Starting phenix.real_space_refine on Tue Aug 4 19:02:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enc_19831/08_2026/9enc_19831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enc_19831/08_2026/9enc_19831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9enc_19831/08_2026/9enc_19831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enc_19831/08_2026/9enc_19831.map" model { file = "/net/cci-nas-00/data/ceres_data/9enc_19831/08_2026/9enc_19831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enc_19831/08_2026/9enc_19831.cif" } resolution = 3.36 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 30 5.16 5 C 3699 2.51 5 N 1089 2.21 5 O 1357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6249 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2304 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 10, 'TRANS': 270} Chain breaks: 2 Chain: "B" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2356 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 3 Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1589 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 32} Link IDs: {'rna2p': 15, 'rna3p': 59} Time building chain proxies: 1.05, per 1000 atoms: 0.17 Number of scatterers: 6249 At special positions: 0 Unit cell: (102.318, 127.686, 65.9568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 74 15.00 O 1357 8.00 N 1089 7.00 C 3699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 327 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 263.9 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 35.3% alpha, 25.1% beta 22 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 159 through 168 removed outlier: 3.924A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.766A pdb=" N TYR A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.746A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 369 Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.503A pdb=" N LYS B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.925A pdb=" N VAL B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 removed outlier: 3.667A pdb=" N GLN B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.791A pdb=" N CYS B 226 " --> pdb=" O ARG B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.659A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.518A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 5.122A pdb=" N PHE A 124 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N TYR A 71 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 63 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS A 64 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 66 " --> pdb=" O TRP A 177 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TRP A 177 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG A 68 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.346A pdb=" N ASP A 326 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN A 126 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LYS A 328 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 11.007A pdb=" N ILE A 128 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N CYS A 327 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 192 " --> pdb=" O CYS A 327 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU A 264 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 248 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN A 266 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 246 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU A 268 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A 244 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A 270 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113 removed outlier: 5.056A pdb=" N PHE B 124 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR B 71 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 61 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS B 64 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 66 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP B 177 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG B 68 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113 removed outlier: 7.226A pdb=" N SER B 122 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ASP B 326 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N PHE B 124 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N LYS B 328 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N GLN B 126 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N CYS B 327 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU B 192 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 199 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 264 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU B 248 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN B 266 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 246 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU B 268 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA B 244 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR B 270 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 239 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1690 1.34 - 1.45: 1630 1.45 - 1.57: 3030 1.57 - 1.69: 148 1.69 - 1.81: 48 Bond restraints: 6546 Sorted by residual: bond pdb=" C GLU B 260 " pdb=" N PRO B 261 " ideal model delta sigma weight residual 1.334 1.352 -0.018 8.40e-03 1.42e+04 4.65e+00 bond pdb=" C3' G D 36 " pdb=" O3' G D 36 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.20e-02 6.94e+03 1.78e+00 bond pdb=" C GLU A 260 " pdb=" N PRO A 261 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.11e-02 8.12e+03 1.69e+00 bond pdb=" O3' G D 36 " pdb=" P A D 37 " ideal model delta sigma weight residual 1.607 1.620 -0.013 1.20e-02 6.94e+03 1.17e+00 bond pdb=" CA ASN A 232 " pdb=" C ASN A 232 " ideal model delta sigma weight residual 1.523 1.535 -0.013 1.41e-02 5.03e+03 8.00e-01 ... (remaining 6541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 8953 2.07 - 4.14: 250 4.14 - 6.20: 9 6.20 - 8.27: 0 8.27 - 10.34: 1 Bond angle restraints: 9213 Sorted by residual: angle pdb=" C3' G D 36 " pdb=" O3' G D 36 " pdb=" P A D 37 " ideal model delta sigma weight residual 119.70 125.79 -6.09 1.20e+00 6.94e-01 2.58e+01 angle pdb=" C1' C D 48 " pdb=" N1 C D 48 " pdb=" C2 C D 48 " ideal model delta sigma weight residual 118.80 123.62 -4.82 1.10e+00 8.26e-01 1.92e+01 angle pdb=" N1 C D 48 " pdb=" C2 C D 48 " pdb=" O2 C D 48 " ideal model delta sigma weight residual 118.90 121.29 -2.39 6.00e-01 2.78e+00 1.59e+01 angle pdb=" O5' G D 17 " pdb=" C5' G D 17 " pdb=" C4' G D 17 " ideal model delta sigma weight residual 109.40 112.43 -3.03 8.00e-01 1.56e+00 1.44e+01 angle pdb=" O5' G D 18 " pdb=" C5' G D 18 " pdb=" C4' G D 18 " ideal model delta sigma weight residual 109.40 112.34 -2.94 8.00e-01 1.56e+00 1.35e+01 ... (remaining 9208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.20: 3647 31.20 - 62.40: 282 62.40 - 93.60: 79 93.60 - 124.80: 2 124.80 - 156.00: 4 Dihedral angle restraints: 4014 sinusoidal: 2349 harmonic: 1665 Sorted by residual: dihedral pdb=" O4' U D 35 " pdb=" C1' U D 35 " pdb=" N1 U D 35 " pdb=" C2 U D 35 " ideal model delta sinusoidal sigma weight residual 200.00 44.00 156.00 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' C D 48 " pdb=" C1' C D 48 " pdb=" N1 C D 48 " pdb=" C2 C D 48 " ideal model delta sinusoidal sigma weight residual -160.00 -25.27 -134.73 1 1.50e+01 4.44e-03 7.27e+01 dihedral pdb=" O4' A D 37 " pdb=" C1' A D 37 " pdb=" N9 A D 37 " pdb=" C4 A D 37 " ideal model delta sinusoidal sigma weight residual 254.00 175.33 78.67 1 1.70e+01 3.46e-03 2.67e+01 ... (remaining 4011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 792 0.042 - 0.084: 164 0.084 - 0.126: 45 0.126 - 0.168: 60 0.168 - 0.210: 2 Chirality restraints: 1063 Sorted by residual: chirality pdb=" P A D 37 " pdb=" OP1 A D 37 " pdb=" OP2 A D 37 " pdb=" O5' A D 37 " both_signs ideal model delta sigma weight residual True 2.41 -2.62 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C1' A D 58 " pdb=" O4' A D 58 " pdb=" C2' A D 58 " pdb=" N9 A D 58 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA PHE A 320 " pdb=" N PHE A 320 " pdb=" C PHE A 320 " pdb=" CB PHE A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1060 not shown) Planarity restraints: 907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 32 " 0.026 2.00e-02 2.50e+03 1.32e-02 3.94e+00 pdb=" N1 C D 32 " -0.029 2.00e-02 2.50e+03 pdb=" C2 C D 32 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C D 32 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C D 32 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C D 32 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C D 32 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C D 32 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C D 32 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 58 " -0.017 2.00e-02 2.50e+03 8.90e-03 2.18e+00 pdb=" N9 A D 58 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A D 58 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A D 58 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A D 58 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 58 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A D 58 " -0.001 2.00e-02 2.50e+03 pdb=" N1 A D 58 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 58 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 58 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A D 58 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 44 " -0.018 2.00e-02 2.50e+03 9.34e-03 1.96e+00 pdb=" N1 C D 44 " 0.020 2.00e-02 2.50e+03 pdb=" C2 C D 44 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C D 44 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C D 44 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C D 44 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C D 44 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C D 44 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C D 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 904 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1073 2.77 - 3.30: 5518 3.30 - 3.83: 10864 3.83 - 4.37: 12384 4.37 - 4.90: 20070 Nonbonded interactions: 49909 Sorted by model distance: nonbonded pdb=" OP2 G D 45 " pdb=" N2 G D 45 " model vdw 2.232 3.120 nonbonded pdb=" O2' U D 35 " pdb=" OP1 A D 37 " model vdw 2.234 3.040 nonbonded pdb=" OG SER B 105 " pdb=" OG1 THR B 108 " model vdw 2.235 3.040 nonbonded pdb=" O2' A D 7 " pdb=" O2 C D 48 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR A 197 " pdb=" O VAL A 318 " model vdw 2.305 3.040 ... (remaining 49904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 61 through 228 or resid 236 through 249 or resid 257 throu \ gh 369)) selection = (chain 'B' and (resid 61 through 134 or resid 157 through 369)) } 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6548 Z= 0.155 Angle : 0.623 10.339 9217 Z= 0.462 Chirality : 0.048 0.210 1063 Planarity : 0.003 0.033 907 Dihedral : 21.396 156.003 2928 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.20 % Allowed : 27.66 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.36), residues: 552 helix: 1.24 (0.40), residues: 172 sheet: 0.61 (0.57), residues: 87 loop : -1.22 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.006 0.001 TYR A 216 PHE 0.017 0.001 PHE B 320 TRP 0.006 0.001 TRP A 352 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 ( 6546) covalent geometry : angle 0.62255 / 0.46 ( 9213) SS BOND : bond 0.00164 / 0.10 ( 2) SS BOND : angle 0.66776 / 0.35 ( 4) hydrogen bonds : bond 0.19239 / 12.49 ( 239) hydrogen bonds : angle 6.40376 / 4.48 ( 618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.151 Fit side-chains REVERT: A 293 MET cc_start: 0.7799 (ttt) cc_final: 0.7593 (ttt) REVERT: A 295 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8216 (ttpp) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0828 time to fit residues: 3.5733 Evaluate side-chains 22 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.072687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052915 restraints weight = 21018.287| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.10 r_work: 0.2964 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6548 Z= 0.148 Angle : 0.517 11.129 9217 Z= 0.284 Chirality : 0.039 0.265 1063 Planarity : 0.004 0.036 907 Dihedral : 20.764 155.356 1796 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.20 % Allowed : 26.05 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.36), residues: 552 helix: 2.25 (0.38), residues: 166 sheet: 0.56 (0.56), residues: 91 loop : -1.17 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 257 TYR 0.011 0.001 TYR B 216 PHE 0.016 0.001 PHE B 320 TRP 0.015 0.002 TRP A 258 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 6546) covalent geometry : angle 0.51711 / 0.28 ( 9213) SS BOND : bond 0.00388 / 0.23 ( 2) SS BOND : angle 0.90975 / 0.48 ( 4) hydrogen bonds : bond 0.06075 / 4.07 ( 239) hydrogen bonds : angle 4.51417 / 3.21 ( 618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.207 Fit side-chains REVERT: A 72 MET cc_start: 0.8470 (mpp) cc_final: 0.8125 (mmm) REVERT: A 258 TRP cc_start: 0.8059 (t60) cc_final: 0.7355 (t60) outliers start: 6 outliers final: 1 residues processed: 26 average time/residue: 0.0482 time to fit residues: 2.1440 Evaluate side-chains 22 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 7 optimal weight: 4.9990 chunk 51 optimal weight: 0.0060 chunk 15 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.071123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.051464 restraints weight = 20922.439| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.08 r_work: 0.2924 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6548 Z= 0.216 Angle : 0.554 11.626 9217 Z= 0.300 Chirality : 0.041 0.238 1063 Planarity : 0.004 0.033 907 Dihedral : 20.767 155.636 1792 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.40 % Allowed : 23.85 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.36), residues: 552 helix: 2.24 (0.38), residues: 167 sheet: 0.27 (0.56), residues: 86 loop : -1.24 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 257 TYR 0.015 0.002 TYR B 216 PHE 0.015 0.002 PHE A 320 TRP 0.015 0.002 TRP B 74 HIS 0.007 0.002 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 ( 6546) covalent geometry : angle 0.55379 / 0.30 ( 9213) SS BOND : bond 0.00529 / 0.31 ( 2) SS BOND : angle 1.14989 / 0.59 ( 4) hydrogen bonds : bond 0.06162 / 4.08 ( 239) hydrogen bonds : angle 4.41103 / 3.11 ( 618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.125 Fit side-chains REVERT: A 72 MET cc_start: 0.8526 (mpp) cc_final: 0.8183 (mmm) REVERT: A 258 TRP cc_start: 0.8168 (t60) cc_final: 0.7495 (t60) REVERT: A 293 MET cc_start: 0.7754 (ttt) cc_final: 0.7419 (ttm) REVERT: B 72 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8293 (mmm) outliers start: 12 outliers final: 3 residues processed: 30 average time/residue: 0.0561 time to fit residues: 2.5016 Evaluate side-chains 25 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051429 restraints weight = 20974.714| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.08 r_work: 0.2920 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6548 Z= 0.192 Angle : 0.528 11.559 9217 Z= 0.287 Chirality : 0.040 0.239 1063 Planarity : 0.004 0.033 907 Dihedral : 20.763 156.345 1792 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.41 % Allowed : 22.24 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.36), residues: 552 helix: 2.22 (0.38), residues: 167 sheet: 0.10 (0.56), residues: 84 loop : -1.32 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.013 0.001 TYR A 195 PHE 0.017 0.002 PHE B 124 TRP 0.026 0.002 TRP B 74 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 6546) covalent geometry : angle 0.52746 / 0.29 ( 9213) SS BOND : bond 0.00466 / 0.28 ( 2) SS BOND : angle 1.13978 / 0.58 ( 4) hydrogen bonds : bond 0.05939 / 3.97 ( 239) hydrogen bonds : angle 4.25828 / 2.99 ( 618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 21 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8503 (mpp) cc_final: 0.8162 (mmm) REVERT: A 229 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8445 (t70) REVERT: A 258 TRP cc_start: 0.8204 (t60) cc_final: 0.7602 (t60) REVERT: A 293 MET cc_start: 0.7755 (ttt) cc_final: 0.7456 (ttm) outliers start: 17 outliers final: 10 residues processed: 35 average time/residue: 0.0479 time to fit residues: 2.4374 Evaluate side-chains 32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.072255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052589 restraints weight = 21193.605| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.12 r_work: 0.2953 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6548 Z= 0.118 Angle : 0.462 11.495 9217 Z= 0.254 Chirality : 0.037 0.238 1063 Planarity : 0.004 0.035 907 Dihedral : 20.719 156.344 1792 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.60 % Allowed : 23.65 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.36), residues: 552 helix: 2.36 (0.38), residues: 167 sheet: 0.20 (0.55), residues: 91 loop : -1.22 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.007 0.001 TYR B 216 PHE 0.016 0.001 PHE B 320 TRP 0.010 0.001 TRP A 352 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 6546) covalent geometry : angle 0.46200 / 0.25 ( 9213) SS BOND : bond 0.00446 / 0.26 ( 2) SS BOND : angle 1.00091 / 0.49 ( 4) hydrogen bonds : bond 0.05319 / 3.59 ( 239) hydrogen bonds : angle 3.96453 / 2.78 ( 618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8516 (mpp) cc_final: 0.8177 (mmm) REVERT: A 229 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8381 (t70) REVERT: A 258 TRP cc_start: 0.8171 (t60) cc_final: 0.7620 (t60) outliers start: 8 outliers final: 7 residues processed: 28 average time/residue: 0.0467 time to fit residues: 1.9989 Evaluate side-chains 29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.070645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050816 restraints weight = 21229.274| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.10 r_work: 0.2890 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6548 Z= 0.218 Angle : 0.545 11.539 9217 Z= 0.291 Chirality : 0.040 0.241 1063 Planarity : 0.004 0.033 907 Dihedral : 20.752 157.153 1792 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.40 % Allowed : 24.05 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.36), residues: 552 helix: 2.18 (0.38), residues: 167 sheet: -0.16 (0.56), residues: 86 loop : -1.26 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.012 0.001 TYR A 216 PHE 0.017 0.002 PHE B 124 TRP 0.009 0.002 TRP A 352 HIS 0.008 0.002 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 ( 6546) covalent geometry : angle 0.54477 / 0.29 ( 9213) SS BOND : bond 0.00504 / 0.30 ( 2) SS BOND : angle 1.06552 / 0.54 ( 4) hydrogen bonds : bond 0.06027 / 4.03 ( 239) hydrogen bonds : angle 4.20081 / 2.95 ( 618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8604 (mpp) cc_final: 0.8234 (mmm) REVERT: A 229 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8325 (t70) REVERT: A 258 TRP cc_start: 0.8256 (t60) cc_final: 0.7757 (t60) REVERT: B 126 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8060 (tp-100) outliers start: 12 outliers final: 7 residues processed: 31 average time/residue: 0.0494 time to fit residues: 2.2507 Evaluate side-chains 30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 39 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 overall best weight: 1.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051046 restraints weight = 21144.576| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.10 r_work: 0.2897 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6548 Z= 0.186 Angle : 0.516 11.279 9217 Z= 0.278 Chirality : 0.039 0.242 1063 Planarity : 0.004 0.035 907 Dihedral : 20.749 157.508 1792 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.20 % Allowed : 24.65 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.36), residues: 552 helix: 2.12 (0.38), residues: 167 sheet: -0.23 (0.56), residues: 84 loop : -1.30 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.011 0.001 TYR A 216 PHE 0.017 0.002 PHE B 124 TRP 0.010 0.001 TRP A 352 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 6546) covalent geometry : angle 0.51525 / 0.28 ( 9213) SS BOND : bond 0.00484 / 0.29 ( 2) SS BOND : angle 1.14821 / 0.58 ( 4) hydrogen bonds : bond 0.05881 / 3.94 ( 239) hydrogen bonds : angle 4.12099 / 2.88 ( 618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8610 (mpp) cc_final: 0.8240 (mmm) REVERT: A 229 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8295 (t70) REVERT: A 258 TRP cc_start: 0.8248 (t60) cc_final: 0.7733 (t60) REVERT: B 126 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8029 (tp-100) outliers start: 11 outliers final: 7 residues processed: 30 average time/residue: 0.0511 time to fit residues: 2.2455 Evaluate side-chains 30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.072117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.052300 restraints weight = 21159.337| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.12 r_work: 0.2935 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6548 Z= 0.116 Angle : 0.460 10.631 9217 Z= 0.252 Chirality : 0.036 0.233 1063 Planarity : 0.004 0.035 907 Dihedral : 20.699 157.105 1792 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.80 % Allowed : 24.05 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.36), residues: 552 helix: 2.27 (0.38), residues: 167 sheet: -0.15 (0.55), residues: 92 loop : -1.20 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.013 0.001 TYR A 216 PHE 0.017 0.001 PHE B 124 TRP 0.010 0.001 TRP A 352 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 6546) covalent geometry : angle 0.45915 / 0.25 ( 9213) SS BOND : bond 0.00449 / 0.27 ( 2) SS BOND : angle 1.00478 / 0.49 ( 4) hydrogen bonds : bond 0.05262 / 3.56 ( 239) hydrogen bonds : angle 3.85339 / 2.70 ( 618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8614 (mpp) cc_final: 0.8241 (mmm) REVERT: A 229 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8301 (t70) REVERT: A 258 TRP cc_start: 0.8208 (t60) cc_final: 0.7690 (t60) REVERT: A 282 MET cc_start: 0.7865 (mtm) cc_final: 0.7424 (mtt) REVERT: A 295 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8226 (tttp) REVERT: B 126 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7921 (tp-100) REVERT: B 259 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5644 (tm-30) outliers start: 9 outliers final: 5 residues processed: 29 average time/residue: 0.0654 time to fit residues: 2.6976 Evaluate side-chains 30 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 259 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.0020 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.073476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053714 restraints weight = 21059.568| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.09 r_work: 0.2974 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6548 Z= 0.092 Angle : 0.440 9.229 9217 Z= 0.239 Chirality : 0.036 0.210 1063 Planarity : 0.003 0.035 907 Dihedral : 20.643 156.395 1792 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.80 % Allowed : 24.05 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.36), residues: 552 helix: 2.49 (0.38), residues: 167 sheet: -0.01 (0.55), residues: 91 loop : -1.13 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.008 0.001 TYR A 216 PHE 0.019 0.001 PHE B 320 TRP 0.011 0.001 TRP B 74 HIS 0.004 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 ( 6546) covalent geometry : angle 0.44025 / 0.24 ( 9213) SS BOND : bond 0.00341 / 0.20 ( 2) SS BOND : angle 0.64427 / 0.31 ( 4) hydrogen bonds : bond 0.04719 / 3.20 ( 239) hydrogen bonds : angle 3.64391 / 2.56 ( 618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.164 Fit side-chains REVERT: A 72 MET cc_start: 0.8633 (mpp) cc_final: 0.8223 (mmm) REVERT: A 229 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8312 (t70) REVERT: A 258 TRP cc_start: 0.8164 (t60) cc_final: 0.7716 (t60) REVERT: A 295 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8249 (tttp) REVERT: B 126 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7857 (tp-100) outliers start: 9 outliers final: 4 residues processed: 30 average time/residue: 0.0513 time to fit residues: 2.3510 Evaluate side-chains 28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.071448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051608 restraints weight = 21180.502| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.11 r_work: 0.2915 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6548 Z= 0.197 Angle : 0.505 8.401 9217 Z= 0.271 Chirality : 0.038 0.199 1063 Planarity : 0.004 0.035 907 Dihedral : 20.674 157.276 1792 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.60 % Allowed : 24.05 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.36), residues: 552 helix: 2.34 (0.38), residues: 167 sheet: -0.19 (0.54), residues: 92 loop : -1.18 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.011 0.001 TYR A 195 PHE 0.016 0.002 PHE A 320 TRP 0.009 0.001 TRP A 352 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 ( 6546) covalent geometry : angle 0.50486 / 0.27 ( 9213) SS BOND : bond 0.00495 / 0.30 ( 2) SS BOND : angle 0.98631 / 0.50 ( 4) hydrogen bonds : bond 0.05461 / 3.66 ( 239) hydrogen bonds : angle 3.94822 / 2.76 ( 618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8700 (mpp) cc_final: 0.8300 (mmm) REVERT: A 229 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8338 (t70) REVERT: A 258 TRP cc_start: 0.8260 (t60) cc_final: 0.7821 (t60) REVERT: A 282 MET cc_start: 0.7997 (mtm) cc_final: 0.7604 (mtt) REVERT: B 126 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8047 (tp-100) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 0.0579 time to fit residues: 2.3673 Evaluate side-chains 28 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.072586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052880 restraints weight = 21008.112| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.08 r_work: 0.2952 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6548 Z= 0.099 Angle : 0.442 7.611 9217 Z= 0.243 Chirality : 0.035 0.186 1063 Planarity : 0.004 0.034 907 Dihedral : 20.662 157.031 1792 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.20 % Allowed : 24.45 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.36), residues: 552 helix: 2.42 (0.38), residues: 167 sheet: -0.05 (0.55), residues: 91 loop : -1.16 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.008 0.001 TYR A 216 PHE 0.018 0.001 PHE B 320 TRP 0.010 0.001 TRP A 352 HIS 0.005 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 ( 6546) covalent geometry : angle 0.44211 / 0.24 ( 9213) SS BOND : bond 0.00394 / 0.23 ( 2) SS BOND : angle 0.84378 / 0.42 ( 4) hydrogen bonds : bond 0.04983 / 3.36 ( 239) hydrogen bonds : angle 3.74974 / 2.63 ( 618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.12 seconds wall clock time: 20 minutes 31.65 seconds (1231.65 seconds total)