Starting phenix.real_space_refine on Sat Jul 4 10:16:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asc_43812/07_2026/9asc_43812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asc_43812/07_2026/9asc_43812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9asc_43812/07_2026/9asc_43812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asc_43812/07_2026/9asc_43812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9asc_43812/07_2026/9asc_43812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asc_43812/07_2026/9asc_43812.map" } resolution = 2.96 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= 0.027 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 8 5.49 5 S 52 5.16 5 C 6416 2.51 5 N 1728 2.21 5 O 1860 1.98 5 H 10224 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 20292 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5036 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 4.52, per 1000 atoms: 0.22 Number of scatterers: 20292 At special positions: 0 Unit cell: (110.7, 110.7, 97.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 52 16.00 P 8 15.00 O 1860 8.00 N 1728 7.00 C 6416 6.00 H 10224 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: 1.83 Conformation dependent library (CDL) restraints added in 491.0 milliseconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 55.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 134 through 153 Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.534A pdb=" N ARG A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.524A pdb=" N ASN A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.651A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 234 through 262 removed outlier: 3.800A pdb=" N LEU A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 304 removed outlier: 3.851A pdb=" N TYR A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 134 through 153 Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.535A pdb=" N ARG B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.523A pdb=" N ASN B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.651A pdb=" N LEU B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 233 Processing helix chain 'B' and resid 234 through 262 removed outlier: 3.800A pdb=" N LEU B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 304 removed outlier: 3.851A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 134 through 153 Processing helix chain 'C' and resid 168 through 176 removed outlier: 3.534A pdb=" N ARG C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.524A pdb=" N ASN C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.652A pdb=" N LEU C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 233 Processing helix chain 'C' and resid 234 through 262 removed outlier: 3.800A pdb=" N LEU C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 304 removed outlier: 3.851A pdb=" N TYR C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 79 through 89 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 134 through 153 Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.533A pdb=" N ARG D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.523A pdb=" N ASN D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.651A pdb=" N LEU D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 233 Processing helix chain 'D' and resid 234 through 262 removed outlier: 3.800A pdb=" N LEU D 238 " --> pdb=" O ARG D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 304 removed outlier: 3.851A pdb=" N TYR D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.798A pdb=" N VAL A 123 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 164 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER A 71 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL B 313 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU A 73 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 removed outlier: 5.717A pdb=" N VAL A 127 " --> pdb=" O VAL A 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 310 through 314 removed outlier: 7.056A pdb=" N LEU D 73 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL A 313 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N SER D 71 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 164 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL D 123 " --> pdb=" O THR D 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 195 through 196 removed outlier: 6.798A pdb=" N VAL B 123 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 164 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER B 71 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL C 313 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 73 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 127 through 128 removed outlier: 5.718A pdb=" N VAL B 127 " --> pdb=" O VAL B 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 195 through 196 removed outlier: 6.797A pdb=" N VAL C 123 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 164 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER C 71 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL D 313 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU C 73 " --> pdb=" O GLN D 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 127 through 128 removed outlier: 5.717A pdb=" N VAL C 127 " --> pdb=" O VAL C 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 128 removed outlier: 5.718A pdb=" N VAL D 127 " --> pdb=" O VAL D 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 584 hydrogen bonds defined for protein. 1728 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: 3.95 Time building geometry restraints manager: 2.30 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: 10208 1.03 - 1.23: 20 1.23 - 1.42: 4192 1.42 - 1.61: 5972 1.61 - 1.81: 88 Bond restraints: 20480 Sorted by residual: bond pdb=" O1A UDP A 401 " pdb=" PA UDP A 401 " ideal model delta sigma weight residual 1.482 1.527 -0.045 1.00e-02 1.00e+04 2.01e+01 bond pdb=" O1A UDP B 401 " pdb=" PA UDP B 401 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.94e+01 bond pdb=" O1A UDP D 401 " pdb=" PA UDP D 401 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" O1A UDP C 401 " pdb=" PA UDP C 401 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" O1B UDP C 401 " pdb=" PB UDP C 401 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.00e-02 1.00e+04 1.42e+01 ... (remaining 20475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 36814 1.83 - 3.65: 194 3.65 - 5.48: 40 5.48 - 7.30: 0 7.30 - 9.13: 8 Bond angle restraints: 37056 Sorted by residual: angle pdb=" O1B UDP A 401 " pdb=" PB UDP A 401 " pdb=" O3A UDP A 401 " ideal model delta sigma weight residual 102.95 112.08 -9.13 1.00e+00 1.00e+00 8.33e+01 angle pdb=" O1B UDP C 401 " pdb=" PB UDP C 401 " pdb=" O3A UDP C 401 " ideal model delta sigma weight residual 102.95 112.06 -9.11 1.00e+00 1.00e+00 8.30e+01 angle pdb=" O1B UDP B 401 " pdb=" PB UDP B 401 " pdb=" O3A UDP B 401 " ideal model delta sigma weight residual 102.95 112.06 -9.11 1.00e+00 1.00e+00 8.29e+01 angle pdb=" O1B UDP D 401 " pdb=" PB UDP D 401 " pdb=" O3A UDP D 401 " ideal model delta sigma weight residual 102.95 112.04 -9.09 1.00e+00 1.00e+00 8.26e+01 angle pdb=" O3A UDP C 401 " pdb=" PB UDP C 401 " pdb=" O3B UDP C 401 " ideal model delta sigma weight residual 112.01 103.03 8.98 1.00e+00 1.00e+00 8.07e+01 ... (remaining 37051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8900 17.07 - 34.14: 448 34.14 - 51.21: 208 51.21 - 68.28: 112 68.28 - 85.35: 4 Dihedral angle restraints: 9672 sinusoidal: 5408 harmonic: 4264 Sorted by residual: dihedral pdb=" CA ILE A 46 " pdb=" CB ILE A 46 " pdb=" CG1 ILE A 46 " pdb=" CD1 ILE A 46 " ideal model delta sinusoidal sigma weight residual 60.00 109.32 -49.32 3 1.50e+01 4.44e-03 8.76e+00 dihedral pdb=" CA ILE C 46 " pdb=" CB ILE C 46 " pdb=" CG1 ILE C 46 " pdb=" CD1 ILE C 46 " ideal model delta sinusoidal sigma weight residual 60.00 109.32 -49.32 3 1.50e+01 4.44e-03 8.76e+00 dihedral pdb=" CA ILE B 46 " pdb=" CB ILE B 46 " pdb=" CG1 ILE B 46 " pdb=" CD1 ILE B 46 " ideal model delta sinusoidal sigma weight residual 60.00 109.32 -49.32 3 1.50e+01 4.44e-03 8.76e+00 ... (remaining 9669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 988 0.025 - 0.050: 386 0.050 - 0.075: 118 0.075 - 0.100: 41 0.100 - 0.125: 83 Chirality restraints: 1616 Sorted by residual: chirality pdb=" CA ILE B 97 " pdb=" N ILE B 97 " pdb=" C ILE B 97 " pdb=" CB ILE B 97 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE A 97 " pdb=" N ILE A 97 " pdb=" C ILE A 97 " pdb=" CB ILE A 97 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE C 97 " pdb=" N ILE C 97 " pdb=" C ILE C 97 " pdb=" CB ILE C 97 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1613 not shown) Planarity restraints: 2976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 14 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 15 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 14 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO B 15 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 15 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 15 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 14 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 15 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 15 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 15 " 0.017 5.00e-02 4.00e+02 ... (remaining 2973 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1484 2.22 - 2.82: 43828 2.82 - 3.41: 51920 3.41 - 4.01: 69593 4.01 - 4.60: 109765 Nonbonded interactions: 276590 Sorted by model distance: nonbonded pdb=" O GLY B 120 " pdb=" HE ARG B 194 " model vdw 1.628 2.450 nonbonded pdb=" O GLY A 120 " pdb=" HE ARG A 194 " model vdw 1.628 2.450 nonbonded pdb=" O GLY D 120 " pdb=" HE ARG D 194 " model vdw 1.628 2.450 nonbonded pdb=" O GLY C 120 " pdb=" HE ARG C 194 " model vdw 1.628 2.450 nonbonded pdb=" O MET A 215 " pdb="HD21 ASN A 219 " model vdw 1.661 2.450 ... (remaining 276585 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: 0.04 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.290 Find NCS groups from input model: 0.130 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: 0.020 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.003 0.046 10256 Z= 0.176 Angle : 0.556 9.126 13912 Z= 0.373 Chirality : 0.039 0.125 1616 Planarity : 0.004 0.031 1760 Dihedral : 11.391 85.347 3892 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: 2.10 (0.24), residues: 1264 helix: 2.82 (0.21), residues: 644 sheet: 0.73 (0.40), residues: 200 loop : -0.59 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 176 TYR 0.009 0.001 TYR B 299 PHE 0.008 0.001 PHE C 136 TRP 0.003 0.000 TRP A 41 HIS 0.002 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.18 (10256) covalent geometry : angle 0.55552 / 0.37 (13912) hydrogen bonds : bond 0.14723 / 9.85 ( 584) hydrogen bonds : angle 6.07764 / 4.26 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 ASP cc_start: 0.7018 (p0) cc_final: 0.6750 (p0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 1.5072 time to fit residues: 290.7389 Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN B 145 ASN C 145 ASN C 202 HIS D 145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.204428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143224 restraints weight = 31165.504| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.26 r_work: 0.3293 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10256 Z= 0.184 Angle : 0.562 4.410 13912 Z= 0.298 Chirality : 0.043 0.156 1616 Planarity : 0.005 0.041 1760 Dihedral : 9.652 87.613 1528 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.02 % Allowed : 9.54 % Favored : 89.44 % 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: 1.48 (0.23), residues: 1264 helix: 2.31 (0.20), residues: 652 sheet: 0.24 (0.37), residues: 200 loop : -0.83 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 303 TYR 0.010 0.002 TYR B 166 PHE 0.010 0.001 PHE B 121 TRP 0.003 0.001 TRP A 41 HIS 0.002 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (10256) covalent geometry : angle 0.56158 / 0.30 (13912) hydrogen bonds : bond 0.07105 / 4.78 ( 584) hydrogen bonds : angle 5.10858 / 3.56 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.562 Fit side-chains REVERT: A 156 MET cc_start: 0.6733 (ptp) cc_final: 0.6518 (ptp) REVERT: A 218 ILE cc_start: 0.8727 (mt) cc_final: 0.8513 (mm) REVERT: B 85 MET cc_start: 0.8970 (mmt) cc_final: 0.8770 (mmt) REVERT: B 156 MET cc_start: 0.6719 (ptm) cc_final: 0.6499 (ptp) REVERT: B 218 ILE cc_start: 0.8696 (mt) cc_final: 0.8477 (mm) REVERT: C 156 MET cc_start: 0.6786 (ptp) cc_final: 0.6584 (ptp) REVERT: C 218 ILE cc_start: 0.8745 (mt) cc_final: 0.8542 (mm) REVERT: D 156 MET cc_start: 0.6850 (ptp) cc_final: 0.6592 (ptp) REVERT: D 218 ILE cc_start: 0.8757 (mt) cc_final: 0.8555 (mm) outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 1.4800 time to fit residues: 207.7660 Evaluate side-chains 118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 36 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.204171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.142613 restraints weight = 31235.750| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.26 r_work: 0.3288 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10256 Z= 0.153 Angle : 0.518 4.452 13912 Z= 0.272 Chirality : 0.041 0.145 1616 Planarity : 0.005 0.044 1760 Dihedral : 9.142 88.895 1528 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.39 % Allowed : 11.20 % Favored : 87.41 % 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: 1.39 (0.23), residues: 1264 helix: 2.29 (0.20), residues: 652 sheet: 0.12 (0.37), residues: 200 loop : -0.94 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 303 TYR 0.008 0.001 TYR A 308 PHE 0.007 0.001 PHE A 214 TRP 0.002 0.001 TRP B 41 HIS 0.004 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (10256) covalent geometry : angle 0.51786 / 0.27 (13912) hydrogen bonds : bond 0.06778 / 4.57 ( 584) hydrogen bonds : angle 4.88596 / 3.40 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.9028 (mmt) cc_final: 0.8721 (mmt) outliers start: 15 outliers final: 12 residues processed: 131 average time/residue: 1.6166 time to fit residues: 224.5343 Evaluate side-chains 129 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 237 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.201791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.145476 restraints weight = 31111.482| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.11 r_work: 0.3275 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10256 Z= 0.130 Angle : 0.488 4.471 13912 Z= 0.255 Chirality : 0.041 0.142 1616 Planarity : 0.005 0.046 1760 Dihedral : 8.593 89.997 1528 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.30 % Allowed : 12.04 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.23), residues: 1264 helix: 2.38 (0.20), residues: 652 sheet: -0.02 (0.36), residues: 200 loop : -0.99 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 303 TYR 0.007 0.001 TYR C 166 PHE 0.006 0.001 PHE D 214 TRP 0.002 0.000 TRP B 41 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10256) covalent geometry : angle 0.48799 / 0.26 (13912) hydrogen bonds : bond 0.06162 / 4.15 ( 584) hydrogen bonds : angle 4.73752 / 3.30 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.9009 (mmt) cc_final: 0.8657 (mmt) REVERT: B 215 MET cc_start: 0.5981 (tpt) cc_final: 0.5641 (tpt) outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 1.6560 time to fit residues: 226.4223 Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 202 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.202881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147354 restraints weight = 29526.326| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.02 r_work: 0.3464 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10256 Z= 0.271 Angle : 0.670 7.240 13912 Z= 0.353 Chirality : 0.045 0.161 1616 Planarity : 0.007 0.050 1760 Dihedral : 8.504 87.067 1528 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.96 % Allowed : 11.02 % Favored : 86.02 % 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: 0.49 (0.22), residues: 1264 helix: 1.57 (0.20), residues: 652 sheet: -0.27 (0.36), residues: 200 loop : -1.37 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 297 TYR 0.015 0.003 TYR C 308 PHE 0.015 0.002 PHE B 207 TRP 0.006 0.001 TRP A 41 HIS 0.004 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.27 (10256) covalent geometry : angle 0.67023 / 0.35 (13912) hydrogen bonds : bond 0.09132 / 6.18 ( 584) hydrogen bonds : angle 5.02968 / 3.53 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TRP cc_start: 0.5506 (m-90) cc_final: 0.4701 (p90) REVERT: B 85 MET cc_start: 0.9088 (mmt) cc_final: 0.8501 (mmt) REVERT: B 215 MET cc_start: 0.6306 (tpt) cc_final: 0.5901 (tpt) REVERT: B 265 TRP cc_start: 0.5621 (m-90) cc_final: 0.4775 (p90) REVERT: C 272 MET cc_start: 0.6760 (mmm) cc_final: 0.6348 (ttt) outliers start: 32 outliers final: 16 residues processed: 139 average time/residue: 1.5039 time to fit residues: 222.5726 Evaluate side-chains 130 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 211 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.204871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149359 restraints weight = 29413.436| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.09 r_work: 0.3490 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10256 Z= 0.197 Angle : 0.567 6.477 13912 Z= 0.297 Chirality : 0.042 0.149 1616 Planarity : 0.006 0.048 1760 Dihedral : 8.151 88.032 1528 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.85 % Allowed : 12.96 % Favored : 85.19 % 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: 0.59 (0.23), residues: 1264 helix: 1.75 (0.20), residues: 652 sheet: -0.34 (0.36), residues: 200 loop : -1.47 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 297 TYR 0.011 0.002 TYR C 308 PHE 0.013 0.001 PHE C 207 TRP 0.004 0.001 TRP B 41 HIS 0.003 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (10256) covalent geometry : angle 0.56683 / 0.30 (13912) hydrogen bonds : bond 0.07810 / 5.26 ( 584) hydrogen bonds : angle 4.89665 / 3.43 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TRP cc_start: 0.5608 (m-90) cc_final: 0.4828 (p90) REVERT: B 85 MET cc_start: 0.9055 (mmt) cc_final: 0.8573 (mmt) REVERT: B 215 MET cc_start: 0.6306 (tpt) cc_final: 0.5900 (tpt) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 1.4574 time to fit residues: 204.2118 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 211 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 HIS D 202 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.206256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146257 restraints weight = 29926.563| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.36 r_work: 0.3400 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10256 Z= 0.249 Angle : 0.630 7.360 13912 Z= 0.332 Chirality : 0.044 0.157 1616 Planarity : 0.006 0.049 1760 Dihedral : 7.952 85.450 1528 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.96 % Allowed : 12.13 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.23), residues: 1264 helix: 1.51 (0.20), residues: 652 sheet: -0.54 (0.35), residues: 200 loop : -1.61 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 297 TYR 0.015 0.002 TYR A 308 PHE 0.010 0.002 PHE D 136 TRP 0.005 0.001 TRP C 41 HIS 0.003 0.001 HIS C 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.25 (10256) covalent geometry : angle 0.63002 / 0.33 (13912) hydrogen bonds : bond 0.08776 / 5.92 ( 584) hydrogen bonds : angle 4.96935 / 3.49 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.9068 (mmt) cc_final: 0.8563 (mmt) REVERT: B 215 MET cc_start: 0.6384 (tpt) cc_final: 0.6003 (tpt) outliers start: 32 outliers final: 22 residues processed: 129 average time/residue: 1.5274 time to fit residues: 209.1309 Evaluate side-chains 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 211 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 0.6980 chunk 116 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 111 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN C 104 GLN D 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.212782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159042 restraints weight = 30283.204| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.33 r_work: 0.3547 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10256 Z= 0.112 Angle : 0.468 4.382 13912 Z= 0.249 Chirality : 0.040 0.133 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.507 88.278 1528 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.11 % Allowed : 13.43 % Favored : 85.46 % 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: 1.06 (0.23), residues: 1264 helix: 2.27 (0.20), residues: 652 sheet: -0.33 (0.37), residues: 200 loop : -1.38 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 258 TYR 0.007 0.001 TYR B 166 PHE 0.008 0.001 PHE B 285 TRP 0.002 0.000 TRP C 265 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (10256) covalent geometry : angle 0.46841 / 0.25 (13912) hydrogen bonds : bond 0.05676 / 3.80 ( 584) hydrogen bonds : angle 4.67188 / 3.27 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.9052 (mmt) cc_final: 0.8634 (mmt) REVERT: B 156 MET cc_start: 0.6853 (ptm) cc_final: 0.6576 (ptp) REVERT: B 215 MET cc_start: 0.6072 (tpt) cc_final: 0.5681 (tpt) REVERT: D 265 TRP cc_start: 0.5282 (OUTLIER) cc_final: 0.4594 (p90) outliers start: 12 outliers final: 4 residues processed: 128 average time/residue: 1.6445 time to fit residues: 223.0851 Evaluate side-chains 116 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 265 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.210181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157299 restraints weight = 30031.939| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.40 r_work: 0.3491 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10256 Z= 0.156 Angle : 0.513 5.000 13912 Z= 0.269 Chirality : 0.041 0.141 1616 Planarity : 0.005 0.046 1760 Dihedral : 7.320 84.899 1528 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.30 % Allowed : 13.52 % Favored : 85.19 % 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: 0.94 (0.23), residues: 1264 helix: 2.16 (0.20), residues: 652 sheet: -0.28 (0.37), residues: 200 loop : -1.48 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 297 TYR 0.009 0.001 TYR B 308 PHE 0.013 0.001 PHE D 207 TRP 0.003 0.001 TRP D 41 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (10256) covalent geometry : angle 0.51264 / 0.27 (13912) hydrogen bonds : bond 0.06813 / 4.59 ( 584) hydrogen bonds : angle 4.66067 / 3.26 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TRP cc_start: 0.5402 (OUTLIER) cc_final: 0.4728 (m-90) REVERT: B 85 MET cc_start: 0.9085 (mmt) cc_final: 0.8608 (mmt) REVERT: B 215 MET cc_start: 0.6201 (tpt) cc_final: 0.5803 (tpt) REVERT: C 265 TRP cc_start: 0.5314 (OUTLIER) cc_final: 0.4699 (m-90) REVERT: D 265 TRP cc_start: 0.5274 (OUTLIER) cc_final: 0.4665 (m-90) outliers start: 14 outliers final: 7 residues processed: 116 average time/residue: 1.6839 time to fit residues: 206.2843 Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 265 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.210667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.151208 restraints weight = 30331.157| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.20 r_work: 0.3448 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10256 Z= 0.141 Angle : 0.498 4.751 13912 Z= 0.262 Chirality : 0.040 0.141 1616 Planarity : 0.005 0.046 1760 Dihedral : 7.134 82.940 1528 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.74 % Allowed : 14.54 % Favored : 84.72 % 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: 0.99 (0.23), residues: 1264 helix: 2.22 (0.20), residues: 652 sheet: -0.27 (0.38), residues: 200 loop : -1.48 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.008 0.001 TYR B 308 PHE 0.006 0.001 PHE D 136 TRP 0.003 0.001 TRP C 41 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10256) covalent geometry : angle 0.49844 / 0.26 (13912) hydrogen bonds : bond 0.06527 / 4.39 ( 584) hydrogen bonds : angle 4.63025 / 3.24 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6854 (ptm) cc_final: 0.6615 (ptp) REVERT: A 265 TRP cc_start: 0.5376 (OUTLIER) cc_final: 0.4730 (m-90) REVERT: B 85 MET cc_start: 0.9081 (mmt) cc_final: 0.8610 (mmt) REVERT: B 215 MET cc_start: 0.6160 (tpt) cc_final: 0.5774 (tpt) REVERT: C 204 GLU cc_start: 0.7076 (tt0) cc_final: 0.6875 (tm-30) REVERT: C 265 TRP cc_start: 0.5313 (OUTLIER) cc_final: 0.4708 (m-90) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 1.7792 time to fit residues: 212.7495 Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 265 TRP Chi-restraints excluded: chain D residue 196 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.211147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151618 restraints weight = 30236.493| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.24 r_work: 0.3465 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10256 Z= 0.131 Angle : 0.485 4.375 13912 Z= 0.254 Chirality : 0.040 0.138 1616 Planarity : 0.005 0.046 1760 Dihedral : 6.893 79.072 1528 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.93 % Allowed : 14.54 % Favored : 84.54 % 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: 1.09 (0.23), residues: 1264 helix: 2.33 (0.20), residues: 652 sheet: -0.29 (0.38), residues: 200 loop : -1.45 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 303 TYR 0.007 0.001 TYR B 308 PHE 0.005 0.001 PHE D 136 TRP 0.003 0.001 TRP A 41 HIS 0.002 0.001 HIS D 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (10256) covalent geometry : angle 0.48497 / 0.25 (13912) hydrogen bonds : bond 0.06207 / 4.17 ( 584) hydrogen bonds : angle 4.57365 / 3.20 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6829.78 seconds wall clock time: 116 minutes 8.67 seconds (6968.67 seconds total)