Starting phenix.real_space_refine on Sun May 3 08:06:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nn_75866/05_2026/11nn_75866.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nn_75866/05_2026/11nn_75866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nn_75866/05_2026/11nn_75866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nn_75866/05_2026/11nn_75866.map" model { file = "/net/cci-nas-00/data/ceres_data/11nn_75866/05_2026/11nn_75866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nn_75866/05_2026/11nn_75866.cif" } resolution = 2.34 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= 0.008 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 3097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11589 Number of models: 1 Model: "" Number of chains: 8 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} Chain: "A" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 270 Classifications: {'water': 270} Link IDs: {None: 269} Chain: "B" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 274 Classifications: {'water': 274} Link IDs: {None: 273} Chain: "C" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 306 Classifications: {'water': 306} Link IDs: {None: 305} Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 267 Classifications: {'water': 267} Link IDs: {None: 266} Time building chain proxies: 3.34, per 1000 atoms: 0.29 Number of scatterers: 11589 At special positions: 0 Unit cell: (100.695, 80.115, 109.515, 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 3097 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: 1.10 Conformation dependent library (CDL) restraints added in 630.2 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: 60 helices and 8 sheets defined 54.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.890A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.757A 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 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.821A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.645A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.541A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 338 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.867A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.816A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 258 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.500A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 45 removed outlier: 3.850A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.732A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.662A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.206A 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 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 47 removed outlier: 4.302A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.528A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 305 removed outlier: 3.620A pdb=" N LEU D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 302 through 305' 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 28 through 31 removed outlier: 6.810A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (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 'B' and resid 28 through 31 removed outlier: 6.690A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 145 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU B 187 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP B 147 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU B 189 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS B 149 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 191 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU B 151 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.784A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.804A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 567 hydrogen bonds defined for protein. 1632 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: 2.04 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2091 1.33 - 1.45: 2321 1.45 - 1.57: 6204 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" N VAL D 260 " pdb=" CA VAL D 260 " ideal model delta sigma weight residual 1.457 1.498 -0.040 9.00e-03 1.23e+04 2.02e+01 bond pdb=" N LEU D 320 " pdb=" CA LEU D 320 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.20e-02 6.94e+03 1.17e+01 bond pdb=" CA PRO D 261 " pdb=" C PRO D 261 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.05e+01 bond pdb=" N ILE C 106 " pdb=" CA ILE C 106 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.11e-02 8.12e+03 1.02e+01 bond pdb=" N ASP C 109 " pdb=" CA ASP C 109 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.27e-02 6.20e+03 1.01e+01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13544 1.42 - 2.84: 773 2.84 - 4.26: 114 4.26 - 5.68: 25 5.68 - 7.10: 8 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " pdb=" CG PHE D 144 " ideal model delta sigma weight residual 113.80 118.68 -4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " pdb=" CG PHE B 144 " ideal model delta sigma weight residual 113.80 118.55 -4.75 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N ASN D 319 " pdb=" CA ASN D 319 " pdb=" C ASN D 319 " ideal model delta sigma weight residual 113.20 107.46 5.74 1.21e+00 6.83e-01 2.25e+01 angle pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " pdb=" CG PHE C 144 " ideal model delta sigma weight residual 113.80 118.39 -4.59 1.00e+00 1.00e+00 2.11e+01 angle pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " pdb=" CG PHE A 144 " ideal model delta sigma weight residual 113.80 118.10 -4.30 1.00e+00 1.00e+00 1.85e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6060 17.44 - 34.87: 333 34.87 - 52.31: 71 52.31 - 69.75: 26 69.75 - 87.19: 14 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA ASP A 109 " pdb=" CB ASP A 109 " pdb=" CG ASP A 109 " pdb=" OD1 ASP A 109 " ideal model delta sinusoidal sigma weight residual -30.00 -88.62 58.62 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" C PHE D 144 " pdb=" N PHE D 144 " pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " ideal model delta harmonic sigma weight residual -122.60 -131.02 8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CA ASP B 67 " pdb=" CB ASP B 67 " pdb=" CG ASP B 67 " pdb=" OD1 ASP B 67 " ideal model delta sinusoidal sigma weight residual -30.00 -85.16 55.16 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1162 0.045 - 0.090: 348 0.090 - 0.135: 112 0.135 - 0.180: 14 0.180 - 0.225: 8 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA ILE D 46 " pdb=" N ILE D 46 " pdb=" C ILE D 46 " pdb=" CB ILE D 46 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE C 106 " pdb=" N ILE C 106 " pdb=" C ILE C 106 " pdb=" CB ILE C 106 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA PHE D 144 " pdb=" N PHE D 144 " pdb=" C PHE D 144 " pdb=" CB PHE D 144 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 185 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C ILE C 185 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE C 185 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 186 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 187 " 0.040 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO C 188 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 326 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C GLU D 326 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU D 326 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR D 327 " 0.013 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2945 2.79 - 3.32: 11729 3.32 - 3.85: 22081 3.85 - 4.37: 27030 4.37 - 4.90: 42493 Nonbonded interactions: 106278 Sorted by model distance: nonbonded pdb=" O GLN A 60 " pdb=" OG1 THR A 64 " model vdw 2.268 3.040 nonbonded pdb=" O GLN D 60 " pdb=" OG1 THR D 64 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR C 84 " pdb=" OD2 ASP C 140 " model vdw 2.286 3.040 nonbonded pdb=" O HOH D 562 " pdb=" O HOH D 628 " model vdw 2.308 3.040 nonbonded pdb=" O HOH A 422 " pdb=" O HOH A 522 " model vdw 2.312 3.040 ... (remaining 106273 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.830 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 0.065 10672 Z= 0.320 Angle : 0.748 7.098 14464 Z= 0.464 Chirality : 0.049 0.225 1644 Planarity : 0.006 0.062 1880 Dihedral : 12.715 87.185 3984 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.99 % Allowed : 0.72 % Favored : 98.29 % 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: 0.89 (0.23), residues: 1364 helix: 1.49 (0.19), residues: 700 sheet: -0.93 (0.33), residues: 232 loop : 0.20 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 172 TYR 0.021 0.002 TYR D 213 PHE 0.025 0.003 PHE D 144 TRP 0.036 0.005 TRP B 147 HIS 0.014 0.003 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00537 (10672) covalent geometry : angle 0.74789 (14464) hydrogen bonds : bond 0.14724 ( 567) hydrogen bonds : angle 5.85971 ( 1632) *********************** 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 188 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.414 Fit side-chains REVERT: A 41 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7511 (mmmm) REVERT: A 52 GLU cc_start: 0.7875 (tt0) cc_final: 0.7636 (tt0) REVERT: A 86 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8203 (mttt) REVERT: A 152 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7749 (tttm) REVERT: A 242 LYS cc_start: 0.8042 (mtpp) cc_final: 0.7756 (mmmt) REVERT: A 303 ARG cc_start: 0.7008 (ttm-80) cc_final: 0.5896 (ttt-90) REVERT: B 42 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6778 (mmp-170) REVERT: B 242 LYS cc_start: 0.8004 (mmmm) cc_final: 0.7707 (mptt) REVERT: B 288 LYS cc_start: 0.8302 (mtpp) cc_final: 0.8101 (mtmt) REVERT: B 303 ARG cc_start: 0.7346 (ttp80) cc_final: 0.6412 (mmm160) REVERT: C 38 SER cc_start: 0.8173 (t) cc_final: 0.7754 (m) REVERT: C 42 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6677 (mmp80) REVERT: C 66 ASP cc_start: 0.7433 (t70) cc_final: 0.7186 (t0) REVERT: C 199 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7414 (mmpt) REVERT: C 303 ARG cc_start: 0.7654 (mtp85) cc_final: 0.6397 (ttt180) REVERT: D 41 LYS cc_start: 0.7681 (mmtm) cc_final: 0.7393 (mppt) REVERT: D 292 LEU cc_start: 0.8270 (tt) cc_final: 0.8027 (tm) REVERT: D 303 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7090 (mmm160) outliers start: 11 outliers final: 4 residues processed: 186 average time/residue: 0.9196 time to fit residues: 180.1658 Evaluate side-chains 94 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 85 GLN B 119 ASN B 219 HIS C 50 ASN C 95 GLN C 241 GLN C 306 GLN D 50 ASN D 95 GLN D 219 HIS D 231 ASN D 241 GLN D 306 GLN D 324 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100045 restraints weight = 11605.613| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.38 r_work: 0.3036 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10672 Z= 0.133 Angle : 0.539 5.426 14464 Z= 0.284 Chirality : 0.042 0.147 1644 Planarity : 0.004 0.044 1880 Dihedral : 5.233 59.170 1480 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.89 % Allowed : 8.00 % Favored : 90.11 % 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: 1.60 (0.23), residues: 1364 helix: 2.30 (0.19), residues: 712 sheet: -1.69 (0.35), residues: 184 loop : 0.43 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.022 0.002 TYR D 213 PHE 0.018 0.002 PHE B 144 TRP 0.018 0.002 TRP A 147 HIS 0.007 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00304 (10672) covalent geometry : angle 0.53933 (14464) hydrogen bonds : bond 0.05360 ( 567) hydrogen bonds : angle 4.30326 ( 1632) *********************** 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 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.393 Fit side-chains REVERT: A 41 LYS cc_start: 0.7536 (mmtm) cc_final: 0.7325 (mmtt) REVERT: A 52 GLU cc_start: 0.7717 (tt0) cc_final: 0.7404 (tt0) REVERT: A 66 ASP cc_start: 0.7020 (t0) cc_final: 0.6778 (t0) REVERT: A 86 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8093 (mttt) REVERT: A 89 ASP cc_start: 0.7618 (p0) cc_final: 0.7216 (p0) REVERT: A 152 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7564 (tttm) REVERT: A 197 ASP cc_start: 0.7845 (p0) cc_final: 0.7543 (p0) REVERT: A 199 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7193 (mmtm) REVERT: A 242 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7540 (mmmt) REVERT: A 303 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.5927 (ttt-90) REVERT: B 42 ARG cc_start: 0.7376 (mtp180) cc_final: 0.6762 (mmp80) REVERT: B 107 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8518 (ttmm) REVERT: B 199 LYS cc_start: 0.8427 (ttpp) cc_final: 0.7377 (tptp) REVERT: B 242 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7643 (mptt) REVERT: B 303 ARG cc_start: 0.7353 (ttp80) cc_final: 0.6213 (mmm160) REVERT: C 38 SER cc_start: 0.8164 (t) cc_final: 0.7742 (m) REVERT: C 41 LYS cc_start: 0.7478 (mptt) cc_final: 0.6336 (ptmm) REVERT: C 199 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7279 (mmpt) REVERT: C 303 ARG cc_start: 0.7623 (mtp85) cc_final: 0.6483 (ttt180) REVERT: C 325 GLU cc_start: 0.7656 (tp30) cc_final: 0.7009 (tp30) REVERT: C 326 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7146 (tp30) REVERT: D 41 LYS cc_start: 0.7297 (mmtm) cc_final: 0.6896 (mppt) REVERT: D 107 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8286 (ttmm) REVERT: D 292 LEU cc_start: 0.8313 (tt) cc_final: 0.7986 (tm) REVERT: D 303 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7307 (mmm160) outliers start: 21 outliers final: 9 residues processed: 117 average time/residue: 0.8919 time to fit residues: 110.3797 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.0050 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 119 ASN C 95 GLN C 241 GLN D 44 GLN D 95 GLN D 168 ASN D 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.095020 restraints weight = 11638.290| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.39 r_work: 0.2946 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10672 Z= 0.195 Angle : 0.603 6.286 14464 Z= 0.318 Chirality : 0.046 0.161 1644 Planarity : 0.005 0.046 1880 Dihedral : 5.541 59.203 1480 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.25 % Allowed : 8.45 % Favored : 89.30 % 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: 1.60 (0.22), residues: 1364 helix: 2.40 (0.19), residues: 688 sheet: -1.43 (0.38), residues: 144 loop : 0.08 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 257 TYR 0.029 0.002 TYR D 213 PHE 0.015 0.002 PHE B 144 TRP 0.020 0.003 TRP A 147 HIS 0.010 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00473 (10672) covalent geometry : angle 0.60309 (14464) hydrogen bonds : bond 0.06665 ( 567) hydrogen bonds : angle 4.32432 ( 1632) *********************** 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 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.457 Fit side-chains REVERT: A 41 LYS cc_start: 0.7630 (mmtm) cc_final: 0.7418 (mmmm) REVERT: A 52 GLU cc_start: 0.7840 (tt0) cc_final: 0.7556 (tt0) REVERT: A 86 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8040 (mttt) REVERT: A 89 ASP cc_start: 0.7616 (p0) cc_final: 0.7220 (p0) REVERT: A 152 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7501 (tttm) REVERT: A 199 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7299 (mmtm) REVERT: A 242 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7489 (mmmt) REVERT: A 303 ARG cc_start: 0.7226 (ttm-80) cc_final: 0.6057 (ttt-90) REVERT: B 42 ARG cc_start: 0.7305 (mtp180) cc_final: 0.6743 (mmp-170) REVERT: B 67 ASP cc_start: 0.7246 (m-30) cc_final: 0.6956 (m-30) REVERT: B 107 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8646 (ttmm) REVERT: B 199 LYS cc_start: 0.8421 (ttpp) cc_final: 0.7338 (tptp) REVERT: B 242 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7674 (mptt) REVERT: C 38 SER cc_start: 0.8200 (t) cc_final: 0.7610 (m) REVERT: C 41 LYS cc_start: 0.7482 (mptt) cc_final: 0.6314 (ptmm) REVERT: C 66 ASP cc_start: 0.7082 (t70) cc_final: 0.6539 (t0) REVERT: C 95 GLN cc_start: 0.8060 (tt0) cc_final: 0.7807 (tt0) REVERT: C 199 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7287 (mmpt) REVERT: C 303 ARG cc_start: 0.7643 (mtp85) cc_final: 0.6390 (ttt180) REVERT: C 325 GLU cc_start: 0.7777 (tp30) cc_final: 0.7165 (tp30) REVERT: C 326 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7193 (mm-30) REVERT: D 41 LYS cc_start: 0.7362 (mmtm) cc_final: 0.6905 (mppt) REVERT: D 49 GLU cc_start: 0.7458 (pm20) cc_final: 0.7155 (pm20) REVERT: D 107 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8424 (ttmm) REVERT: D 292 LEU cc_start: 0.8461 (tt) cc_final: 0.8114 (tm) REVERT: D 325 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7323 (mm-30) outliers start: 25 outliers final: 9 residues processed: 119 average time/residue: 0.8851 time to fit residues: 111.4405 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 129 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 119 ASN C 241 GLN D 44 GLN D 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097255 restraints weight = 11730.553| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.38 r_work: 0.2995 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.121 Angle : 0.496 5.774 14464 Z= 0.262 Chirality : 0.041 0.147 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.260 59.660 1480 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.61 % Allowed : 8.45 % Favored : 88.94 % 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: 1.80 (0.23), residues: 1364 helix: 2.50 (0.19), residues: 712 sheet: -1.50 (0.37), residues: 144 loop : 0.22 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 257 TYR 0.020 0.002 TYR D 213 PHE 0.014 0.001 PHE D 144 TRP 0.015 0.002 TRP A 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00279 (10672) covalent geometry : angle 0.49593 (14464) hydrogen bonds : bond 0.05080 ( 567) hydrogen bonds : angle 4.10570 ( 1632) *********************** 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 123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.439 Fit side-chains REVERT: A 41 LYS cc_start: 0.7598 (mmtm) cc_final: 0.7380 (mmmm) REVERT: A 52 GLU cc_start: 0.7835 (tt0) cc_final: 0.7559 (tt0) REVERT: A 86 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8047 (mttt) REVERT: A 89 ASP cc_start: 0.7534 (p0) cc_final: 0.7129 (p0) REVERT: A 152 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7500 (tttm) REVERT: A 197 ASP cc_start: 0.7839 (p0) cc_final: 0.7571 (p0) REVERT: A 199 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7120 (mmtm) REVERT: A 242 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7509 (mmmt) REVERT: A 303 ARG cc_start: 0.7160 (ttm-80) cc_final: 0.5984 (ttt-90) REVERT: B 42 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6753 (mmp-170) REVERT: B 49 GLU cc_start: 0.7126 (pm20) cc_final: 0.6758 (pm20) REVERT: B 67 ASP cc_start: 0.7198 (m-30) cc_final: 0.6878 (m-30) REVERT: B 95 GLN cc_start: 0.7860 (tt0) cc_final: 0.7623 (tt0) REVERT: B 152 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8082 (pttm) REVERT: B 199 LYS cc_start: 0.8358 (ttpp) cc_final: 0.7308 (mmtt) REVERT: B 242 LYS cc_start: 0.8034 (mmmm) cc_final: 0.7689 (mptt) REVERT: B 311 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7483 (tttm) REVERT: C 38 SER cc_start: 0.8309 (t) cc_final: 0.7703 (m) REVERT: C 41 LYS cc_start: 0.7482 (mptt) cc_final: 0.6338 (ptmm) REVERT: C 66 ASP cc_start: 0.7011 (t70) cc_final: 0.6494 (t0) REVERT: C 95 GLN cc_start: 0.8120 (tt0) cc_final: 0.7873 (tt0) REVERT: C 152 LYS cc_start: 0.8318 (pttt) cc_final: 0.8004 (pttp) REVERT: C 199 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7259 (mmpt) REVERT: C 303 ARG cc_start: 0.7550 (mtp85) cc_final: 0.6395 (ttt180) REVERT: C 325 GLU cc_start: 0.7786 (tp30) cc_final: 0.7168 (tp30) REVERT: C 326 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 41 LYS cc_start: 0.7389 (mmtm) cc_final: 0.6897 (mppt) REVERT: D 49 GLU cc_start: 0.7472 (pm20) cc_final: 0.7162 (pm20) REVERT: D 53 GLU cc_start: 0.7861 (tp30) cc_final: 0.7608 (tp30) REVERT: D 189 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: D 292 LEU cc_start: 0.8431 (tt) cc_final: 0.8089 (tm) REVERT: D 325 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7270 (mm-30) outliers start: 29 outliers final: 10 residues processed: 119 average time/residue: 0.9124 time to fit residues: 114.6371 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 119 ASN C 166 ASN C 241 GLN D 44 GLN D 95 GLN D 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097959 restraints weight = 11661.883| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.38 r_work: 0.3021 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.114 Angle : 0.482 5.675 14464 Z= 0.253 Chirality : 0.040 0.144 1644 Planarity : 0.004 0.036 1880 Dihedral : 5.166 59.730 1480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.25 % Allowed : 8.81 % Favored : 88.94 % 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: 1.88 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 720 sheet: -1.48 (0.38), residues: 144 loop : 0.21 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 42 TYR 0.019 0.002 TYR D 213 PHE 0.012 0.001 PHE D 144 TRP 0.013 0.001 TRP A 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00263 (10672) covalent geometry : angle 0.48234 (14464) hydrogen bonds : bond 0.04808 ( 567) hydrogen bonds : angle 3.99632 ( 1632) *********************** 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 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.488 Fit side-chains REVERT: A 41 LYS cc_start: 0.7588 (mmtm) cc_final: 0.7266 (mmtt) REVERT: A 52 GLU cc_start: 0.7813 (tt0) cc_final: 0.7572 (tt0) REVERT: A 86 LYS cc_start: 0.8437 (mtmm) cc_final: 0.7978 (mttt) REVERT: A 89 ASP cc_start: 0.7493 (p0) cc_final: 0.7092 (p0) REVERT: A 152 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7416 (tttm) REVERT: A 197 ASP cc_start: 0.7641 (p0) cc_final: 0.7363 (p0) REVERT: A 199 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7040 (mmtm) REVERT: A 242 LYS cc_start: 0.7933 (mtpp) cc_final: 0.7433 (mmmt) REVERT: A 303 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.5862 (ttt-90) REVERT: B 42 ARG cc_start: 0.7402 (mtp180) cc_final: 0.6714 (mmp-170) REVERT: B 49 GLU cc_start: 0.7024 (pm20) cc_final: 0.6589 (pm20) REVERT: B 67 ASP cc_start: 0.7190 (m-30) cc_final: 0.6854 (m-30) REVERT: B 95 GLN cc_start: 0.7844 (tt0) cc_final: 0.7607 (tt0) REVERT: B 199 LYS cc_start: 0.8287 (ttpp) cc_final: 0.7227 (mmtt) REVERT: B 242 LYS cc_start: 0.7996 (mmmm) cc_final: 0.7646 (mptt) REVERT: C 38 SER cc_start: 0.8267 (t) cc_final: 0.7636 (m) REVERT: C 41 LYS cc_start: 0.7428 (mptt) cc_final: 0.6267 (ptmm) REVERT: C 95 GLN cc_start: 0.8082 (tt0) cc_final: 0.7850 (tt0) REVERT: C 152 LYS cc_start: 0.8291 (pttt) cc_final: 0.7966 (pttp) REVERT: C 199 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7191 (mmpt) REVERT: C 288 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7694 (mttp) REVERT: C 303 ARG cc_start: 0.7499 (mtp85) cc_final: 0.6345 (ttt180) REVERT: C 325 GLU cc_start: 0.7748 (tp30) cc_final: 0.7067 (tp30) REVERT: D 41 LYS cc_start: 0.7336 (mmtm) cc_final: 0.6824 (mppt) REVERT: D 49 GLU cc_start: 0.7437 (pm20) cc_final: 0.7107 (pm20) REVERT: D 53 GLU cc_start: 0.7826 (tp30) cc_final: 0.7547 (tp30) REVERT: D 173 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8756 (t80) REVERT: D 189 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: D 292 LEU cc_start: 0.8365 (tt) cc_final: 0.8077 (tm) outliers start: 25 outliers final: 11 residues processed: 118 average time/residue: 0.9056 time to fit residues: 112.7993 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 85 GLN B 119 ASN C 241 GLN D 44 GLN D 95 GLN D 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.098143 restraints weight = 11755.862| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.37 r_work: 0.3024 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.114 Angle : 0.478 5.571 14464 Z= 0.250 Chirality : 0.040 0.142 1644 Planarity : 0.004 0.036 1880 Dihedral : 5.122 59.852 1480 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 9.35 % Favored : 88.67 % 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: 1.95 (0.23), residues: 1364 helix: 2.64 (0.19), residues: 720 sheet: -1.46 (0.38), residues: 144 loop : 0.21 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 303 TYR 0.019 0.001 TYR D 213 PHE 0.012 0.001 PHE D 144 TRP 0.012 0.001 TRP A 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00262 (10672) covalent geometry : angle 0.47783 (14464) hydrogen bonds : bond 0.04733 ( 567) hydrogen bonds : angle 3.94327 ( 1632) *********************** 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 116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.464 Fit side-chains REVERT: A 41 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7400 (mmmm) REVERT: A 52 GLU cc_start: 0.7803 (tt0) cc_final: 0.7579 (tt0) REVERT: A 86 LYS cc_start: 0.8437 (mtmm) cc_final: 0.7970 (mttt) REVERT: A 89 ASP cc_start: 0.7443 (p0) cc_final: 0.7079 (p0) REVERT: A 152 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7387 (tttm) REVERT: A 197 ASP cc_start: 0.7582 (p0) cc_final: 0.7291 (p0) REVERT: A 199 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7057 (mmtm) REVERT: A 242 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7385 (mmmt) REVERT: A 303 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.5834 (ttt-90) REVERT: B 42 ARG cc_start: 0.7401 (mtp180) cc_final: 0.6731 (mmp-170) REVERT: B 49 GLU cc_start: 0.6975 (pm20) cc_final: 0.6499 (pm20) REVERT: B 67 ASP cc_start: 0.7185 (m-30) cc_final: 0.6851 (m-30) REVERT: B 95 GLN cc_start: 0.7851 (tt0) cc_final: 0.7615 (tt0) REVERT: B 152 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8016 (pttm) REVERT: B 199 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7199 (mmtt) REVERT: B 242 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7642 (mptt) REVERT: C 38 SER cc_start: 0.8270 (t) cc_final: 0.7640 (m) REVERT: C 41 LYS cc_start: 0.7420 (mptt) cc_final: 0.6248 (ptmm) REVERT: C 52 GLU cc_start: 0.8116 (tt0) cc_final: 0.7835 (tt0) REVERT: C 95 GLN cc_start: 0.8089 (tt0) cc_final: 0.7870 (tt0) REVERT: C 107 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8246 (tmmm) REVERT: C 152 LYS cc_start: 0.8284 (pttt) cc_final: 0.7954 (pttp) REVERT: C 199 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7166 (mmpt) REVERT: C 288 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7696 (mttp) REVERT: C 303 ARG cc_start: 0.7495 (mtp85) cc_final: 0.6355 (ttt180) REVERT: C 325 GLU cc_start: 0.7742 (tp30) cc_final: 0.7073 (tp30) REVERT: D 41 LYS cc_start: 0.7345 (mmtm) cc_final: 0.6820 (mppt) REVERT: D 49 GLU cc_start: 0.7421 (pm20) cc_final: 0.7093 (pm20) REVERT: D 53 GLU cc_start: 0.7789 (tp30) cc_final: 0.7495 (tp30) REVERT: D 173 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8816 (t80) REVERT: D 189 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: D 292 LEU cc_start: 0.8343 (tt) cc_final: 0.8058 (tm) outliers start: 22 outliers final: 9 residues processed: 114 average time/residue: 0.8930 time to fit residues: 107.6463 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 0.0170 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 241 GLN B 119 ASN C 241 GLN D 44 GLN D 95 GLN D 166 ASN D 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099122 restraints weight = 11662.401| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.37 r_work: 0.3035 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10672 Z= 0.106 Angle : 0.467 5.518 14464 Z= 0.244 Chirality : 0.040 0.136 1644 Planarity : 0.004 0.039 1880 Dihedral : 5.056 59.842 1480 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.89 % Allowed : 9.44 % Favored : 88.67 % 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: 2.03 (0.23), residues: 1364 helix: 2.71 (0.19), residues: 720 sheet: -1.45 (0.38), residues: 144 loop : 0.24 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.018 0.001 TYR D 213 PHE 0.012 0.001 PHE D 144 TRP 0.012 0.001 TRP A 147 HIS 0.003 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00242 (10672) covalent geometry : angle 0.46685 (14464) hydrogen bonds : bond 0.04488 ( 567) hydrogen bonds : angle 3.88855 ( 1632) *********************** 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 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.470 Fit side-chains REVERT: A 41 LYS cc_start: 0.7658 (mmtm) cc_final: 0.7336 (mmtt) REVERT: A 52 GLU cc_start: 0.7831 (tt0) cc_final: 0.7618 (tt0) REVERT: A 86 LYS cc_start: 0.8431 (mtmm) cc_final: 0.7969 (mttt) REVERT: A 89 ASP cc_start: 0.7417 (p0) cc_final: 0.7068 (p0) REVERT: A 152 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7358 (tttm) REVERT: A 197 ASP cc_start: 0.7533 (p0) cc_final: 0.7258 (p0) REVERT: A 199 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7052 (mmtm) REVERT: A 242 LYS cc_start: 0.7889 (mtpp) cc_final: 0.7392 (mmmt) REVERT: A 303 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.5844 (ttt-90) REVERT: B 42 ARG cc_start: 0.7420 (mtp180) cc_final: 0.6752 (mmp-170) REVERT: B 49 GLU cc_start: 0.6984 (pm20) cc_final: 0.6592 (pm20) REVERT: B 67 ASP cc_start: 0.7151 (m-30) cc_final: 0.6826 (m-30) REVERT: B 95 GLN cc_start: 0.7859 (tt0) cc_final: 0.7621 (tt0) REVERT: B 152 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8069 (pttm) REVERT: B 199 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7188 (mmtt) REVERT: B 242 LYS cc_start: 0.7984 (mmmm) cc_final: 0.7640 (mptt) REVERT: C 38 SER cc_start: 0.8293 (t) cc_final: 0.7669 (m) REVERT: C 41 LYS cc_start: 0.7414 (mptt) cc_final: 0.6238 (ptmm) REVERT: C 52 GLU cc_start: 0.8132 (tt0) cc_final: 0.7823 (tt0) REVERT: C 152 LYS cc_start: 0.8283 (pttt) cc_final: 0.7951 (pttp) REVERT: C 199 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7191 (mmpt) REVERT: C 246 GLU cc_start: 0.7825 (mp0) cc_final: 0.7518 (mp0) REVERT: C 288 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7695 (mttp) REVERT: C 303 ARG cc_start: 0.7471 (mtp85) cc_final: 0.6340 (ttt180) REVERT: C 325 GLU cc_start: 0.7714 (tp30) cc_final: 0.7052 (tp30) REVERT: D 41 LYS cc_start: 0.7379 (mmtm) cc_final: 0.6844 (mppt) REVERT: D 49 GLU cc_start: 0.7442 (pm20) cc_final: 0.7108 (pm20) REVERT: D 53 GLU cc_start: 0.7741 (tp30) cc_final: 0.7366 (tp30) REVERT: D 173 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8742 (t80) REVERT: D 189 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8431 (tt0) REVERT: D 292 LEU cc_start: 0.8319 (tt) cc_final: 0.8029 (tm) outliers start: 21 outliers final: 9 residues processed: 114 average time/residue: 0.9048 time to fit residues: 109.1773 Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 241 GLN B 119 ASN C 95 GLN C 241 GLN D 44 GLN D 95 GLN D 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.098001 restraints weight = 11735.428| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.38 r_work: 0.3024 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.116 Angle : 0.483 5.794 14464 Z= 0.252 Chirality : 0.040 0.139 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.092 59.914 1480 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.71 % Allowed : 9.71 % Favored : 88.58 % 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: 1.98 (0.23), residues: 1364 helix: 2.67 (0.19), residues: 720 sheet: -1.46 (0.38), residues: 144 loop : 0.22 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 303 TYR 0.020 0.002 TYR D 213 PHE 0.012 0.001 PHE D 144 TRP 0.011 0.001 TRP A 147 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00267 (10672) covalent geometry : angle 0.48270 (14464) hydrogen bonds : bond 0.04764 ( 567) hydrogen bonds : angle 3.89273 ( 1632) *********************** 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 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.473 Fit side-chains REVERT: A 41 LYS cc_start: 0.7656 (mmtm) cc_final: 0.7418 (mmmm) REVERT: A 52 GLU cc_start: 0.7839 (tt0) cc_final: 0.7624 (tt0) REVERT: A 86 LYS cc_start: 0.8465 (mtmm) cc_final: 0.7994 (mttt) REVERT: A 89 ASP cc_start: 0.7422 (p0) cc_final: 0.7079 (p0) REVERT: A 152 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7381 (tttm) REVERT: A 197 ASP cc_start: 0.7598 (p0) cc_final: 0.7330 (p0) REVERT: A 199 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7125 (mmtm) REVERT: A 242 LYS cc_start: 0.7906 (mtpp) cc_final: 0.7417 (mmmt) REVERT: A 303 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.5895 (ttt-90) REVERT: B 42 ARG cc_start: 0.7422 (mtp180) cc_final: 0.6769 (mmp-170) REVERT: B 49 GLU cc_start: 0.7013 (pm20) cc_final: 0.6605 (pm20) REVERT: B 67 ASP cc_start: 0.7189 (m-30) cc_final: 0.6874 (m-30) REVERT: B 95 GLN cc_start: 0.7900 (tt0) cc_final: 0.7661 (tt0) REVERT: B 152 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8088 (pttm) REVERT: B 199 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7255 (mmtt) REVERT: B 242 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7681 (mptt) REVERT: C 38 SER cc_start: 0.8313 (t) cc_final: 0.7692 (m) REVERT: C 41 LYS cc_start: 0.7429 (mptt) cc_final: 0.6255 (ptmm) REVERT: C 52 GLU cc_start: 0.8154 (tt0) cc_final: 0.7835 (tt0) REVERT: C 107 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8268 (tmmm) REVERT: C 152 LYS cc_start: 0.8314 (pttt) cc_final: 0.7987 (pttp) REVERT: C 199 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7253 (mmpt) REVERT: C 246 GLU cc_start: 0.7862 (mp0) cc_final: 0.7553 (mp0) REVERT: C 288 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7758 (mttp) REVERT: C 303 ARG cc_start: 0.7524 (mtp85) cc_final: 0.6389 (ttt180) REVERT: C 325 GLU cc_start: 0.7743 (tp30) cc_final: 0.7086 (tp30) REVERT: D 41 LYS cc_start: 0.7384 (mmtm) cc_final: 0.6856 (mppt) REVERT: D 49 GLU cc_start: 0.7470 (pm20) cc_final: 0.7135 (pm20) REVERT: D 53 GLU cc_start: 0.7755 (tp30) cc_final: 0.7385 (tp30) REVERT: D 173 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8835 (t80) REVERT: D 189 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: D 292 LEU cc_start: 0.8346 (tt) cc_final: 0.8060 (tm) outliers start: 19 outliers final: 10 residues processed: 112 average time/residue: 0.9186 time to fit residues: 108.6736 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 41 optimal weight: 0.0040 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 119 ASN C 241 GLN D 44 GLN D 95 GLN D 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.099742 restraints weight = 11484.903| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.40 r_work: 0.3034 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10672 Z= 0.107 Angle : 0.470 5.863 14464 Z= 0.245 Chirality : 0.040 0.134 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.022 59.920 1480 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 9.80 % Favored : 88.49 % 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: 2.05 (0.23), residues: 1364 helix: 2.74 (0.19), residues: 720 sheet: -1.45 (0.38), residues: 144 loop : 0.24 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.018 0.001 TYR D 213 PHE 0.012 0.001 PHE D 144 TRP 0.011 0.001 TRP A 147 HIS 0.003 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00247 (10672) covalent geometry : angle 0.46996 (14464) hydrogen bonds : bond 0.04465 ( 567) hydrogen bonds : angle 3.85117 ( 1632) *********************** 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 114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.454 Fit side-chains REVERT: A 41 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7302 (mmtt) REVERT: A 52 GLU cc_start: 0.7872 (tt0) cc_final: 0.7651 (tt0) REVERT: A 86 LYS cc_start: 0.8458 (mtmm) cc_final: 0.7982 (mttt) REVERT: A 89 ASP cc_start: 0.7412 (p0) cc_final: 0.7058 (p0) REVERT: A 152 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7360 (tttm) REVERT: A 197 ASP cc_start: 0.7560 (p0) cc_final: 0.7294 (p0) REVERT: A 199 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7121 (mmtm) REVERT: A 242 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7404 (mmmt) REVERT: A 303 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.5844 (ttt-90) REVERT: B 42 ARG cc_start: 0.7422 (mtp180) cc_final: 0.6769 (mmp-170) REVERT: B 49 GLU cc_start: 0.7005 (pm20) cc_final: 0.6586 (pm20) REVERT: B 67 ASP cc_start: 0.7144 (m-30) cc_final: 0.6818 (m-30) REVERT: B 95 GLN cc_start: 0.7889 (tt0) cc_final: 0.7652 (tt0) REVERT: B 152 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8104 (pttm) REVERT: B 199 LYS cc_start: 0.8282 (ttpp) cc_final: 0.7237 (mmtt) REVERT: B 242 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7657 (mptt) REVERT: C 38 SER cc_start: 0.8314 (t) cc_final: 0.7689 (m) REVERT: C 41 LYS cc_start: 0.7422 (mptt) cc_final: 0.6242 (ptmm) REVERT: C 52 GLU cc_start: 0.8160 (tt0) cc_final: 0.7863 (tt0) REVERT: C 107 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8231 (tmmm) REVERT: C 152 LYS cc_start: 0.8302 (pttt) cc_final: 0.7291 (tttt) REVERT: C 199 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7249 (mmpt) REVERT: C 246 GLU cc_start: 0.7850 (mp0) cc_final: 0.7507 (mp0) REVERT: C 288 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7729 (mttp) REVERT: C 303 ARG cc_start: 0.7481 (mtp85) cc_final: 0.6360 (ttt180) REVERT: C 325 GLU cc_start: 0.7734 (tp30) cc_final: 0.7083 (tp30) REVERT: D 41 LYS cc_start: 0.7374 (mmtm) cc_final: 0.6847 (mppt) REVERT: D 49 GLU cc_start: 0.7471 (pm20) cc_final: 0.7115 (pm20) REVERT: D 53 GLU cc_start: 0.7742 (tp30) cc_final: 0.7377 (tp30) REVERT: D 173 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.8825 (t80) REVERT: D 189 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: D 292 LEU cc_start: 0.8325 (tt) cc_final: 0.8034 (tm) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 0.9048 time to fit residues: 108.1393 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 chunk 104 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 241 GLN B 119 ASN C 241 GLN D 44 GLN D 95 GLN D 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099705 restraints weight = 11625.781| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.41 r_work: 0.3018 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10672 Z= 0.107 Angle : 0.472 6.484 14464 Z= 0.246 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.011 59.750 1480 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.62 % Allowed : 9.98 % Favored : 88.40 % 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: 2.07 (0.23), residues: 1364 helix: 2.75 (0.19), residues: 720 sheet: -1.43 (0.38), residues: 144 loop : 0.25 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.018 0.001 TYR D 213 PHE 0.012 0.001 PHE D 144 TRP 0.011 0.001 TRP A 147 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00247 (10672) covalent geometry : angle 0.47211 (14464) hydrogen bonds : bond 0.04463 ( 567) hydrogen bonds : angle 3.84032 ( 1632) ********************** 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 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.340 Fit side-chains REVERT: A 41 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7391 (mmtt) REVERT: A 52 GLU cc_start: 0.7896 (tt0) cc_final: 0.7680 (tt0) REVERT: A 86 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8021 (mttt) REVERT: A 89 ASP cc_start: 0.7433 (p0) cc_final: 0.7094 (p0) REVERT: A 152 LYS cc_start: 0.7979 (ttpp) cc_final: 0.7410 (tttm) REVERT: A 199 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7176 (mmtm) REVERT: A 242 LYS cc_start: 0.7931 (mtpp) cc_final: 0.7461 (mmmt) REVERT: A 303 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.5907 (ttt-90) REVERT: B 42 ARG cc_start: 0.7411 (mtp180) cc_final: 0.6780 (mmp-170) REVERT: B 49 GLU cc_start: 0.7035 (pm20) cc_final: 0.6610 (pm20) REVERT: B 67 ASP cc_start: 0.7179 (m-30) cc_final: 0.6849 (m-30) REVERT: B 95 GLN cc_start: 0.7945 (tt0) cc_final: 0.7709 (tt0) REVERT: B 152 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8150 (pttm) REVERT: B 199 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7313 (mmtt) REVERT: B 242 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7702 (mptt) REVERT: C 38 SER cc_start: 0.8356 (t) cc_final: 0.7737 (m) REVERT: C 41 LYS cc_start: 0.7461 (mptt) cc_final: 0.6285 (ptmm) REVERT: C 52 GLU cc_start: 0.8187 (tt0) cc_final: 0.7886 (tt0) REVERT: C 95 GLN cc_start: 0.8140 (tt0) cc_final: 0.7893 (tt0) REVERT: C 107 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8296 (tmmm) REVERT: C 152 LYS cc_start: 0.8333 (pttt) cc_final: 0.7350 (tttt) REVERT: C 199 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7336 (mmpt) REVERT: C 246 GLU cc_start: 0.7892 (mp0) cc_final: 0.7562 (mp0) REVERT: C 288 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7794 (mttp) REVERT: C 303 ARG cc_start: 0.7533 (mtp85) cc_final: 0.6422 (ttt180) REVERT: C 325 GLU cc_start: 0.7771 (tp30) cc_final: 0.7128 (tp30) REVERT: D 41 LYS cc_start: 0.7414 (mmtm) cc_final: 0.6881 (mppt) REVERT: D 49 GLU cc_start: 0.7502 (pm20) cc_final: 0.7163 (pm20) REVERT: D 53 GLU cc_start: 0.7764 (tp30) cc_final: 0.7408 (tp30) REVERT: D 173 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8850 (t80) REVERT: D 189 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: D 292 LEU cc_start: 0.8359 (tt) cc_final: 0.8076 (tm) outliers start: 18 outliers final: 10 residues processed: 110 average time/residue: 0.8718 time to fit residues: 101.3747 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 119 ASN C 241 GLN D 44 GLN D 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096653 restraints weight = 11736.322| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.37 r_work: 0.3000 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10672 Z= 0.132 Angle : 0.508 6.165 14464 Z= 0.265 Chirality : 0.041 0.146 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.169 59.827 1480 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.71 % Allowed : 9.98 % 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: 1.91 (0.23), residues: 1364 helix: 2.62 (0.19), residues: 720 sheet: -1.43 (0.38), residues: 144 loop : 0.16 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.023 0.002 TYR D 213 PHE 0.013 0.001 PHE C 144 TRP 0.013 0.002 TRP A 147 HIS 0.005 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00309 (10672) covalent geometry : angle 0.50809 (14464) hydrogen bonds : bond 0.05197 ( 567) hydrogen bonds : angle 3.95141 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.04 seconds wall clock time: 73 minutes 28.17 seconds (4408.17 seconds total)