Starting phenix.real_space_refine on Thu Mar 13 17:41:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uxu_26862/03_2025/7uxu_26862_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uxu_26862/03_2025/7uxu_26862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2025/7uxu_26862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2025/7uxu_26862.map" model { file = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2025/7uxu_26862_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uxu_26862/03_2025/7uxu_26862_trim.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 8 5.16 5 C 2852 2.51 5 N 744 2.21 5 O 896 1.98 5 H 4268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8776 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "B" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "C" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "D" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2148 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'1O4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.53, per 1000 atoms: 0.52 Number of scatterers: 8776 At special positions: 0 Unit cell: (77.6, 64, 111.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 8 16.00 P 8 15.00 O 896 8.00 N 744 7.00 C 2852 6.00 H 4268 1.00 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: 1.96 Conformation dependent library (CDL) restraints added in 632.9 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 64.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.580A pdb=" N LYS A 146 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 196 through 202 removed outlier: 3.956A pdb=" N LYS A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.841A pdb=" N ASN A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.820A pdb=" N VAL A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.574A pdb=" N LYS B 146 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 196 through 202 removed outlier: 4.009A pdb=" N LYS B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.918A pdb=" N ASN B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.768A pdb=" N VAL B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.596A pdb=" N LYS C 146 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 161 Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 176 through 187 Processing helix chain 'C' and resid 196 through 202 removed outlier: 4.068A pdb=" N LYS C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.913A pdb=" N ASN C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 254 through 267 removed outlier: 3.783A pdb=" N VAL C 265 " --> pdb=" O GLN C 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.641A pdb=" N LYS D 146 " --> pdb=" O SER D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 161 Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 176 through 187 Processing helix chain 'D' and resid 196 through 202 removed outlier: 4.009A pdb=" N LYS D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.901A pdb=" N ASN D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 241 through 245 Processing helix chain 'D' and resid 254 through 267 removed outlier: 3.810A pdb=" N VAL D 265 " --> pdb=" O GLN D 261 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 165 removed outlier: 6.900A pdb=" N LEU A 137 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE A 138 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 194 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N SER A 140 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 193 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 165 removed outlier: 6.876A pdb=" N LEU B 137 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE B 138 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL B 194 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER B 140 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 193 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 164 through 165 removed outlier: 6.872A pdb=" N LEU C 137 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE C 138 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL C 194 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER C 140 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 193 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 164 through 165 removed outlier: 6.874A pdb=" N LEU D 137 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE D 138 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 194 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N SER D 140 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 193 " --> pdb=" O LEU D 224 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 585 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: 2.86 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4268 1.03 - 1.22: 4 1.22 - 1.42: 1936 1.42 - 1.61: 2656 1.61 - 1.80: 16 Bond restraints: 8880 Sorted by residual: bond pdb=" O1 1O4 A 301 " pdb=" P 1O4 A 301 " ideal model delta sigma weight residual 1.656 1.599 0.057 2.00e-02 2.50e+03 8.16e+00 bond pdb=" O1 1O4 C 301 " pdb=" P 1O4 C 301 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" O1 1O4 D 301 " pdb=" P 1O4 D 301 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.82e+00 bond pdb=" O1 1O4 B 301 " pdb=" P 1O4 B 301 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.77e+00 bond pdb=" O 1O4 B 301 " pdb=" P 1O4 B 301 " ideal model delta sigma weight residual 1.647 1.593 0.054 2.00e-02 2.50e+03 7.41e+00 ... (remaining 8875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 15575 1.87 - 3.74: 383 3.74 - 5.62: 45 5.62 - 7.49: 9 7.49 - 9.36: 4 Bond angle restraints: 16016 Sorted by residual: angle pdb=" O 1O4 C 301 " pdb=" P 1O4 C 301 " pdb=" O1 1O4 C 301 " ideal model delta sigma weight residual 96.18 105.54 -9.36 3.00e+00 1.11e-01 9.74e+00 angle pdb=" N PRO A 225 " pdb=" CA PRO A 225 " pdb=" C PRO A 225 " ideal model delta sigma weight residual 111.68 116.75 -5.07 1.67e+00 3.59e-01 9.23e+00 angle pdb=" O 1O4 A 301 " pdb=" P 1O4 A 301 " pdb=" O1 1O4 A 301 " ideal model delta sigma weight residual 96.18 105.09 -8.91 3.00e+00 1.11e-01 8.81e+00 angle pdb=" N PRO C 225 " pdb=" CA PRO C 225 " pdb=" C PRO C 225 " ideal model delta sigma weight residual 111.68 116.51 -4.83 1.67e+00 3.59e-01 8.36e+00 angle pdb=" O 1O4 D 301 " pdb=" P 1O4 D 301 " pdb=" O1 1O4 D 301 " ideal model delta sigma weight residual 96.18 104.75 -8.57 3.00e+00 1.11e-01 8.16e+00 ... (remaining 16011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 3847 16.56 - 33.12: 245 33.12 - 49.68: 107 49.68 - 66.24: 62 66.24 - 82.80: 11 Dihedral angle restraints: 4272 sinusoidal: 2416 harmonic: 1856 Sorted by residual: dihedral pdb=" CA MET B 222 " pdb=" C MET B 222 " pdb=" N ILE B 223 " pdb=" CA ILE B 223 " ideal model delta harmonic sigma weight residual -180.00 -156.06 -23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA MET D 222 " pdb=" C MET D 222 " pdb=" N ILE D 223 " pdb=" CA ILE D 223 " ideal model delta harmonic sigma weight residual 180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA MET C 222 " pdb=" C MET C 222 " pdb=" N ILE C 223 " pdb=" CA ILE C 223 " ideal model delta harmonic sigma weight residual 180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 4269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 432 0.043 - 0.085: 215 0.085 - 0.128: 41 0.128 - 0.171: 20 0.171 - 0.214: 8 Chirality restraints: 716 Sorted by residual: chirality pdb=" C1 1O4 C 301 " pdb=" C 1O4 C 301 " pdb=" C2 1O4 C 301 " pdb=" O12 1O4 C 301 " both_signs ideal model delta sigma weight residual False -2.49 -2.70 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 1O4 B 301 " pdb=" C 1O4 B 301 " pdb=" C2 1O4 B 301 " pdb=" O12 1O4 B 301 " both_signs ideal model delta sigma weight residual False -2.49 -2.70 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1 1O4 A 301 " pdb=" C 1O4 A 301 " pdb=" C2 1O4 A 301 " pdb=" O12 1O4 A 301 " both_signs ideal model delta sigma weight residual False -2.49 -2.70 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 713 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C 1O4 B 301 " -0.369 2.00e-02 2.50e+03 1.47e-01 6.53e+02 pdb=" C15 1O4 B 301 " 0.121 2.00e-02 2.50e+03 pdb=" C16 1O4 B 301 " 0.089 2.00e-02 2.50e+03 pdb=" C17 1O4 B 301 " 0.035 2.00e-02 2.50e+03 pdb=" C18 1O4 B 301 " -0.111 2.00e-02 2.50e+03 pdb=" C19 1O4 B 301 " -0.171 2.00e-02 2.50e+03 pdb=" C20 1O4 B 301 " -0.073 2.00e-02 2.50e+03 pdb=" C21 1O4 B 301 " 0.052 2.00e-02 2.50e+03 pdb=" C22 1O4 B 301 " 0.110 2.00e-02 2.50e+03 pdb=" C23 1O4 B 301 " 0.153 2.00e-02 2.50e+03 pdb=" N5 1O4 B 301 " 0.047 2.00e-02 2.50e+03 pdb=" N6 1O4 B 301 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C 1O4 C 301 " 0.351 2.00e-02 2.50e+03 1.41e-01 5.94e+02 pdb=" C15 1O4 C 301 " -0.111 2.00e-02 2.50e+03 pdb=" C16 1O4 C 301 " -0.085 2.00e-02 2.50e+03 pdb=" C17 1O4 C 301 " -0.034 2.00e-02 2.50e+03 pdb=" C18 1O4 C 301 " 0.108 2.00e-02 2.50e+03 pdb=" C19 1O4 C 301 " 0.164 2.00e-02 2.50e+03 pdb=" C20 1O4 C 301 " 0.070 2.00e-02 2.50e+03 pdb=" C21 1O4 C 301 " -0.052 2.00e-02 2.50e+03 pdb=" C22 1O4 C 301 " -0.106 2.00e-02 2.50e+03 pdb=" C23 1O4 C 301 " -0.145 2.00e-02 2.50e+03 pdb=" N5 1O4 C 301 " -0.045 2.00e-02 2.50e+03 pdb=" N6 1O4 C 301 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C 1O4 A 301 " -0.347 2.00e-02 2.50e+03 1.39e-01 5.81e+02 pdb=" C15 1O4 A 301 " 0.104 2.00e-02 2.50e+03 pdb=" C16 1O4 A 301 " 0.082 2.00e-02 2.50e+03 pdb=" C17 1O4 A 301 " 0.034 2.00e-02 2.50e+03 pdb=" C18 1O4 A 301 " -0.107 2.00e-02 2.50e+03 pdb=" C19 1O4 A 301 " -0.163 2.00e-02 2.50e+03 pdb=" C20 1O4 A 301 " -0.068 2.00e-02 2.50e+03 pdb=" C21 1O4 A 301 " 0.051 2.00e-02 2.50e+03 pdb=" C22 1O4 A 301 " 0.105 2.00e-02 2.50e+03 pdb=" C23 1O4 A 301 " 0.146 2.00e-02 2.50e+03 pdb=" N5 1O4 A 301 " 0.046 2.00e-02 2.50e+03 pdb=" N6 1O4 A 301 " 0.117 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 920 2.27 - 2.85: 18795 2.85 - 3.43: 20434 3.43 - 4.02: 29483 4.02 - 4.60: 45114 Nonbonded interactions: 114746 Sorted by model distance: nonbonded pdb=" HG SER A 140 " pdb=" OE1 GLU A 208 " model vdw 1.686 2.450 nonbonded pdb=" HG SER B 140 " pdb=" OE1 GLU B 208 " model vdw 1.696 2.450 nonbonded pdb=" HG SER C 140 " pdb=" OE1 GLU C 208 " model vdw 1.709 2.450 nonbonded pdb=" HG SER D 140 " pdb=" OE1 GLU D 208 " model vdw 1.732 2.450 nonbonded pdb=" HE ARG A 178 " pdb=" OD1 ASP C 210 " model vdw 1.790 2.450 ... (remaining 114741 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: 0.03 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: 1.630 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: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.080 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 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 : 0.007 0.057 4612 Z= 0.441 Angle : 1.006 9.361 6292 Z= 0.565 Chirality : 0.056 0.214 716 Planarity : 0.013 0.147 768 Dihedral : 17.352 82.799 1844 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.34), residues: 528 helix: -0.82 (0.28), residues: 256 sheet: -0.19 (0.47), residues: 84 loop : 0.82 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 204 HIS 0.007 0.003 HIS C 228 PHE 0.019 0.003 PHE C 138 TYR 0.018 0.004 TYR D 238 ARG 0.013 0.002 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.756 Fit side-chains REVERT: A 189 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7524 (mtmt) REVERT: A 222 MET cc_start: 0.8702 (mtp) cc_final: 0.8450 (mtp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 2.8016 time to fit residues: 191.2743 Evaluate side-chains 46 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN C 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102423 restraints weight = 16655.752| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.58 r_work: 0.3165 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4612 Z= 0.207 Angle : 0.600 5.089 6292 Z= 0.325 Chirality : 0.041 0.145 716 Planarity : 0.005 0.043 768 Dihedral : 13.090 70.401 800 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.24 % Allowed : 7.85 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.34), residues: 528 helix: 0.62 (0.31), residues: 248 sheet: -1.00 (0.45), residues: 84 loop : 0.40 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 204 HIS 0.005 0.001 HIS D 228 PHE 0.009 0.002 PHE C 138 TYR 0.013 0.002 TYR D 207 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.755 Fit side-chains REVERT: A 189 LYS cc_start: 0.7666 (mmmm) cc_final: 0.7291 (ttmt) REVERT: A 222 MET cc_start: 0.8544 (mtp) cc_final: 0.8252 (mtp) REVERT: B 216 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: C 189 LYS cc_start: 0.7815 (mttt) cc_final: 0.7274 (ttmt) outliers start: 6 outliers final: 1 residues processed: 52 average time/residue: 2.4209 time to fit residues: 131.0861 Evaluate side-chains 44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104092 restraints weight = 16873.301| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.58 r_work: 0.3194 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4612 Z= 0.152 Angle : 0.493 4.200 6292 Z= 0.269 Chirality : 0.039 0.138 716 Planarity : 0.004 0.044 768 Dihedral : 12.272 66.616 800 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.03 % Allowed : 9.30 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.35), residues: 528 helix: 1.34 (0.33), residues: 248 sheet: -1.54 (0.44), residues: 84 loop : 0.30 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 204 HIS 0.003 0.001 HIS D 228 PHE 0.007 0.001 PHE A 138 TYR 0.012 0.001 TYR D 207 ARG 0.002 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.665 Fit side-chains REVERT: A 155 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6272 (mp0) REVERT: A 189 LYS cc_start: 0.7679 (mmmm) cc_final: 0.7276 (ttmt) REVERT: B 216 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: C 189 LYS cc_start: 0.7773 (mttt) cc_final: 0.7107 (mtmt) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 2.5227 time to fit residues: 125.8684 Evaluate side-chains 44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109037 restraints weight = 16640.586| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.51 r_work: 0.3265 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4612 Z= 0.122 Angle : 0.440 3.755 6292 Z= 0.240 Chirality : 0.038 0.135 716 Planarity : 0.004 0.042 768 Dihedral : 11.561 64.613 800 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.24 % Allowed : 10.33 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.36), residues: 528 helix: 1.89 (0.34), residues: 248 sheet: -1.66 (0.45), residues: 84 loop : 0.21 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 204 HIS 0.002 0.001 HIS A 228 PHE 0.006 0.001 PHE B 138 TYR 0.011 0.001 TYR D 207 ARG 0.002 0.000 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.767 Fit side-chains REVERT: A 155 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6468 (mp0) REVERT: A 189 LYS cc_start: 0.7717 (mmmm) cc_final: 0.7295 (ttmt) REVERT: B 155 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6067 (mp0) REVERT: B 222 MET cc_start: 0.8413 (mtp) cc_final: 0.8202 (mtp) REVERT: C 189 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7233 (ttmt) outliers start: 6 outliers final: 1 residues processed: 48 average time/residue: 2.8053 time to fit residues: 140.2849 Evaluate side-chains 43 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN C 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.113076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102577 restraints weight = 16947.999| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.49 r_work: 0.3171 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4612 Z= 0.252 Angle : 0.585 4.335 6292 Z= 0.311 Chirality : 0.042 0.145 716 Planarity : 0.005 0.051 768 Dihedral : 13.080 72.348 800 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.41 % Allowed : 10.95 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.35), residues: 528 helix: 1.35 (0.33), residues: 248 sheet: -2.02 (0.44), residues: 84 loop : -0.05 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 204 HIS 0.005 0.001 HIS D 228 PHE 0.010 0.002 PHE B 138 TYR 0.011 0.002 TYR C 207 ARG 0.004 0.001 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.634 Fit side-chains REVERT: A 189 LYS cc_start: 0.7881 (mmmm) cc_final: 0.7514 (ttmt) REVERT: C 189 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7358 (mtmt) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 2.5924 time to fit residues: 113.3948 Evaluate side-chains 44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111112 restraints weight = 16727.899| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.28 r_work: 0.3270 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4612 Z= 0.153 Angle : 0.482 4.057 6292 Z= 0.259 Chirality : 0.039 0.137 716 Planarity : 0.004 0.046 768 Dihedral : 12.128 67.479 800 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.62 % Allowed : 11.57 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.36), residues: 528 helix: 1.73 (0.33), residues: 248 sheet: -2.00 (0.45), residues: 84 loop : 0.01 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 204 HIS 0.002 0.001 HIS D 228 PHE 0.007 0.001 PHE A 138 TYR 0.011 0.001 TYR D 207 ARG 0.003 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.684 Fit side-chains REVERT: A 155 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6522 (mp0) REVERT: A 189 LYS cc_start: 0.7876 (mmmm) cc_final: 0.7524 (ttmt) REVERT: B 222 MET cc_start: 0.8566 (mtp) cc_final: 0.8299 (mtp) REVERT: C 189 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7401 (ttmt) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 2.6155 time to fit residues: 117.1387 Evaluate side-chains 45 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108844 restraints weight = 16952.021| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.28 r_work: 0.3240 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4612 Z= 0.205 Angle : 0.541 4.076 6292 Z= 0.288 Chirality : 0.041 0.141 716 Planarity : 0.005 0.049 768 Dihedral : 12.721 70.764 800 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.62 % Allowed : 12.60 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.35), residues: 528 helix: 1.56 (0.32), residues: 248 sheet: -2.12 (0.46), residues: 84 loop : -0.04 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 204 HIS 0.003 0.001 HIS A 228 PHE 0.009 0.002 PHE D 138 TYR 0.012 0.002 TYR C 207 ARG 0.003 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.635 Fit side-chains REVERT: A 155 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6534 (mp0) REVERT: A 189 LYS cc_start: 0.7897 (mmmm) cc_final: 0.7523 (ttmt) REVERT: B 222 MET cc_start: 0.8656 (mtp) cc_final: 0.8448 (mtp) REVERT: C 189 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7424 (mtmt) REVERT: D 189 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7376 (tttt) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 2.4343 time to fit residues: 114.1434 Evaluate side-chains 46 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112251 restraints weight = 17008.353| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.33 r_work: 0.3289 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4612 Z= 0.128 Angle : 0.448 3.910 6292 Z= 0.240 Chirality : 0.038 0.134 716 Planarity : 0.004 0.044 768 Dihedral : 11.665 65.204 800 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.62 % Allowed : 13.22 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.36), residues: 528 helix: 2.12 (0.33), residues: 248 sheet: -2.03 (0.46), residues: 84 loop : 0.14 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 204 HIS 0.002 0.001 HIS C 220 PHE 0.005 0.001 PHE B 138 TYR 0.010 0.001 TYR C 207 ARG 0.002 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 1.275 Fit side-chains REVERT: A 155 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6620 (mp0) REVERT: A 189 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7567 (ttmt) REVERT: B 155 GLU cc_start: 0.6896 (mt-10) cc_final: 0.6293 (mp0) REVERT: C 189 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7441 (ttmt) REVERT: D 189 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7370 (tttt) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 3.1651 time to fit residues: 151.3315 Evaluate side-chains 46 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 50 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108418 restraints weight = 17161.580| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.30 r_work: 0.3231 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4612 Z= 0.214 Angle : 0.550 4.075 6292 Z= 0.291 Chirality : 0.041 0.142 716 Planarity : 0.005 0.050 768 Dihedral : 12.759 71.386 800 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.41 % Allowed : 13.64 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.35), residues: 528 helix: 1.71 (0.32), residues: 248 sheet: -2.18 (0.46), residues: 84 loop : 0.02 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 204 HIS 0.003 0.001 HIS A 228 PHE 0.009 0.002 PHE D 138 TYR 0.013 0.002 TYR D 207 ARG 0.003 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.684 Fit side-chains REVERT: A 155 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6609 (mp0) REVERT: A 189 LYS cc_start: 0.7938 (mmmm) cc_final: 0.7582 (ttmt) REVERT: C 189 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7481 (mtmt) REVERT: D 189 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7425 (tttt) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 2.6004 time to fit residues: 113.7051 Evaluate side-chains 44 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.118345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109012 restraints weight = 16987.273| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.31 r_work: 0.3240 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4612 Z= 0.192 Angle : 0.523 4.108 6292 Z= 0.278 Chirality : 0.040 0.140 716 Planarity : 0.005 0.049 768 Dihedral : 12.535 69.636 800 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.41 % Allowed : 13.64 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.35), residues: 528 helix: 1.70 (0.32), residues: 248 sheet: -2.20 (0.46), residues: 84 loop : 0.00 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 204 HIS 0.003 0.001 HIS D 228 PHE 0.008 0.001 PHE B 138 TYR 0.012 0.002 TYR D 207 ARG 0.002 0.001 ARG A 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.756 Fit side-chains REVERT: A 155 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6549 (mp0) REVERT: A 189 LYS cc_start: 0.7908 (mmmm) cc_final: 0.7530 (ttmt) REVERT: C 189 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7434 (mtmt) REVERT: D 189 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7357 (tttt) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 2.7007 time to fit residues: 115.2470 Evaluate side-chains 43 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain D residue 210 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109061 restraints weight = 17044.561| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.30 r_work: 0.3241 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4612 Z= 0.189 Angle : 0.522 4.174 6292 Z= 0.277 Chirality : 0.040 0.140 716 Planarity : 0.005 0.049 768 Dihedral : 12.500 69.496 800 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.41 % Allowed : 13.64 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.36), residues: 528 helix: 1.73 (0.32), residues: 248 sheet: -2.23 (0.46), residues: 84 loop : -0.00 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 204 HIS 0.003 0.001 HIS A 228 PHE 0.008 0.001 PHE D 138 TYR 0.012 0.002 TYR D 207 ARG 0.002 0.000 ARG B 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6519.87 seconds wall clock time: 114 minutes 18.87 seconds (6858.87 seconds total)