 47 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8264 (mttm) REVERT: D 57 GLN cc_start: 0.8508 (mt0) cc_final: 0.8095 (mm-40) REVERT: D 67 LYS cc_start: 0.8410 (mttp) cc_final: 0.8048 (mtmt) REVERT: D 93 ILE cc_start: 0.9385 (mm) cc_final: 0.9178 (mt) REVERT: D 199 MET cc_start: 0.9338 (mtm) cc_final: 0.9107 (mtp) REVERT: D 278 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7086 (m-70) REVERT: D 305 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8976 (mm) REVERT: D 338 LYS cc_start: 0.8551 (mtpp) cc_final: 0.7874 (tptt) outliers start: 41 outliers final: 19 residues processed: 175 average time/residue: 0.2639 time to fit residues: 61.8924 Evaluate side-chains 160 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 334 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 119 optimal weight: 0.0770 chunk 27 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN B 277 HIS C 41 ASN D 277 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.092204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.081655 restraints weight = 16174.895| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.01 r_work: 0.2877 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10308 Z= 0.129 Angle : 0.458 6.023 14016 Z= 0.247 Chirality : 0.044 0.193 1652 Planarity : 0.003 0.033 1764 Dihedral : 5.295 47.321 1383 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.42 % Allowed : 16.64 % Favored : 79.95 % 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: 0.42 (0.24), residues: 1276 helix: 1.81 (0.27), residues: 400 sheet: -0.31 (0.35), residues: 220 loop : -0.43 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 68 HIS 0.006 0.001 HIS B 277 PHE 0.014 0.001 PHE D 75 TYR 0.008 0.001 TYR A 258 ARG 0.001 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 439) hydrogen bonds : angle 3.89419 ( 1224) SS BOND : bond 0.00213 ( 4) SS BOND : angle 1.13977 ( 8) covalent geometry : bond 0.00291 (10304) covalent geometry : angle 0.45711 (14008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 1.084 Fit side-chains REVERT: A 67 LYS cc_start: 0.8636 (mttp) cc_final: 0.7997 (mmmt) REVERT: A 77 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8489 (mpp) REVERT: A 160 ASN cc_start: 0.8747 (m-40) cc_final: 0.8385 (m110) REVERT: A 258 TYR cc_start: 0.9030 (p90) cc_final: 0.8520 (p90) REVERT: A 268 TYR cc_start: 0.9235 (t80) cc_final: 0.8938 (t80) REVERT: B 47 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8146 (mmmt) REVERT: B 137 MET cc_start: 0.9355 (ptt) cc_final: 0.8901 (ptm) REVERT: B 160 ASN cc_start: 0.8733 (m-40) cc_final: 0.8525 (m110) REVERT: B 169 MET cc_start: 0.9084 (ttm) cc_final: 0.8860 (ttm) REVERT: B 185 LYS cc_start: 0.9071 (ttpp) cc_final: 0.8722 (ttpt) REVERT: B 258 TYR cc_start: 0.9045 (p90) cc_final: 0.8599 (p90) REVERT: C 67 LYS cc_start: 0.8594 (mttp) cc_final: 0.7890 (mmmt) REVERT: C 185 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8705 (tptt) REVERT: C 207 LYS cc_start: 0.8957 (tptm) cc_final: 0.8627 (tptt) REVERT: C 334 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8493 (m-30) REVERT: D 47 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8327 (mttm) REVERT: D 57 GLN cc_start: 0.8469 (mt0) cc_final: 0.8100 (mm-40) REVERT: D 67 LYS cc_start: 0.8508 (mttp) cc_final: 0.8155 (mtmt) REVERT: D 199 MET cc_start: 0.9334 (mtm) cc_final: 0.9094 (mtp) REVERT: D 278 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7109 (m-70) REVERT: D 305 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9109 (mm) REVERT: D 338 LYS cc_start: 0.8517 (mtpp) cc_final: 0.7902 (tptt) outliers start: 38 outliers final: 21 residues processed: 171 average time/residue: 0.2696 time to fit residues: 61.4798 Evaluate side-chains 164 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 HIS B 277 HIS C 41 ASN C 234 HIS ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS D 348 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.087408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.077151 restraints weight = 16465.823| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.91 r_work: 0.2801 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 10308 Z= 0.307 Angle : 0.578 6.026 14016 Z= 0.307 Chirality : 0.047 0.181 1652 Planarity : 0.003 0.035 1764 Dihedral : 5.294 50.445 1375 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.60 % Allowed : 16.82 % Favored : 79.59 % 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: 0.04 (0.24), residues: 1276 helix: 1.64 (0.27), residues: 400 sheet: -0.91 (0.31), residues: 256 loop : -0.57 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 311 HIS 0.005 0.001 HIS B 276 PHE 0.019 0.002 PHE A 117 TYR 0.009 0.002 TYR A 258 ARG 0.004 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 439) hydrogen bonds : angle 4.17461 ( 1224) SS BOND : bond 0.00383 ( 4) SS BOND : angle 1.44520 ( 8) covalent geometry : bond 0.00720 (10304) covalent geometry : angle 0.57728 (14008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.119 Fit side-chains REVERT: A 67 LYS cc_start: 0.8573 (mttp) cc_final: 0.7916 (mmmt) REVERT: A 77 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8508 (mpp) REVERT: B 47 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8213 (mmmt) REVERT: B 67 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8259 (mtpt) REVERT: B 137 MET cc_start: 0.9401 (ptt) cc_final: 0.8880 (ptm) REVERT: B 185 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8768 (ttpt) REVERT: B 222 LYS cc_start: 0.9359 (ttmm) cc_final: 0.8961 (ttpp) REVERT: C 67 LYS cc_start: 0.8543 (mttp) cc_final: 0.7791 (mmmt) REVERT: C 108 GLU cc_start: 0.8353 (pt0) cc_final: 0.8041 (pt0) REVERT: C 185 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8603 (tptt) REVERT: C 207 LYS cc_start: 0.8948 (tptm) cc_final: 0.8592 (tptt) REVERT: C 304 TYR cc_start: 0.9396 (m-80) cc_final: 0.9119 (m-80) REVERT: C 334 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: D 47 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8284 (mttm) REVERT: D 57 GLN cc_start: 0.8467 (mt0) cc_final: 0.8057 (mm-40) REVERT: D 67 LYS cc_start: 0.8379 (mttp) cc_final: 0.8020 (mtmt) REVERT: D 199 MET cc_start: 0.9379 (mtm) cc_final: 0.9075 (mtp) REVERT: D 278 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7242 (m-70) REVERT: D 305 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8942 (mm) REVERT: D 338 LYS cc_start: 0.8647 (mtpp) cc_final: 0.7934 (tptt) outliers start: 40 outliers final: 26 residues processed: 172 average time/residue: 0.2626 time to fit residues: 60.3668 Evaluate side-chains 172 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN C 41 ASN D 43 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.091604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.080857 restraints weight = 16236.664| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.06 r_work: 0.2864 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10308 Z= 0.117 Angle : 0.454 5.504 14016 Z= 0.246 Chirality : 0.044 0.143 1652 Planarity : 0.003 0.036 1764 Dihedral : 4.880 45.026 1375 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.52 % Allowed : 18.17 % Favored : 79.32 % 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: 0.52 (0.24), residues: 1276 helix: 1.90 (0.27), residues: 400 sheet: -0.27 (0.35), residues: 220 loop : -0.36 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 68 HIS 0.003 0.001 HIS B 277 PHE 0.015 0.001 PHE A 75 TYR 0.014 0.001 TYR D 330 ARG 0.001 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 439) hydrogen bonds : angle 3.91578 ( 1224) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.04621 ( 8) covalent geometry : bond 0.00263 (10304) covalent geometry : angle 0.45361 (14008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.154 Fit side-chains REVERT: A 67 LYS cc_start: 0.8646 (mttp) cc_final: 0.8013 (mmmt) REVERT: A 77 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8500 (mpp) REVERT: A 268 TYR cc_start: 0.9181 (t80) cc_final: 0.8928 (t80) REVERT: B 47 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8203 (mmmt) REVERT: B 67 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8208 (mtpt) REVERT: B 137 MET cc_start: 0.9355 (ptt) cc_final: 0.8869 (ptm) REVERT: B 185 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8777 (ttpt) REVERT: B 222 LYS cc_start: 0.9291 (ttmm) cc_final: 0.8934 (ttpp) REVERT: C 67 LYS cc_start: 0.8630 (mttp) cc_final: 0.7907 (mmmt) REVERT: C 108 GLU cc_start: 0.8250 (pt0) cc_final: 0.7941 (pt0) REVERT: C 185 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8678 (tptt) REVERT: C 207 LYS cc_start: 0.8933 (tptm) cc_final: 0.8569 (mptt) REVERT: C 268 TYR cc_start: 0.9057 (t80) cc_final: 0.8681 (t80) REVERT: C 304 TYR cc_start: 0.9372 (m-80) cc_final: 0.9091 (m-80) REVERT: C 334 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8468 (m-30) REVERT: D 47 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8346 (mmtm) REVERT: D 57 GLN cc_start: 0.8367 (mt0) cc_final: 0.8013 (mm-40) REVERT: D 67 LYS cc_start: 0.8434 (mttp) cc_final: 0.8080 (mtmt) REVERT: D 199 MET cc_start: 0.9354 (mtm) cc_final: 0.9090 (mtp) REVERT: D 278 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7294 (m-70) REVERT: D 305 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9112 (mm) REVERT: D 338 LYS cc_start: 0.8637 (mtpp) cc_final: 0.7920 (tptt) outliers start: 28 outliers final: 16 residues processed: 166 average time/residue: 0.2704 time to fit residues: 60.3528 Evaluate side-chains 163 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 117 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN C 41 ASN D 277 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.080825 restraints weight = 16229.439| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.04 r_work: 0.2841 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10308 Z= 0.143 Angle : 0.463 5.871 14016 Z= 0.250 Chirality : 0.044 0.136 1652 Planarity : 0.003 0.039 1764 Dihedral : 4.776 42.113 1374 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.24 % Allowed : 17.54 % Favored : 79.23 % 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: 0.62 (0.24), residues: 1276 helix: 1.95 (0.27), residues: 400 sheet: -0.20 (0.35), residues: 220 loop : -0.29 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.003 0.001 HIS D 276 PHE 0.014 0.001 PHE C 75 TYR 0.008 0.001 TYR D 330 ARG 0.001 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 439) hydrogen bonds : angle 3.86676 ( 1224) SS BOND : bond 0.00245 ( 4) SS BOND : angle 1.04533 ( 8) covalent geometry : bond 0.00329 (10304) covalent geometry : angle 0.46261 (14008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.189 Fit side-chains REVERT: A 67 LYS cc_start: 0.8461 (mttp) cc_final: 0.7816 (mmmt) REVERT: A 77 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8433 (mpp) REVERT: A 140 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: A 160 ASN cc_start: 0.8684 (m-40) cc_final: 0.8245 (m110) REVERT: A 268 TYR cc_start: 0.9219 (t80) cc_final: 0.8886 (t80) REVERT: B 47 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8037 (mmmt) REVERT: B 67 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8057 (mtpt) REVERT: B 137 MET cc_start: 0.9318 (ptt) cc_final: 0.8791 (ptm) REVERT: B 185 LYS cc_start: 0.9095 (ttpp) cc_final: 0.8712 (ttpt) REVERT: B 222 LYS cc_start: 0.9300 (ttmm) cc_final: 0.8881 (ttpp) REVERT: B 247 ASN cc_start: 0.9228 (p0) cc_final: 0.8724 (p0) REVERT: C 39 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8952 (mtmm) REVERT: C 67 LYS cc_start: 0.8414 (mttp) cc_final: 0.7664 (mmmt) REVERT: C 108 GLU cc_start: 0.8315 (pt0) cc_final: 0.7941 (pt0) REVERT: C 185 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8621 (tptt) REVERT: C 207 LYS cc_start: 0.8945 (tptm) cc_final: 0.8548 (tptt) REVERT: C 268 TYR cc_start: 0.9139 (t80) cc_final: 0.8671 (t80) REVERT: C 304 TYR cc_start: 0.9370 (m-80) cc_final: 0.9135 (m-80) REVERT: D 47 LYS cc_start: 0.8525 (mtpp) cc_final: 0.8185 (mmtm) REVERT: D 57 GLN cc_start: 0.8417 (mt0) cc_final: 0.7999 (mm-40) REVERT: D 67 LYS cc_start: 0.8242 (mttp) cc_final: 0.7476 (tptt) REVERT: D 199 MET cc_start: 0.9352 (mtm) cc_final: 0.9065 (mtp) REVERT: D 278 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7328 (m-70) REVERT: D 305 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8959 (mm) REVERT: D 338 LYS cc_start: 0.8692 (mtpp) cc_final: 0.7889 (tptt) outliers start: 36 outliers final: 21 residues processed: 172 average time/residue: 0.2624 time to fit residues: 60.9541 Evaluate side-chains 171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN C 41 ASN D 277 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.080917 restraints weight = 16112.356| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.01 r_work: 0.2848 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10308 Z= 0.143 Angle : 0.466 5.531 14016 Z= 0.252 Chirality : 0.044 0.130 1652 Planarity : 0.003 0.035 1764 Dihedral : 4.693 41.920 1372 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.33 % Allowed : 17.18 % Favored : 79.50 % 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: 0.67 (0.24), residues: 1276 helix: 1.97 (0.27), residues: 400 sheet: -0.16 (0.35), residues: 220 loop : -0.24 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 311 HIS 0.003 0.001 HIS D 276 PHE 0.015 0.001 PHE D 75 TYR 0.007 0.001 TYR D 330 ARG 0.001 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 439) hydrogen bonds : angle 3.87143 ( 1224) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.04608 ( 8) covalent geometry : bond 0.00328 (10304) covalent geometry : angle 0.46583 (14008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.183 Fit side-chains REVERT: A 67 LYS cc_start: 0.8509 (mttp) cc_final: 0.8306 (mtpt) REVERT: A 77 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8460 (mpp) REVERT: A 140 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: A 160 ASN cc_start: 0.8665 (m-40) cc_final: 0.8222 (m110) REVERT: A 258 TYR cc_start: 0.9091 (p90) cc_final: 0.8523 (p90) REVERT: A 268 TYR cc_start: 0.9211 (t80) cc_final: 0.8834 (t80) REVERT: B 47 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8096 (mmmt) REVERT: B 50 ARG cc_start: 0.6625 (mmt-90) cc_final: 0.6390 (mmp80) REVERT: B 67 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8124 (mtpt) REVERT: B 137 MET cc_start: 0.9332 (ptt) cc_final: 0.8815 (ptm) REVERT: B 185 LYS cc_start: 0.9070 (ttpp) cc_final: 0.8717 (ttpt) REVERT: B 222 LYS cc_start: 0.9301 (ttmm) cc_final: 0.8901 (ttpp) REVERT: B 247 ASN cc_start: 0.9234 (p0) cc_final: 0.8698 (p0) REVERT: C 39 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8941 (mtmm) REVERT: C 67 LYS cc_start: 0.8444 (mttp) cc_final: 0.7713 (mmmt) REVERT: C 108 GLU cc_start: 0.8265 (pt0) cc_final: 0.7908 (pt0) REVERT: C 185 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8653 (tptt) REVERT: C 207 LYS cc_start: 0.9017 (tptm) cc_final: 0.8595 (tptt) REVERT: C 268 TYR cc_start: 0.9107 (t80) cc_final: 0.8739 (t80) REVERT: D 47 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8154 (mtpp) REVERT: D 57 GLN cc_start: 0.8389 (mt0) cc_final: 0.7986 (mm-40) REVERT: D 67 LYS cc_start: 0.8273 (mttp) cc_final: 0.7527 (tptt) REVERT: D 199 MET cc_start: 0.9348 (mtm) cc_final: 0.9068 (mtp) REVERT: D 278 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7338 (m-70) REVERT: D 305 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8989 (mm) REVERT: D 338 LYS cc_start: 0.8655 (mtpp) cc_final: 0.7903 (tptt) outliers start: 37 outliers final: 25 residues processed: 172 average time/residue: 0.2635 time to fit residues: 60.9987 Evaluate side-chains 176 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 0 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 0.0030 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN D 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.092241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.081726 restraints weight = 16024.204| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.03 r_work: 0.2880 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10308 Z= 0.127 Angle : 0.461 5.904 14016 Z= 0.248 Chirality : 0.044 0.165 1652 Planarity : 0.003 0.036 1764 Dihedral : 4.599 41.971 1372 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.97 % Allowed : 17.45 % Favored : 79.59 % 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 (0.24), residues: 1276 helix: 2.01 (0.27), residues: 400 sheet: -0.02 (0.35), residues: 216 loop : -0.27 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 311 HIS 0.003 0.000 HIS D 276 PHE 0.014 0.001 PHE D 75 TYR 0.007 0.001 TYR B 258 ARG 0.001 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 439) hydrogen bonds : angle 3.82389 ( 1224) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.01028 ( 8) covalent geometry : bond 0.00288 (10304) covalent geometry : angle 0.46013 (14008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.059 Fit side-chains REVERT: A 77 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8402 (mpp) REVERT: A 140 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8510 (mp0) REVERT: A 160 ASN cc_start: 0.8637 (m-40) cc_final: 0.8173 (m110) REVERT: A 258 TYR cc_start: 0.9101 (p90) cc_final: 0.8532 (p90) REVERT: A 268 TYR cc_start: 0.9211 (t80) cc_final: 0.8836 (t80) REVERT: B 47 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8048 (mmmt) REVERT: B 67 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8103 (mtpt) REVERT: B 137 MET cc_start: 0.9273 (ptt) cc_final: 0.8754 (ptm) REVERT: B 185 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8702 (ttpt) REVERT: B 247 ASN cc_start: 0.9254 (p0) cc_final: 0.8717 (p0) REVERT: C 39 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8949 (mtmm) REVERT: C 67 LYS cc_start: 0.8418 (mttp) cc_final: 0.7544 (tptp) REVERT: C 108 GLU cc_start: 0.8264 (pt0) cc_final: 0.7902 (pt0) REVERT: C 185 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8719 (tptt) REVERT: C 207 LYS cc_start: 0.9021 (tptm) cc_final: 0.8521 (mptt) REVERT: C 268 TYR cc_start: 0.9099 (t80) cc_final: 0.8689 (t80) REVERT: C 304 TYR cc_start: 0.9350 (m-80) cc_final: 0.8928 (m-80) REVERT: D 47 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8010 (mtpp) REVERT: D 67 LYS cc_start: 0.8247 (mttp) cc_final: 0.7501 (tptt) REVERT: D 199 MET cc_start: 0.9342 (mtm) cc_final: 0.9067 (mtp) REVERT: D 278 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7400 (m-70) REVERT: D 305 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8971 (mm) REVERT: D 338 LYS cc_start: 0.8651 (mtpp) cc_final: 0.7888 (tptt) outliers start: 33 outliers final: 24 residues processed: 171 average time/residue: 0.2604 time to fit residues: 60.1512 Evaluate side-chains 173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 277 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.091319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.081097 restraints weight = 16166.989| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.93 r_work: 0.2843 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10308 Z= 0.163 Angle : 0.485 5.532 14016 Z= 0.262 Chirality : 0.045 0.140 1652 Planarity : 0.003 0.035 1764 Dihedral : 4.674 41.646 1372 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.97 % Allowed : 17.63 % Favored : 79.41 % 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 (0.24), residues: 1276 helix: 1.98 (0.27), residues: 400 sheet: -0.02 (0.35), residues: 216 loop : -0.26 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.004 0.001 HIS D 216 PHE 0.015 0.001 PHE C 75 TYR 0.007 0.001 TYR D 330 ARG 0.001 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 439) hydrogen bonds : angle 3.88030 ( 1224) SS BOND : bond 0.00264 ( 4) SS BOND : angle 1.05467 ( 8) covalent geometry : bond 0.00379 (10304) covalent geometry : angle 0.48485 (14008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.186 Fit side-chains REVERT: A 77 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8481 (mpp) REVERT: A 140 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: A 160 ASN cc_start: 0.8653 (m-40) cc_final: 0.8188 (m110) REVERT: A 258 TYR cc_start: 0.9077 (p90) cc_final: 0.8558 (p90) REVERT: A 268 TYR cc_start: 0.9176 (t80) cc_final: 0.8853 (t80) REVERT: B 47 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8205 (mmmt) REVERT: B 67 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8304 (mtpt) REVERT: B 137 MET cc_start: 0.9359 (ptt) cc_final: 0.8864 (ptm) REVERT: B 185 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8750 (ttpt) REVERT: B 222 LYS cc_start: 0.9303 (ttmm) cc_final: 0.8932 (ttpp) REVERT: B 247 ASN cc_start: 0.9239 (p0) cc_final: 0.8712 (p0) REVERT: C 39 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8940 (mtmm) REVERT: C 67 LYS cc_start: 0.8551 (mttp) cc_final: 0.7634 (tptp) REVERT: C 108 GLU cc_start: 0.8234 (pt0) cc_final: 0.7940 (pt0) REVERT: C 185 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8711 (tptt) REVERT: C 207 LYS cc_start: 0.9074 (tptm) cc_final: 0.8613 (mptt) REVERT: C 268 TYR cc_start: 0.9060 (t80) cc_final: 0.8705 (t80) REVERT: C 304 TYR cc_start: 0.9349 (m-80) cc_final: 0.9063 (m-80) REVERT: D 47 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8227 (mtpp) REVERT: D 67 LYS cc_start: 0.8387 (mttp) cc_final: 0.7684 (tptt) REVERT: D 199 MET cc_start: 0.9344 (mtm) cc_final: 0.9051 (mtp) REVERT: D 247 ASN cc_start: 0.9218 (p0) cc_final: 0.8708 (p0) REVERT: D 278 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7348 (m-70) REVERT: D 305 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9097 (mm) REVERT: D 338 LYS cc_start: 0.8564 (mtpp) cc_final: 0.7904 (tptt) outliers start: 33 outliers final: 26 residues processed: 166 average time/residue: 0.2621 time to fit residues: 58.7912 Evaluate side-chains 173 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 115 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 115 HIS Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 259 HIS Chi-restraints excluded: chain D residue 278 HIS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 119 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 264 ASN D 277 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.091515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.081123 restraints weight = 16009.590| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.97 r_work: 0.2866 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10308 Z= 0.146 Angle : 0.475 5.463 14016 Z= 0.256 Chirality : 0.044 0.134 1652 Planarity : 0.003 0.035 1764 Dihedral : 4.637 41.979 1372 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.33 % Allowed : 17.27 % Favored : 79.41 % 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: 0.73 (0.24), residues: 1276 helix: 2.01 (0.27), residues: 400 sheet: -0.03 (0.34), residues: 216 loop : -0.24 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 311 HIS 0.003 0.001 HIS D 276 PHE 0.014 0.001 PHE C 75 TYR 0.007 0.001 TYR B 258 ARG 0.001 0.000 ARG A 206 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 439) hydrogen bonds : angle 3.85241 ( 1224) SS BOND : bond 0.00246 ( 4) SS BOND : angle 1.02462 ( 8) covalent geometry : bond 0.00335 (10304) covalent geometry : angle 0.47436 (14008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5389.51 seconds wall clock time: 93 minutes 48.97 seconds (5628.97 seconds total)