Starting phenix.real_space_refine on Thu Jul 2 14:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khg_62339/07_2026/9khg_62339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khg_62339/07_2026/9khg_62339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9khg_62339/07_2026/9khg_62339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khg_62339/07_2026/9khg_62339.map" model { file = "/net/cci-nas-00/data/ceres_data/9khg_62339/07_2026/9khg_62339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khg_62339/07_2026/9khg_62339.cif" } resolution = 3.2 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= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 40 5.16 5 C 5828 2.51 5 N 1384 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "B" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "C" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "D" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2167 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8670 At special positions: 0 Unit cell: (112.36, 113.42, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 40 16.00 O 1416 8.00 N 1384 7.00 C 5828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 326.0 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 3 sheets defined 73.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 62 through 90 Proline residue: A 84 - end of helix removed outlier: 3.630A pdb=" N PHE A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 116 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 164 through 170 removed outlier: 4.013A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 177 through 191 removed outlier: 4.207A pdb=" N VAL A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.617A pdb=" N ALA A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 313 removed outlier: 3.724A pdb=" N VAL A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Proline residue: B 84 - end of helix removed outlier: 3.621A pdb=" N PHE B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 116 Processing helix chain 'B' and resid 131 through 142 removed outlier: 3.509A pdb=" N ILE B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.910A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.502A pdb=" N ARG B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 removed outlier: 4.220A pdb=" N VAL B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 225 removed outlier: 3.608A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 313 removed outlier: 3.722A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Proline residue: C 84 - end of helix removed outlier: 3.644A pdb=" N PHE C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 118 removed outlier: 4.124A pdb=" N PHE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 164 through 170 removed outlier: 4.100A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 191 removed outlier: 4.199A pdb=" N VAL C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 225 removed outlier: 3.616A pdb=" N ALA C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 224 " --> pdb=" O TYR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 Processing helix chain 'C' and resid 281 through 313 removed outlier: 3.745A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Proline residue: D 84 - end of helix removed outlier: 3.576A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 164 through 170 removed outlier: 4.125A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 4.054A pdb=" N PHE D 176 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 191 removed outlier: 4.240A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 225 removed outlier: 3.614A pdb=" N ALA D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 224 " --> pdb=" O TYR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 313 removed outlier: 3.704A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.828A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 129 " --> pdb=" O TYR A 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.822A pdb=" N TYR C 120 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 129 " --> pdb=" O TYR C 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.853A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 129 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP D 122 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG D 127 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 538 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1256 1.31 - 1.44: 2836 1.44 - 1.56: 4779 1.56 - 1.68: 1 1.68 - 1.81: 68 Bond restraints: 8940 Sorted by residual: bond pdb=" C TYR D 139 " pdb=" N LEU D 140 " ideal model delta sigma weight residual 1.334 1.210 0.124 1.27e-02 6.20e+03 9.59e+01 bond pdb=" C ARG D 96 " pdb=" N LEU D 97 " ideal model delta sigma weight residual 1.332 1.417 -0.086 1.52e-02 4.33e+03 3.18e+01 bond pdb=" C ARG D 168 " pdb=" O ARG D 168 " ideal model delta sigma weight residual 1.236 1.189 0.046 1.28e-02 6.10e+03 1.31e+01 bond pdb=" CA ALA B 270 " pdb=" CB ALA B 270 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.74e-02 3.30e+03 1.23e+01 bond pdb=" CA ALA C 270 " pdb=" CB ALA C 270 " ideal model delta sigma weight residual 1.529 1.468 0.061 1.74e-02 3.30e+03 1.23e+01 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11624 1.81 - 3.61: 359 3.61 - 5.42: 113 5.42 - 7.23: 22 7.23 - 9.04: 18 Bond angle restraints: 12136 Sorted by residual: angle pdb=" N VAL A 272 " pdb=" CA VAL A 272 " pdb=" C VAL A 272 " ideal model delta sigma weight residual 110.74 102.19 8.55 9.10e-01 1.21e+00 8.82e+01 angle pdb=" N VAL D 272 " pdb=" CA VAL D 272 " pdb=" C VAL D 272 " ideal model delta sigma weight residual 110.74 102.26 8.48 9.10e-01 1.21e+00 8.69e+01 angle pdb=" N VAL C 272 " pdb=" CA VAL C 272 " pdb=" C VAL C 272 " ideal model delta sigma weight residual 110.74 102.34 8.40 9.10e-01 1.21e+00 8.52e+01 angle pdb=" N VAL B 272 " pdb=" CA VAL B 272 " pdb=" C VAL B 272 " ideal model delta sigma weight residual 110.74 102.36 8.38 9.10e-01 1.21e+00 8.48e+01 angle pdb=" N TRP B 64 " pdb=" CA TRP B 64 " pdb=" C TRP B 64 " ideal model delta sigma weight residual 111.28 119.70 -8.42 1.09e+00 8.42e-01 5.96e+01 ... (remaining 12131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4284 17.99 - 35.98: 628 35.98 - 53.97: 158 53.97 - 71.97: 25 71.97 - 89.96: 5 Dihedral angle restraints: 5100 sinusoidal: 2056 harmonic: 3044 Sorted by residual: dihedral pdb=" CA SER B 142 " pdb=" C SER B 142 " pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PHE A 176 " pdb=" C PHE A 176 " pdb=" N ARG A 177 " pdb=" CA ARG A 177 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PHE D 176 " pdb=" C PHE D 176 " pdb=" N ARG D 177 " pdb=" CA ARG D 177 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1163 0.063 - 0.126: 125 0.126 - 0.190: 21 0.190 - 0.253: 12 0.253 - 0.316: 3 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA THR A 271 " pdb=" N THR A 271 " pdb=" C THR A 271 " pdb=" CB THR A 271 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA THR C 271 " pdb=" N THR C 271 " pdb=" C THR C 271 " pdb=" CB THR C 271 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1321 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 268 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C THR A 268 " -0.061 2.00e-02 2.50e+03 pdb=" O THR A 268 " 0.022 2.00e-02 2.50e+03 pdb=" N MET A 269 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 272 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL D 272 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL D 272 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY D 273 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 272 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C VAL B 272 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL B 272 " -0.022 2.00e-02 2.50e+03 pdb=" N GLY B 273 " -0.021 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 2479 2.80 - 3.39: 9994 3.39 - 3.97: 15860 3.97 - 4.56: 22574 4.56 - 5.14: 32716 Nonbonded interactions: 83623 Sorted by model distance: nonbonded pdb=" O ALA A 270 " pdb=" OG1 THR A 271 " model vdw 2.217 3.040 nonbonded pdb=" O ILE C 157 " pdb=" OG SER C 161 " model vdw 2.221 3.040 nonbonded pdb=" O ARG D 168 " pdb=" N LEU D 171 " model vdw 2.223 3.120 nonbonded pdb=" O ILE B 157 " pdb=" OG SER B 161 " model vdw 2.225 3.040 nonbonded pdb=" O ILE D 157 " pdb=" OG SER D 161 " model vdw 2.238 3.040 ... (remaining 83618 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 58 through 313) 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.110 Find NCS groups from input model: 0.100 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 8940 Z= 0.305 Angle : 0.856 9.037 12136 Z= 0.558 Chirality : 0.049 0.316 1324 Planarity : 0.006 0.039 1464 Dihedral : 17.395 89.958 3156 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.05 % Favored : 96.56 % Rotamer: Outliers : 1.32 % Allowed : 26.86 % Favored : 71.82 % 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: 0.73 (0.26), residues: 1016 helix: 0.91 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -0.28 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 174 TYR 0.013 0.002 TYR A 120 PHE 0.018 0.002 PHE A 98 TRP 0.009 0.001 TRP B 255 HIS 0.004 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.30 ( 8940) covalent geometry : angle 0.85640 / 0.56 (12136) hydrogen bonds : bond 0.13225 / 8.69 ( 538) hydrogen bonds : angle 5.50097 / 3.97 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 PHE cc_start: 0.8485 (t80) cc_final: 0.8275 (t80) REVERT: A 96 ARG cc_start: 0.7699 (mtm180) cc_final: 0.7429 (mtm-85) REVERT: A 146 MET cc_start: 0.7855 (ttm) cc_final: 0.7527 (ttm) REVERT: A 269 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7879 (ttt) REVERT: A 276 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7684 (p0) REVERT: B 131 LYS cc_start: 0.8383 (tppt) cc_final: 0.7814 (mmmt) REVERT: C 96 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7515 (mtm-85) REVERT: C 121 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7548 (tpp80) REVERT: C 151 CYS cc_start: 0.8268 (t) cc_final: 0.7772 (m) REVERT: C 244 TYR cc_start: 0.7976 (t80) cc_final: 0.7544 (t80) REVERT: C 269 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7796 (ttt) REVERT: D 153 PRO cc_start: 0.7779 (Cg_exo) cc_final: 0.7479 (Cg_endo) REVERT: D 164 HIS cc_start: 0.7888 (m-70) cc_final: 0.7495 (m-70) REVERT: D 276 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7793 (p0) outliers start: 12 outliers final: 2 residues processed: 209 average time/residue: 0.0752 time to fit residues: 22.2345 Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 309 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.200213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134272 restraints weight = 9645.480| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.46 r_work: 0.3337 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8940 Z= 0.144 Angle : 0.555 9.801 12136 Z= 0.298 Chirality : 0.039 0.201 1324 Planarity : 0.004 0.032 1464 Dihedral : 6.202 59.884 1183 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.40 % Allowed : 21.82 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.26), residues: 1016 helix: 1.45 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -0.65 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 174 TYR 0.012 0.001 TYR D 220 PHE 0.021 0.002 PHE A 98 TRP 0.011 0.001 TRP B 255 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 8940) covalent geometry : angle 0.55472 / 0.30 (12136) hydrogen bonds : bond 0.05118 / 3.21 ( 538) hydrogen bonds : angle 4.11688 / 2.96 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8079 (mtm180) cc_final: 0.7355 (mtm180) REVERT: A 295 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6325 (t70) REVERT: B 175 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8110 (mp) REVERT: B 251 GLU cc_start: 0.8556 (mp0) cc_final: 0.8229 (mp0) REVERT: C 86 GLU cc_start: 0.7836 (tp30) cc_final: 0.7415 (tt0) REVERT: C 96 ARG cc_start: 0.8176 (mtm180) cc_final: 0.7448 (mtm180) REVERT: C 244 TYR cc_start: 0.8149 (t80) cc_final: 0.7571 (t80) REVERT: D 72 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7306 (tp) REVERT: D 151 CYS cc_start: 0.8382 (t) cc_final: 0.7535 (m) REVERT: D 164 HIS cc_start: 0.8153 (m-70) cc_final: 0.7892 (m-70) REVERT: D 251 GLU cc_start: 0.8536 (mp0) cc_final: 0.8204 (mp0) outliers start: 31 outliers final: 14 residues processed: 204 average time/residue: 0.0677 time to fit residues: 19.9062 Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.0770 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 92 optimal weight: 0.0060 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6156 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.203772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.130436 restraints weight = 9525.436| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.37 r_work: 0.3381 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8940 Z= 0.130 Angle : 0.528 9.376 12136 Z= 0.274 Chirality : 0.040 0.272 1324 Planarity : 0.003 0.031 1464 Dihedral : 4.955 37.080 1177 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.62 % Allowed : 22.15 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1016 helix: 1.74 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.30 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 174 TYR 0.012 0.001 TYR B 220 PHE 0.018 0.002 PHE D 117 TRP 0.009 0.001 TRP D 255 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 8940) covalent geometry : angle 0.52830 / 0.27 (12136) hydrogen bonds : bond 0.04648 / 2.90 ( 538) hydrogen bonds : angle 3.87185 / 2.77 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8055 (mtm180) cc_final: 0.7359 (mtm180) REVERT: A 157 ILE cc_start: 0.8564 (mt) cc_final: 0.8336 (mt) REVERT: A 295 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6487 (t70) REVERT: B 175 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8083 (mp) REVERT: C 86 GLU cc_start: 0.7866 (tp30) cc_final: 0.7545 (tt0) REVERT: C 96 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7467 (mtm180) REVERT: C 121 ARG cc_start: 0.7591 (tpp80) cc_final: 0.6862 (tpp80) REVERT: C 233 TYR cc_start: 0.8557 (t80) cc_final: 0.8351 (t80) REVERT: D 72 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7342 (tp) REVERT: D 109 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7773 (mm) REVERT: D 146 MET cc_start: 0.8522 (tpp) cc_final: 0.8295 (tpp) REVERT: D 156 LEU cc_start: 0.8493 (mm) cc_final: 0.8265 (mm) REVERT: D 164 HIS cc_start: 0.8088 (m-70) cc_final: 0.7766 (m-70) REVERT: D 178 VAL cc_start: 0.8177 (m) cc_final: 0.7956 (t) REVERT: D 251 GLU cc_start: 0.8528 (mp0) cc_final: 0.8156 (mp0) outliers start: 33 outliers final: 13 residues processed: 203 average time/residue: 0.0739 time to fit residues: 21.9253 Evaluate side-chains 190 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 HIS C 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.204689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129920 restraints weight = 9739.803| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.57 r_work: 0.3361 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8940 Z= 0.144 Angle : 0.532 9.238 12136 Z= 0.278 Chirality : 0.042 0.407 1324 Planarity : 0.003 0.025 1464 Dihedral : 4.383 23.727 1168 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.39 % Allowed : 21.60 % Favored : 74.01 % 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: 1.83 (0.26), residues: 1016 helix: 1.78 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.05 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.015 0.001 TYR A 220 PHE 0.020 0.002 PHE C 98 TRP 0.009 0.001 TRP D 255 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 8940) covalent geometry : angle 0.53208 / 0.28 (12136) hydrogen bonds : bond 0.04526 / 2.80 ( 538) hydrogen bonds : angle 3.73031 / 2.68 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 96 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7418 (mtm180) REVERT: A 234 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8869 (p) REVERT: A 251 GLU cc_start: 0.8647 (mp0) cc_final: 0.8424 (mp0) REVERT: A 295 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6634 (t70) REVERT: B 175 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8186 (mp) REVERT: B 234 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8802 (p) REVERT: B 251 GLU cc_start: 0.8630 (mp0) cc_final: 0.8348 (mp0) REVERT: C 86 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: C 96 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7435 (mtm180) REVERT: C 121 ARG cc_start: 0.7616 (tpp80) cc_final: 0.6754 (tpp80) REVERT: C 201 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6772 (mt) REVERT: C 234 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8808 (p) REVERT: C 251 GLU cc_start: 0.8629 (mp0) cc_final: 0.8411 (mp0) REVERT: C 295 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6617 (t70) REVERT: D 71 PHE cc_start: 0.8213 (t80) cc_final: 0.7910 (t80) REVERT: D 109 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7862 (mm) REVERT: D 156 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8268 (mm) REVERT: D 164 HIS cc_start: 0.8093 (m-70) cc_final: 0.7729 (m-70) REVERT: D 178 VAL cc_start: 0.8245 (m) cc_final: 0.8020 (t) REVERT: D 234 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8730 (p) REVERT: D 295 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6429 (t70) outliers start: 40 outliers final: 16 residues processed: 199 average time/residue: 0.0685 time to fit residues: 20.4291 Evaluate side-chains 196 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 50 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 18 optimal weight: 0.0030 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.204840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136012 restraints weight = 9472.959| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.14 r_work: 0.3427 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8940 Z= 0.117 Angle : 0.509 10.767 12136 Z= 0.262 Chirality : 0.039 0.233 1324 Planarity : 0.003 0.026 1464 Dihedral : 4.293 22.115 1168 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.07 % Allowed : 22.81 % Favored : 74.12 % 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: 2.04 (0.27), residues: 1016 helix: 1.90 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.14 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.012 0.001 TYR A 220 PHE 0.022 0.002 PHE D 98 TRP 0.008 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 8940) covalent geometry : angle 0.50928 / 0.26 (12136) hydrogen bonds : bond 0.04255 / 2.65 ( 538) hydrogen bonds : angle 3.64964 / 2.61 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.341 Fit side-chains REVERT: A 96 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7285 (mtm180) REVERT: A 117 PHE cc_start: 0.5417 (t80) cc_final: 0.5079 (t80) REVERT: B 234 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8783 (p) REVERT: C 86 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: C 96 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7381 (mtm180) REVERT: C 121 ARG cc_start: 0.7743 (tpp80) cc_final: 0.6841 (tpp80) REVERT: C 201 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6714 (mt) REVERT: C 244 TYR cc_start: 0.8311 (t80) cc_final: 0.7691 (t80) REVERT: C 269 MET cc_start: 0.8112 (ttp) cc_final: 0.7811 (ptt) REVERT: D 71 PHE cc_start: 0.8177 (t80) cc_final: 0.7876 (t80) REVERT: D 109 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7874 (mm) REVERT: D 164 HIS cc_start: 0.8000 (m-70) cc_final: 0.7554 (m-70) REVERT: D 234 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8739 (p) REVERT: D 251 GLU cc_start: 0.8650 (mp0) cc_final: 0.8317 (mp0) outliers start: 28 outliers final: 13 residues processed: 185 average time/residue: 0.0663 time to fit residues: 18.1647 Evaluate side-chains 185 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.0000 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.205510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131496 restraints weight = 9640.663| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.49 r_work: 0.3376 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8940 Z= 0.127 Angle : 0.506 7.747 12136 Z= 0.264 Chirality : 0.038 0.230 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.276 22.486 1168 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.29 % Allowed : 23.14 % Favored : 73.57 % 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: 2.13 (0.27), residues: 1016 helix: 1.93 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.27 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.018 0.001 TYR D 233 PHE 0.023 0.002 PHE D 184 TRP 0.008 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8940) covalent geometry : angle 0.50589 / 0.26 (12136) hydrogen bonds : bond 0.04196 / 2.59 ( 538) hydrogen bonds : angle 3.58840 / 2.57 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.207 Fit side-chains REVERT: A 96 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7294 (mtm180) REVERT: A 117 PHE cc_start: 0.5336 (t80) cc_final: 0.5065 (t80) REVERT: A 234 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8905 (p) REVERT: A 251 GLU cc_start: 0.8875 (mp0) cc_final: 0.8650 (mp0) REVERT: A 295 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6620 (t70) REVERT: B 109 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7920 (mm) REVERT: B 156 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8307 (mm) REVERT: B 234 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 251 GLU cc_start: 0.8712 (mp0) cc_final: 0.8377 (mp0) REVERT: C 86 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: C 96 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7383 (mtm180) REVERT: C 121 ARG cc_start: 0.7675 (tpp80) cc_final: 0.6752 (tpp80) REVERT: C 234 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8840 (p) REVERT: C 244 TYR cc_start: 0.8322 (t80) cc_final: 0.7720 (t80) REVERT: C 251 GLU cc_start: 0.8823 (mp0) cc_final: 0.8552 (mp0) REVERT: C 269 MET cc_start: 0.8167 (ttp) cc_final: 0.7962 (ptt) REVERT: C 295 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6598 (t70) REVERT: D 71 PHE cc_start: 0.8301 (t80) cc_final: 0.7977 (t80) REVERT: D 96 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7900 (mmm-85) REVERT: D 109 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7876 (mm) REVERT: D 164 HIS cc_start: 0.7973 (m-70) cc_final: 0.7441 (m-70) REVERT: D 234 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8632 (p) REVERT: D 295 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6451 (t70) outliers start: 30 outliers final: 14 residues processed: 181 average time/residue: 0.0695 time to fit residues: 18.6980 Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 HIS C 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.204904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129541 restraints weight = 9743.348| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.36 r_work: 0.3378 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8940 Z= 0.147 Angle : 0.514 6.806 12136 Z= 0.271 Chirality : 0.039 0.228 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.278 21.377 1168 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.18 % Allowed : 23.68 % Favored : 73.14 % 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: 2.12 (0.27), residues: 1016 helix: 1.91 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.31 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.015 0.001 TYR A 220 PHE 0.022 0.002 PHE D 184 TRP 0.009 0.001 TRP D 255 HIS 0.004 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8940) covalent geometry : angle 0.51421 / 0.27 (12136) hydrogen bonds : bond 0.04258 / 2.63 ( 538) hydrogen bonds : angle 3.56380 / 2.55 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.278 Fit side-chains REVERT: A 96 ARG cc_start: 0.7952 (mtm180) cc_final: 0.7270 (mtm180) REVERT: A 116 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7941 (t80) REVERT: A 234 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8828 (p) REVERT: A 295 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6618 (t70) REVERT: B 109 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7958 (mm) REVERT: B 156 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8325 (mm) REVERT: B 234 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8794 (p) REVERT: C 86 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: C 96 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7371 (mtm180) REVERT: C 117 PHE cc_start: 0.5281 (t80) cc_final: 0.4980 (t80) REVERT: C 121 ARG cc_start: 0.7776 (tpp80) cc_final: 0.6855 (tpp80) REVERT: C 234 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8839 (p) REVERT: C 295 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6533 (t70) REVERT: D 71 PHE cc_start: 0.8263 (t80) cc_final: 0.7944 (t80) REVERT: D 96 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7919 (mmm-85) REVERT: D 109 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7934 (mm) REVERT: D 164 HIS cc_start: 0.7975 (m-70) cc_final: 0.7389 (m-70) REVERT: D 234 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8702 (p) REVERT: D 295 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6502 (t70) outliers start: 29 outliers final: 12 residues processed: 184 average time/residue: 0.0678 time to fit residues: 18.3691 Evaluate side-chains 191 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 86 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.199001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122419 restraints weight = 9572.397| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.51 r_work: 0.3247 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8940 Z= 0.129 Angle : 0.516 6.967 12136 Z= 0.269 Chirality : 0.038 0.227 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.215 21.442 1168 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.29 % Allowed : 24.23 % Favored : 72.48 % 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: 2.24 (0.27), residues: 1016 helix: 2.00 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.35 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.013 0.001 TYR D 220 PHE 0.023 0.002 PHE C 98 TRP 0.008 0.001 TRP D 255 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8940) covalent geometry : angle 0.51616 / 0.27 (12136) hydrogen bonds : bond 0.04125 / 2.56 ( 538) hydrogen bonds : angle 3.51174 / 2.52 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.257 Fit side-chains REVERT: A 96 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7223 (mtm180) REVERT: A 234 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8665 (p) REVERT: A 251 GLU cc_start: 0.8786 (mp0) cc_final: 0.8515 (mp0) REVERT: A 295 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6345 (t70) REVERT: B 109 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7865 (mm) REVERT: B 156 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8233 (mm) REVERT: B 234 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 86 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: C 96 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7324 (mtm180) REVERT: C 117 PHE cc_start: 0.5035 (t80) cc_final: 0.4701 (t80) REVERT: C 121 ARG cc_start: 0.7688 (tpp80) cc_final: 0.6774 (tpp80) REVERT: C 234 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 251 GLU cc_start: 0.8726 (mp0) cc_final: 0.8432 (mp0) REVERT: C 295 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6322 (t70) REVERT: D 71 PHE cc_start: 0.8112 (t80) cc_final: 0.7786 (t80) REVERT: D 96 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7944 (mmm-85) REVERT: D 109 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7855 (mm) REVERT: D 234 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8598 (p) REVERT: D 295 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6289 (t70) outliers start: 30 outliers final: 12 residues processed: 182 average time/residue: 0.0720 time to fit residues: 19.1821 Evaluate side-chains 182 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 67 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.198265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126595 restraints weight = 9423.920| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.52 r_work: 0.3251 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.003 0.040 8940 Z= 0.128 Angle : 0.533 6.922 12136 Z= 0.277 Chirality : 0.038 0.224 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.207 21.295 1168 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.85 % Allowed : 25.00 % Favored : 72.15 % 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: 2.27 (0.27), residues: 1016 helix: 2.02 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.37 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.013 0.001 TYR D 220 PHE 0.036 0.002 PHE D 117 TRP 0.009 0.001 TRP D 64 HIS 0.004 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8940) covalent geometry : angle 0.53343 / 0.28 (12136) hydrogen bonds : bond 0.04072 / 2.52 ( 538) hydrogen bonds : angle 3.48368 / 2.50 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.325 Fit side-chains REVERT: A 96 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7220 (mtm180) REVERT: A 117 PHE cc_start: 0.4492 (t80) cc_final: 0.4248 (t80) REVERT: A 234 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 251 GLU cc_start: 0.8718 (mp0) cc_final: 0.8463 (mp0) REVERT: A 295 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6394 (t70) REVERT: B 109 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7889 (mm) REVERT: B 116 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7986 (t80) REVERT: B 156 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8247 (mm) REVERT: B 234 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8676 (p) REVERT: B 247 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6934 (tp30) REVERT: C 86 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: C 96 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7312 (mtm180) REVERT: C 117 PHE cc_start: 0.4894 (t80) cc_final: 0.4600 (t80) REVERT: C 121 ARG cc_start: 0.7717 (tpp80) cc_final: 0.6818 (tpp80) REVERT: C 234 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8658 (p) REVERT: C 251 GLU cc_start: 0.8675 (mp0) cc_final: 0.8410 (mp0) REVERT: D 71 PHE cc_start: 0.8146 (t80) cc_final: 0.7829 (t80) REVERT: D 96 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7919 (mmm-85) REVERT: D 109 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (mm) REVERT: D 234 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8613 (p) REVERT: D 295 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6344 (t70) outliers start: 26 outliers final: 13 residues processed: 176 average time/residue: 0.0707 time to fit residues: 18.1824 Evaluate side-chains 187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 0.0570 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.197805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125263 restraints weight = 9492.334| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.69 r_work: 0.3240 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8940 Z= 0.137 Angle : 0.543 7.521 12136 Z= 0.284 Chirality : 0.038 0.222 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.165 21.048 1168 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.74 % Allowed : 25.33 % Favored : 71.93 % 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: 2.27 (0.27), residues: 1016 helix: 2.01 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.39 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.014 0.001 TYR A 220 PHE 0.028 0.002 PHE D 184 TRP 0.008 0.001 TRP D 255 HIS 0.003 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8940) covalent geometry : angle 0.54322 / 0.28 (12136) hydrogen bonds : bond 0.04095 / 2.53 ( 538) hydrogen bonds : angle 3.47026 / 2.49 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.316 Fit side-chains REVERT: A 96 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7218 (mtm180) REVERT: A 117 PHE cc_start: 0.4500 (t80) cc_final: 0.4274 (t80) REVERT: A 234 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 251 GLU cc_start: 0.8836 (mp0) cc_final: 0.8579 (mp0) REVERT: A 295 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6413 (t70) REVERT: B 109 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7935 (mm) REVERT: B 116 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8028 (t80) REVERT: B 156 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 234 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 247 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6933 (tp30) REVERT: C 86 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: C 96 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7298 (mtm180) REVERT: C 117 PHE cc_start: 0.4888 (t80) cc_final: 0.4664 (t80) REVERT: C 121 ARG cc_start: 0.7716 (tpp80) cc_final: 0.6803 (tpp80) REVERT: C 234 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 251 GLU cc_start: 0.8678 (mp0) cc_final: 0.8409 (mp0) REVERT: C 295 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6302 (t70) REVERT: D 96 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7833 (mmm-85) REVERT: D 109 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7868 (mm) REVERT: D 234 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8584 (p) REVERT: D 295 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6376 (t70) outliers start: 25 outliers final: 13 residues processed: 174 average time/residue: 0.0725 time to fit residues: 18.3763 Evaluate side-chains 188 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.199543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125942 restraints weight = 9517.917| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.87 r_work: 0.3232 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8940 Z= 0.132 Angle : 0.535 6.757 12136 Z= 0.280 Chirality : 0.038 0.222 1324 Planarity : 0.003 0.028 1464 Dihedral : 4.116 21.135 1168 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.74 % Allowed : 25.66 % Favored : 71.60 % 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: 2.30 (0.27), residues: 1016 helix: 2.03 (0.19), residues: 712 sheet: None (None), residues: 0 loop : 0.43 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.014 0.001 TYR D 233 PHE 0.032 0.002 PHE B 117 TRP 0.007 0.001 TRP D 255 HIS 0.003 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8940) covalent geometry : angle 0.53486 / 0.28 (12136) hydrogen bonds : bond 0.04050 / 2.50 ( 538) hydrogen bonds : angle 3.45161 / 2.48 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.71 seconds wall clock time: 43 minutes 48.74 seconds (2628.74 seconds total)