Starting phenix.real_space_refine on Wed Feb 4 10:31:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vdc_31913/02_2026/7vdc_31913.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdc_31913/02_2026/7vdc_31913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vdc_31913/02_2026/7vdc_31913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdc_31913/02_2026/7vdc_31913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vdc_31913/02_2026/7vdc_31913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdc_31913/02_2026/7vdc_31913.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Time building chain proxies: 2.51, per 1000 atoms: 0.24 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.5, 81.25, 107.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 469.8 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 54.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.956A pdb=" N ILE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.829A pdb=" N VAL A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.635A pdb=" N LEU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.937A pdb=" N ARG A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.657A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.816A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.728A pdb=" N ALA A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 37 through 46 removed outlier: 4.056A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 73 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.584A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.803A pdb=" N ARG B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 181 Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.582A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.784A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.498A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 37 through 47 removed outlier: 4.077A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 66 through 73 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 159 through 181 Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.679A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.790A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.546A pdb=" N ALA C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 removed outlier: 3.516A pdb=" N ARG C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.821A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.514A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 removed outlier: 4.172A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.774A pdb=" N ARG D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 181 Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.721A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.792A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.894A pdb=" N TYR A 301 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 152 removed outlier: 7.038A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.298A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 301 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 151 Processing sheet with id=AA7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.528A pdb=" N ILE C 185 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 144 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR C 301 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'D' and resid 296 through 297 removed outlier: 3.859A pdb=" N PHE D 144 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR D 301 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 112 through 114 537 hydrogen bonds defined for protein. 1569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3503 1.34 - 1.46: 1330 1.46 - 1.57: 5782 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.331 1.348 -0.017 7.90e-03 1.60e+04 4.44e+00 bond pdb=" CB PRO A 92 " pdb=" CG PRO A 92 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 bond pdb=" CG PRO A 158 " pdb=" CD PRO A 158 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.52e-01 bond pdb=" CB PRO A 158 " pdb=" CG PRO A 158 " ideal model delta sigma weight residual 1.506 1.473 0.033 3.90e-02 6.57e+02 7.05e-01 bond pdb=" C THR A 343 " pdb=" O THR A 343 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.65e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 14113 1.43 - 2.86: 281 2.86 - 4.29: 57 4.29 - 5.72: 11 5.72 - 7.15: 2 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 112.00 108.01 3.99 1.40e+00 5.10e-01 8.11e+00 angle pdb=" N VAL A 260 " pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 107.76 110.60 -2.84 1.01e+00 9.80e-01 7.90e+00 angle pdb=" N GLY A 47 " pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 114.85 111.86 2.99 1.35e+00 5.49e-01 4.92e+00 angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 120.60 115.73 4.87 2.20e+00 2.07e-01 4.91e+00 angle pdb=" C LYS C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta sigma weight residual 121.58 117.50 4.08 1.95e+00 2.63e-01 4.38e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5759 16.81 - 33.61: 580 33.61 - 50.42: 125 50.42 - 67.23: 34 67.23 - 84.03: 6 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CG ARG D 172 " pdb=" CD ARG D 172 " pdb=" NE ARG D 172 " pdb=" CZ ARG D 172 " ideal model delta sinusoidal sigma weight residual 90.00 134.39 -44.39 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG C 257 " pdb=" CD ARG C 257 " pdb=" NE ARG C 257 " pdb=" CZ ARG C 257 " ideal model delta sinusoidal sigma weight residual -90.00 -133.53 43.53 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG C 172 " pdb=" CD ARG C 172 " pdb=" NE ARG C 172 " pdb=" CZ ARG C 172 " ideal model delta sinusoidal sigma weight residual 180.00 136.86 43.14 2 1.50e+01 4.44e-03 9.98e+00 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 980 0.027 - 0.054: 378 0.054 - 0.080: 169 0.080 - 0.107: 90 0.107 - 0.134: 27 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL B 23 " pdb=" CA VAL B 23 " pdb=" CG1 VAL B 23 " pdb=" CG2 VAL B 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE C 190 " pdb=" N ILE C 190 " pdb=" C ILE C 190 " pdb=" CB ILE C 190 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 157 " -0.063 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO B 158 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 187 " -0.049 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO D 188 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 188 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 188 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 91 " -0.044 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 92 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.036 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 97 2.63 - 3.20: 9371 3.20 - 3.77: 16904 3.77 - 4.33: 22564 4.33 - 4.90: 37030 Nonbonded interactions: 85966 Sorted by model distance: nonbonded pdb=" O GLU C 224 " pdb=" OG1 THR C 265 " model vdw 2.066 3.040 nonbonded pdb=" O GLU D 224 " pdb=" OG1 THR D 265 " model vdw 2.075 3.040 nonbonded pdb=" O GLU A 224 " pdb=" OG1 THR A 265 " model vdw 2.155 3.040 nonbonded pdb=" O GLU B 224 " pdb=" OG1 THR B 265 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 275 " pdb=" OE1 GLU C 276 " model vdw 2.209 3.040 ... (remaining 85961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 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 : 0.002 0.087 10672 Z= 0.105 Angle : 0.516 7.148 14464 Z= 0.266 Chirality : 0.040 0.134 1644 Planarity : 0.005 0.097 1880 Dihedral : 14.497 84.033 3984 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.23), residues: 1364 helix: 1.77 (0.19), residues: 672 sheet: -1.80 (0.31), residues: 248 loop : -1.30 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 330 TYR 0.014 0.002 TYR B 203 PHE 0.008 0.001 PHE C 144 TRP 0.032 0.003 TRP C 295 HIS 0.002 0.000 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00232 (10672) covalent geometry : angle 0.51632 (14464) hydrogen bonds : bond 0.13271 ( 537) hydrogen bonds : angle 4.68638 ( 1569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.361 Fit side-chains REVERT: A 170 LEU cc_start: 0.8677 (mt) cc_final: 0.8449 (mt) REVERT: B 72 CYS cc_start: 0.6881 (m) cc_final: 0.6358 (t) REVERT: B 139 LYS cc_start: 0.7843 (pttt) cc_final: 0.6882 (ttpt) REVERT: C 130 LEU cc_start: 0.7920 (tp) cc_final: 0.7701 (tp) REVERT: C 139 LYS cc_start: 0.7884 (pttt) cc_final: 0.6888 (ttpt) REVERT: C 298 THR cc_start: 0.7512 (m) cc_final: 0.6974 (p) REVERT: D 189 GLU cc_start: 0.7332 (tp30) cc_final: 0.7121 (tp30) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.0973 time to fit residues: 38.5329 Evaluate side-chains 229 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN D 156 HIS D 339 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150089 restraints weight = 12492.909| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.43 r_work: 0.3707 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10672 Z= 0.141 Angle : 0.551 6.585 14464 Z= 0.280 Chirality : 0.042 0.144 1644 Planarity : 0.005 0.060 1880 Dihedral : 3.695 15.241 1472 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.99 % Allowed : 8.63 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1364 helix: 1.94 (0.19), residues: 676 sheet: -1.94 (0.41), residues: 152 loop : -1.40 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 59 TYR 0.021 0.002 TYR A 58 PHE 0.015 0.002 PHE C 144 TRP 0.007 0.001 TRP D 313 HIS 0.007 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00325 (10672) covalent geometry : angle 0.55067 (14464) hydrogen bonds : bond 0.04120 ( 537) hydrogen bonds : angle 3.75300 ( 1569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 242 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8034 (Cg_endo) cc_final: 0.7760 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7562 (pttt) cc_final: 0.7222 (ttpt) REVERT: C 130 LEU cc_start: 0.7983 (tp) cc_final: 0.7729 (tp) outliers start: 11 outliers final: 11 residues processed: 247 average time/residue: 0.1054 time to fit residues: 35.7002 Evaluate side-chains 237 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 102 optimal weight: 0.0010 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 70 ASN B 324 GLN C 54 ASN C 80 HIS ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 339 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.191015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151768 restraints weight = 12397.156| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.38 r_work: 0.3723 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10672 Z= 0.109 Angle : 0.500 6.513 14464 Z= 0.253 Chirality : 0.040 0.140 1644 Planarity : 0.004 0.049 1880 Dihedral : 3.609 14.862 1472 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.44 % Allowed : 10.25 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1364 helix: 2.10 (0.19), residues: 676 sheet: -1.90 (0.39), residues: 160 loop : -1.32 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 55 TYR 0.020 0.002 TYR A 58 PHE 0.012 0.001 PHE D 144 TRP 0.009 0.001 TRP D 313 HIS 0.008 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00247 (10672) covalent geometry : angle 0.49960 (14464) hydrogen bonds : bond 0.03492 ( 537) hydrogen bonds : angle 3.52924 ( 1569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 0.330 Fit side-chains REVERT: A 114 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.7770 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7602 (pttt) cc_final: 0.7215 (ttpt) REVERT: A 298 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7057 (p) REVERT: B 170 LEU cc_start: 0.8735 (mt) cc_final: 0.8483 (mt) REVERT: C 130 LEU cc_start: 0.7983 (tp) cc_final: 0.7711 (tp) REVERT: D 139 LYS cc_start: 0.7822 (pttp) cc_final: 0.7538 (pttt) outliers start: 16 outliers final: 14 residues processed: 246 average time/residue: 0.1143 time to fit residues: 38.4757 Evaluate side-chains 233 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 218 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 0.0980 chunk 127 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN C 54 ASN C 80 HIS ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.191714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151988 restraints weight = 12610.386| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.45 r_work: 0.3729 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10672 Z= 0.124 Angle : 0.507 6.870 14464 Z= 0.258 Chirality : 0.040 0.143 1644 Planarity : 0.004 0.050 1880 Dihedral : 3.611 14.756 1472 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.44 % Allowed : 12.95 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1364 helix: 2.11 (0.19), residues: 676 sheet: -1.73 (0.40), residues: 152 loop : -1.45 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 148 TYR 0.019 0.002 TYR A 58 PHE 0.015 0.002 PHE C 144 TRP 0.008 0.001 TRP D 313 HIS 0.008 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00290 (10672) covalent geometry : angle 0.50741 (14464) hydrogen bonds : bond 0.03556 ( 537) hydrogen bonds : angle 3.48372 ( 1569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.291 Fit side-chains REVERT: A 114 PRO cc_start: 0.8014 (Cg_endo) cc_final: 0.7739 (Cg_exo) REVERT: A 298 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7062 (p) REVERT: B 170 LEU cc_start: 0.8775 (mt) cc_final: 0.8524 (mt) REVERT: C 57 PHE cc_start: 0.6922 (t80) cc_final: 0.6688 (t80) REVERT: C 130 LEU cc_start: 0.8003 (tp) cc_final: 0.7761 (tp) outliers start: 16 outliers final: 13 residues processed: 242 average time/residue: 0.1119 time to fit residues: 37.1546 Evaluate side-chains 233 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 0.0030 chunk 91 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 324 GLN C 54 ASN C 80 HIS D 2 HIS D 11 GLN D 156 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.192250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152919 restraints weight = 12464.650| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.44 r_work: 0.3742 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10672 Z= 0.110 Angle : 0.494 7.289 14464 Z= 0.251 Chirality : 0.040 0.140 1644 Planarity : 0.004 0.050 1880 Dihedral : 3.568 14.458 1472 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.62 % Allowed : 14.75 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1364 helix: 2.24 (0.19), residues: 676 sheet: -2.03 (0.38), residues: 164 loop : -1.28 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 330 TYR 0.018 0.002 TYR A 58 PHE 0.012 0.001 PHE C 144 TRP 0.009 0.001 TRP D 313 HIS 0.009 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00253 (10672) covalent geometry : angle 0.49388 (14464) hydrogen bonds : bond 0.03370 ( 537) hydrogen bonds : angle 3.39765 ( 1569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.494 Fit side-chains REVERT: A 114 PRO cc_start: 0.7979 (Cg_endo) cc_final: 0.7702 (Cg_exo) REVERT: A 298 THR cc_start: 0.7589 (OUTLIER) cc_final: 0.7028 (p) REVERT: A 330 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7715 (mmm160) REVERT: B 170 LEU cc_start: 0.8748 (mt) cc_final: 0.8474 (mt) REVERT: B 189 GLU cc_start: 0.7457 (tp30) cc_final: 0.7039 (tp30) REVERT: C 57 PHE cc_start: 0.6870 (t80) cc_final: 0.6656 (t80) REVERT: C 58 TYR cc_start: 0.7009 (t80) cc_final: 0.6793 (t80) REVERT: C 130 LEU cc_start: 0.8011 (tp) cc_final: 0.7776 (tp) REVERT: C 342 TYR cc_start: 0.6784 (t80) cc_final: 0.6386 (t80) REVERT: D 170 LEU cc_start: 0.8805 (mt) cc_final: 0.8569 (mt) REVERT: D 320 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.6065 (mp) outliers start: 18 outliers final: 13 residues processed: 249 average time/residue: 0.1122 time to fit residues: 38.5723 Evaluate side-chains 234 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 0.0370 chunk 79 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 324 GLN C 54 ASN C 80 HIS D 156 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.192114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152888 restraints weight = 12596.637| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.45 r_work: 0.3738 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.112 Angle : 0.497 7.463 14464 Z= 0.252 Chirality : 0.040 0.140 1644 Planarity : 0.004 0.052 1880 Dihedral : 3.535 14.394 1472 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.07 % Allowed : 16.10 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1364 helix: 2.26 (0.19), residues: 676 sheet: -1.71 (0.40), residues: 152 loop : -1.38 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 330 TYR 0.024 0.002 TYR A 58 PHE 0.012 0.001 PHE C 144 TRP 0.010 0.001 TRP C 147 HIS 0.009 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00261 (10672) covalent geometry : angle 0.49685 (14464) hydrogen bonds : bond 0.03360 ( 537) hydrogen bonds : angle 3.36345 ( 1569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.417 Fit side-chains REVERT: A 114 PRO cc_start: 0.7975 (Cg_endo) cc_final: 0.7690 (Cg_exo) REVERT: A 298 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7034 (p) REVERT: A 325 GLU cc_start: 0.8291 (tt0) cc_final: 0.7969 (mt-10) REVERT: B 139 LYS cc_start: 0.7945 (pttt) cc_final: 0.6915 (ttpt) REVERT: B 170 LEU cc_start: 0.8767 (mt) cc_final: 0.8514 (mt) REVERT: B 189 GLU cc_start: 0.7460 (tp30) cc_final: 0.7054 (tp30) REVERT: C 57 PHE cc_start: 0.6899 (t80) cc_final: 0.6653 (t80) REVERT: C 58 TYR cc_start: 0.6960 (t80) cc_final: 0.6739 (t80) REVERT: C 130 LEU cc_start: 0.8023 (tp) cc_final: 0.7774 (tp) REVERT: C 330 ARG cc_start: 0.7664 (tpp-160) cc_final: 0.6525 (mmm-85) REVERT: D 139 LYS cc_start: 0.7663 (pttp) cc_final: 0.7309 (pttt) REVERT: D 170 LEU cc_start: 0.8810 (mt) cc_final: 0.8579 (mt) REVERT: D 320 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6059 (mp) outliers start: 23 outliers final: 18 residues processed: 241 average time/residue: 0.1124 time to fit residues: 37.5192 Evaluate side-chains 236 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 60 GLN B 168 ASN B 324 GLN C 54 ASN C 80 HIS ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.189642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150208 restraints weight = 12540.299| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.43 r_work: 0.3708 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10672 Z= 0.162 Angle : 0.545 7.537 14464 Z= 0.279 Chirality : 0.042 0.146 1644 Planarity : 0.005 0.056 1880 Dihedral : 3.737 14.594 1472 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.70 % Allowed : 16.01 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1364 helix: 2.05 (0.19), residues: 676 sheet: -2.03 (0.38), residues: 160 loop : -1.35 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 330 TYR 0.022 0.002 TYR A 213 PHE 0.016 0.002 PHE D 144 TRP 0.014 0.002 TRP C 147 HIS 0.009 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00381 (10672) covalent geometry : angle 0.54474 (14464) hydrogen bonds : bond 0.03872 ( 537) hydrogen bonds : angle 3.48255 ( 1569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.393 Fit side-chains REVERT: A 114 PRO cc_start: 0.8005 (Cg_endo) cc_final: 0.7723 (Cg_exo) REVERT: A 330 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7857 (mmm160) REVERT: B 110 LYS cc_start: 0.6906 (mmmt) cc_final: 0.6613 (mmtt) REVERT: B 189 GLU cc_start: 0.7509 (tp30) cc_final: 0.7093 (tp30) REVERT: C 57 PHE cc_start: 0.6890 (t80) cc_final: 0.6632 (t80) REVERT: C 58 TYR cc_start: 0.7091 (t80) cc_final: 0.6836 (t80) REVERT: C 130 LEU cc_start: 0.8035 (tp) cc_final: 0.7812 (tp) REVERT: D 320 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6047 (mp) outliers start: 30 outliers final: 24 residues processed: 237 average time/residue: 0.1110 time to fit residues: 35.9427 Evaluate side-chains 236 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 129 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 117 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 60 GLN B 324 GLN C 54 ASN C 80 HIS ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.193412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154248 restraints weight = 12499.889| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.45 r_work: 0.3758 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10672 Z= 0.097 Angle : 0.487 8.157 14464 Z= 0.247 Chirality : 0.040 0.136 1644 Planarity : 0.004 0.056 1880 Dihedral : 3.497 13.764 1472 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.62 % Allowed : 17.18 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1364 helix: 2.29 (0.19), residues: 676 sheet: -1.82 (0.34), residues: 200 loop : -1.23 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.023 0.002 TYR A 58 PHE 0.008 0.001 PHE C 144 TRP 0.010 0.001 TRP D 313 HIS 0.010 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00218 (10672) covalent geometry : angle 0.48673 (14464) hydrogen bonds : bond 0.03120 ( 537) hydrogen bonds : angle 3.31915 ( 1569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.394 Fit side-chains REVERT: A 114 PRO cc_start: 0.7972 (Cg_endo) cc_final: 0.7681 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7894 (pttt) cc_final: 0.6809 (ttpt) REVERT: A 170 LEU cc_start: 0.8775 (mt) cc_final: 0.8571 (mt) REVERT: A 298 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.6994 (p) REVERT: A 330 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7362 (mmt180) REVERT: B 72 CYS cc_start: 0.7345 (m) cc_final: 0.6676 (t) REVERT: B 110 LYS cc_start: 0.6834 (mmmt) cc_final: 0.6551 (mmtt) REVERT: B 139 LYS cc_start: 0.7912 (pttt) cc_final: 0.6852 (ttpt) REVERT: B 170 LEU cc_start: 0.8722 (mt) cc_final: 0.8447 (mt) REVERT: B 189 GLU cc_start: 0.7456 (tp30) cc_final: 0.7054 (tp30) REVERT: C 57 PHE cc_start: 0.6879 (t80) cc_final: 0.6637 (t80) REVERT: C 58 TYR cc_start: 0.6957 (t80) cc_final: 0.6733 (t80) REVERT: C 130 LEU cc_start: 0.8032 (tp) cc_final: 0.7780 (tp) REVERT: C 139 LYS cc_start: 0.7860 (pttt) cc_final: 0.6783 (ttpt) REVERT: C 170 LEU cc_start: 0.8743 (mt) cc_final: 0.8511 (mt) REVERT: C 330 ARG cc_start: 0.7671 (tpp-160) cc_final: 0.6649 (mmm-85) REVERT: D 139 LYS cc_start: 0.7615 (pttp) cc_final: 0.6731 (ttpt) REVERT: D 170 LEU cc_start: 0.8763 (mt) cc_final: 0.8537 (mt) REVERT: D 320 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6103 (mp) outliers start: 18 outliers final: 11 residues processed: 251 average time/residue: 0.1116 time to fit residues: 38.5812 Evaluate side-chains 239 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 226 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 128 optimal weight: 0.0070 chunk 133 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 overall best weight: 1.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 168 ASN B 324 GLN C 54 ASN C 80 HIS ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.191371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151690 restraints weight = 12677.381| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.47 r_work: 0.3723 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10672 Z= 0.134 Angle : 0.529 8.519 14464 Z= 0.270 Chirality : 0.041 0.215 1644 Planarity : 0.005 0.059 1880 Dihedral : 3.604 14.488 1472 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.44 % Allowed : 17.63 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.23), residues: 1364 helix: 2.16 (0.19), residues: 676 sheet: -1.76 (0.39), residues: 152 loop : -1.37 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.029 0.002 TYR C 173 PHE 0.014 0.002 PHE D 144 TRP 0.016 0.001 TRP C 147 HIS 0.010 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00313 (10672) covalent geometry : angle 0.52949 (14464) hydrogen bonds : bond 0.03564 ( 537) hydrogen bonds : angle 3.38907 ( 1569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.343 Fit side-chains REVERT: A 114 PRO cc_start: 0.8005 (Cg_endo) cc_final: 0.7711 (Cg_exo) REVERT: A 330 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7803 (mmm160) REVERT: B 110 LYS cc_start: 0.6883 (mmmt) cc_final: 0.6623 (mmtt) REVERT: B 139 LYS cc_start: 0.8059 (pttt) cc_final: 0.6883 (ttpt) REVERT: B 189 GLU cc_start: 0.7487 (tp30) cc_final: 0.7085 (tp30) REVERT: C 57 PHE cc_start: 0.6908 (t80) cc_final: 0.6642 (t80) REVERT: C 58 TYR cc_start: 0.7046 (t80) cc_final: 0.6811 (t80) REVERT: C 130 LEU cc_start: 0.8004 (tp) cc_final: 0.7772 (tp) REVERT: C 330 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.6569 (mmm-85) outliers start: 16 outliers final: 13 residues processed: 229 average time/residue: 0.1081 time to fit residues: 33.9755 Evaluate side-chains 229 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.0170 chunk 132 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 324 GLN C 54 ASN C 80 HIS ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.192070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152817 restraints weight = 12496.847| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.45 r_work: 0.3740 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10672 Z= 0.115 Angle : 0.517 8.530 14464 Z= 0.263 Chirality : 0.041 0.180 1644 Planarity : 0.005 0.060 1880 Dihedral : 3.585 14.478 1472 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.71 % Allowed : 17.72 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1364 helix: 2.17 (0.19), residues: 676 sheet: -1.72 (0.39), residues: 152 loop : -1.35 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 330 TYR 0.024 0.002 TYR C 173 PHE 0.012 0.001 PHE D 144 TRP 0.015 0.001 TRP C 147 HIS 0.011 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00268 (10672) covalent geometry : angle 0.51687 (14464) hydrogen bonds : bond 0.03385 ( 537) hydrogen bonds : angle 3.34517 ( 1569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.254 Fit side-chains REVERT: A 114 PRO cc_start: 0.7978 (Cg_endo) cc_final: 0.7684 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7938 (pttt) cc_final: 0.6845 (ttpt) REVERT: A 330 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7766 (mmm160) REVERT: B 110 LYS cc_start: 0.6898 (mmmt) cc_final: 0.6620 (mmtt) REVERT: B 139 LYS cc_start: 0.8009 (pttt) cc_final: 0.6870 (ttpt) REVERT: B 170 LEU cc_start: 0.8744 (mt) cc_final: 0.8494 (mt) REVERT: B 189 GLU cc_start: 0.7463 (tp30) cc_final: 0.7056 (tp30) REVERT: C 57 PHE cc_start: 0.6886 (t80) cc_final: 0.6635 (t80) REVERT: C 58 TYR cc_start: 0.7036 (t80) cc_final: 0.6802 (t80) REVERT: C 130 LEU cc_start: 0.7992 (tp) cc_final: 0.7763 (tp) REVERT: C 139 LYS cc_start: 0.7856 (pttt) cc_final: 0.6790 (ttpt) REVERT: C 330 ARG cc_start: 0.7704 (tpp-160) cc_final: 0.6558 (mmm-85) REVERT: D 170 LEU cc_start: 0.8804 (mt) cc_final: 0.8563 (mt) REVERT: D 320 LEU cc_start: 0.6557 (tp) cc_final: 0.6069 (mp) outliers start: 19 outliers final: 17 residues processed: 232 average time/residue: 0.0971 time to fit residues: 31.0157 Evaluate side-chains 236 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 219 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 101 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN B 324 GLN C 54 ASN C 80 HIS ** D 156 HIS ** 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 = 0.4309 r_free = 0.4309 target = 0.193315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154465 restraints weight = 12550.627| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.46 r_work: 0.3761 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10672 Z= 0.099 Angle : 0.502 8.553 14464 Z= 0.255 Chirality : 0.040 0.166 1644 Planarity : 0.004 0.059 1880 Dihedral : 3.496 14.438 1472 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.53 % Allowed : 18.08 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1364 helix: 2.24 (0.19), residues: 676 sheet: -1.77 (0.34), residues: 200 loop : -1.17 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 330 TYR 0.044 0.002 TYR C 173 PHE 0.009 0.001 PHE D 144 TRP 0.017 0.002 TRP C 147 HIS 0.011 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00224 (10672) covalent geometry : angle 0.50151 (14464) hydrogen bonds : bond 0.03152 ( 537) hydrogen bonds : angle 3.28887 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2283.63 seconds wall clock time: 40 minutes 10.02 seconds (2410.02 seconds total)