Starting phenix.real_space_refine on Thu Sep 18 21:02:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asc_43812/09_2025/9asc_43812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asc_43812/09_2025/9asc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9asc_43812/09_2025/9asc_43812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asc_43812/09_2025/9asc_43812.map" model { file = "/net/cci-nas-00/data/ceres_data/9asc_43812/09_2025/9asc_43812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asc_43812/09_2025/9asc_43812.cif" } 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-2.0-5805/lib/python3.9/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, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.20, per 1000 atoms: 0.26 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: 2.28 Conformation dependent library (CDL) restraints added in 605.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.54 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: 4.75 Time building geometry restraints manager: 3.05 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: 1.880 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: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.210 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 aren 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 covalent geometry : bond 0.00312 (10256) covalent geometry : angle 0.55552 (13912) hydrogen bonds : bond 0.14723 ( 584) hydrogen bonds : angle 6.07764 ( 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 : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 1.8732 time to fit residues: 358.7877 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 : 0.515 ------------------------------------------------------------------------------- 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 145 ASN C 145 ASN D 145 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.204246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.142482 restraints weight = 31100.935| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.24 r_work: 0.3281 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10256 Z= 0.181 Angle : 0.560 4.737 13912 Z= 0.296 Chirality : 0.043 0.156 1616 Planarity : 0.005 0.041 1760 Dihedral : 9.193 77.276 1528 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 9.35 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.23), residues: 1264 helix: 2.28 (0.20), residues: 652 sheet: 0.21 (0.37), residues: 200 loop : -0.85 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 303 TYR 0.011 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 B 202 Details of bonding type rmsd covalent geometry : bond 0.00430 (10256) covalent geometry : angle 0.56037 (13912) hydrogen bonds : bond 0.07187 ( 584) hydrogen bonds : angle 5.10399 ( 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 135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8973 (mmt) cc_final: 0.8732 (mmt) REVERT: A 156 MET cc_start: 0.6775 (ptp) cc_final: 0.6542 (ptp) REVERT: A 218 ILE cc_start: 0.8751 (mt) cc_final: 0.8538 (mm) REVERT: B 85 MET cc_start: 0.8956 (mmt) cc_final: 0.8701 (mmt) REVERT: B 156 MET cc_start: 0.6727 (ptm) cc_final: 0.6519 (ptp) REVERT: B 218 ILE cc_start: 0.8735 (mt) cc_final: 0.8517 (mm) REVERT: D 156 MET cc_start: 0.6841 (ptp) cc_final: 0.6589 (ptp) REVERT: D 218 ILE cc_start: 0.8778 (mt) cc_final: 0.8577 (mm) outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 1.7080 time to fit residues: 243.9190 Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 C residue 35 GLU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 196 THR 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: 3.9990 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 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: 4.9990 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.201663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139314 restraints weight = 31140.789| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.28 r_work: 0.3228 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10256 Z= 0.190 Angle : 0.559 5.280 13912 Z= 0.295 Chirality : 0.042 0.151 1616 Planarity : 0.006 0.044 1760 Dihedral : 8.895 87.327 1528 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 11.67 % Favored : 86.76 % 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 aren not related in a simple way. whole: 1.11 (0.23), residues: 1264 helix: 2.04 (0.20), residues: 652 sheet: 0.05 (0.37), residues: 200 loop : -1.05 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 303 TYR 0.010 0.002 TYR D 308 PHE 0.009 0.001 PHE A 214 TRP 0.003 0.001 TRP A 41 HIS 0.003 0.001 HIS C 81 Details of bonding type rmsd covalent geometry : bond 0.00458 (10256) covalent geometry : angle 0.55930 (13912) hydrogen bonds : bond 0.07636 ( 584) hydrogen bonds : angle 4.95809 ( 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 139 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.554 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: A 85 MET cc_start: 0.9083 (mmt) cc_final: 0.8717 (mmt) REVERT: B 85 MET cc_start: 0.9081 (mmt) cc_final: 0.8692 (mmt) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 1.7300 time to fit residues: 244.5938 Evaluate side-chains 128 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 211 LYS 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: 0.0070 chunk 7 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.194894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143600 restraints weight = 31275.495| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.18 r_work: 0.3319 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10256 Z= 0.117 Angle : 0.471 4.508 13912 Z= 0.248 Chirality : 0.040 0.139 1616 Planarity : 0.005 0.045 1760 Dihedral : 7.964 81.680 1528 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.20 % Allowed : 12.50 % Favored : 86.30 % 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 aren not related in a simple way. whole: 1.38 (0.23), residues: 1264 helix: 2.39 (0.20), residues: 652 sheet: -0.09 (0.36), residues: 200 loop : -1.01 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 28 TYR 0.007 0.001 TYR A 166 PHE 0.006 0.001 PHE B 285 TRP 0.001 0.000 TRP C 41 HIS 0.002 0.001 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00249 (10256) covalent geometry : angle 0.47107 (13912) hydrogen bonds : bond 0.05895 ( 584) hydrogen bonds : angle 4.75195 ( 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 133 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9122 (mmt) cc_final: 0.8819 (mmt) REVERT: B 85 MET cc_start: 0.9122 (mmt) cc_final: 0.8798 (mmt) REVERT: B 215 MET cc_start: 0.6200 (tpt) cc_final: 0.5844 (tpt) outliers start: 13 outliers final: 5 residues processed: 130 average time/residue: 1.7057 time to fit residues: 233.7195 Evaluate side-chains 115 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS B 202 HIS C 202 HIS D 202 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.206366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.145184 restraints weight = 29984.302| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.28 r_work: 0.3383 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 10256 Z= 0.263 Angle : 0.639 6.895 13912 Z= 0.339 Chirality : 0.045 0.158 1616 Planarity : 0.007 0.049 1760 Dihedral : 7.628 76.334 1528 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.69 % Allowed : 11.20 % Favored : 86.11 % 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 aren not related in a simple way. whole: 0.57 (0.22), residues: 1264 helix: 1.65 (0.20), residues: 652 sheet: -0.24 (0.36), residues: 200 loop : -1.38 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 297 TYR 0.015 0.002 TYR B 308 PHE 0.014 0.002 PHE D 207 TRP 0.006 0.001 TRP D 41 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00650 (10256) covalent geometry : angle 0.63921 (13912) hydrogen bonds : bond 0.08933 ( 584) hydrogen bonds : angle 4.97923 ( 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 138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9080 (mmt) cc_final: 0.8544 (mmt) REVERT: A 265 TRP cc_start: 0.5469 (m-90) cc_final: 0.4624 (p90) REVERT: B 85 MET cc_start: 0.9088 (mmt) cc_final: 0.8541 (mmt) REVERT: B 215 MET cc_start: 0.6377 (tpt) cc_final: 0.5994 (tpt) REVERT: B 265 TRP cc_start: 0.5554 (m-90) cc_final: 0.4685 (p90) outliers start: 29 outliers final: 16 residues processed: 125 average time/residue: 1.7421 time to fit residues: 229.9169 Evaluate side-chains 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 237 SER 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 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 Chi-restraints excluded: chain D residue 237 SER 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: 2.9990 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.208282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147579 restraints weight = 30051.691| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.32 r_work: 0.3418 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10256 Z= 0.187 Angle : 0.549 6.147 13912 Z= 0.288 Chirality : 0.042 0.149 1616 Planarity : 0.006 0.048 1760 Dihedral : 7.387 77.731 1528 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.94 % Allowed : 12.41 % Favored : 85.65 % 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 aren not related in a simple way. whole: 0.66 (0.23), residues: 1264 helix: 1.82 (0.20), residues: 652 sheet: -0.32 (0.36), residues: 200 loop : -1.45 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.002 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00451 (10256) covalent geometry : angle 0.54909 (13912) hydrogen bonds : bond 0.07643 ( 584) hydrogen bonds : angle 4.84945 ( 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 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9059 (mmt) cc_final: 0.8620 (mmt) REVERT: B 58 MET cc_start: 0.7699 (mtp) cc_final: 0.7462 (mtp) REVERT: B 85 MET cc_start: 0.9056 (mmt) cc_final: 0.8605 (mmt) REVERT: B 215 MET cc_start: 0.6263 (tpt) cc_final: 0.5868 (tpt) outliers start: 21 outliers final: 15 residues processed: 126 average time/residue: 1.7116 time to fit residues: 228.3238 Evaluate side-chains 121 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER 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 211 LYS Chi-restraints excluded: chain B residue 237 SER 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 Chi-restraints excluded: chain D residue 237 SER 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: 3.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 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: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.203430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147700 restraints weight = 29767.248| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.10 r_work: 0.3470 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10256 Z= 0.212 Angle : 0.580 6.597 13912 Z= 0.305 Chirality : 0.043 0.151 1616 Planarity : 0.006 0.049 1760 Dihedral : 7.356 77.609 1528 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.41 % Allowed : 12.22 % Favored : 85.37 % 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 aren not related in a simple way. whole: 0.50 (0.23), residues: 1264 helix: 1.72 (0.20), residues: 652 sheet: -0.44 (0.36), residues: 200 loop : -1.56 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 297 TYR 0.013 0.002 TYR D 308 PHE 0.009 0.002 PHE D 136 TRP 0.004 0.001 TRP B 41 HIS 0.002 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00520 (10256) covalent geometry : angle 0.57974 (13912) hydrogen bonds : bond 0.08127 ( 584) hydrogen bonds : angle 4.86417 ( 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 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9076 (mmt) cc_final: 0.8575 (mmt) REVERT: A 265 TRP cc_start: 0.5524 (OUTLIER) cc_final: 0.4886 (m-90) REVERT: B 58 MET cc_start: 0.7790 (mtp) cc_final: 0.7541 (mtp) REVERT: B 85 MET cc_start: 0.9077 (mmt) cc_final: 0.8568 (mmt) REVERT: B 215 MET cc_start: 0.6412 (tpt) cc_final: 0.5993 (tpt) REVERT: B 265 TRP cc_start: 0.5512 (OUTLIER) cc_final: 0.4893 (m-90) REVERT: D 265 TRP cc_start: 0.5485 (OUTLIER) cc_final: 0.4893 (m-90) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 1.7004 time to fit residues: 219.7066 Evaluate side-chains 132 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 SER Chi-restraints excluded: chain A residue 265 TRP 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 B residue 265 TRP 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 Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 111 optimal weight: 0.0010 chunk 67 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.212089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154144 restraints weight = 30448.430| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.55 r_work: 0.3515 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3301 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= 0.111 Angle : 0.464 4.369 13912 Z= 0.246 Chirality : 0.039 0.134 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.124 80.996 1528 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.93 % Allowed : 12.96 % Favored : 86.11 % 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 aren not related in a simple way. whole: 1.11 (0.23), residues: 1264 helix: 2.30 (0.20), residues: 652 sheet: -0.33 (0.37), residues: 200 loop : -1.33 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 303 TYR 0.007 0.001 TYR D 166 PHE 0.006 0.001 PHE C 285 TRP 0.002 0.000 TRP B 41 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00229 (10256) covalent geometry : angle 0.46448 (13912) hydrogen bonds : bond 0.05704 ( 584) hydrogen bonds : angle 4.61966 ( 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 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9012 (mmt) cc_final: 0.8608 (mmt) REVERT: A 265 TRP cc_start: 0.5351 (OUTLIER) cc_final: 0.4724 (m-90) REVERT: B 85 MET cc_start: 0.9007 (mmt) cc_final: 0.8597 (mmt) REVERT: B 215 MET cc_start: 0.6046 (tpt) cc_final: 0.5660 (tpt) REVERT: B 265 TRP cc_start: 0.5338 (OUTLIER) cc_final: 0.4729 (m-90) REVERT: C 156 MET cc_start: 0.6640 (ptm) cc_final: 0.6416 (ptp) REVERT: D 265 TRP cc_start: 0.5245 (OUTLIER) cc_final: 0.4663 (m-90) outliers start: 10 outliers final: 0 residues processed: 117 average time/residue: 1.9428 time to fit residues: 238.9007 Evaluate side-chains 114 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain B residue 265 TRP 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: 1.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.210549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150951 restraints weight = 30192.891| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.26 r_work: 0.3447 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3407 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= 0.133 Angle : 0.489 4.566 13912 Z= 0.256 Chirality : 0.040 0.137 1616 Planarity : 0.005 0.046 1760 Dihedral : 7.025 79.834 1528 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.02 % Allowed : 13.70 % Favored : 85.28 % 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 aren not related in a simple way. whole: 1.09 (0.23), residues: 1264 helix: 2.29 (0.20), residues: 652 sheet: -0.23 (0.37), residues: 200 loop : -1.41 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.008 0.001 TYR C 308 PHE 0.014 0.001 PHE C 207 TRP 0.003 0.000 TRP D 41 HIS 0.002 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00303 (10256) covalent geometry : angle 0.48921 (13912) hydrogen bonds : bond 0.06322 ( 584) hydrogen bonds : angle 4.58611 ( 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 121 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.9094 (mmt) cc_final: 0.8648 (mmt) REVERT: A 265 TRP cc_start: 0.5339 (OUTLIER) cc_final: 0.4718 (m-90) REVERT: B 85 MET cc_start: 0.9091 (mmt) cc_final: 0.8636 (mmt) REVERT: B 215 MET cc_start: 0.6298 (tpt) cc_final: 0.5899 (tpt) REVERT: B 265 TRP cc_start: 0.5333 (OUTLIER) cc_final: 0.4736 (m-90) REVERT: C 156 MET cc_start: 0.6620 (ptm) cc_final: 0.6397 (ptp) REVERT: C 265 TRP cc_start: 0.5250 (OUTLIER) cc_final: 0.4664 (m-90) outliers start: 11 outliers final: 4 residues processed: 111 average time/residue: 1.9731 time to fit residues: 230.2585 Evaluate side-chains 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 265 TRP Chi-restraints excluded: chain C residue 196 THR 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 71 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.209670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149265 restraints weight = 30261.390| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.31 r_work: 0.3440 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10256 Z= 0.148 Angle : 0.502 4.782 13912 Z= 0.263 Chirality : 0.041 0.144 1616 Planarity : 0.005 0.046 1760 Dihedral : 7.023 79.018 1528 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.46 % Allowed : 14.44 % Favored : 85.09 % 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 aren not related in a simple way. whole: 1.02 (0.23), residues: 1264 helix: 2.24 (0.20), residues: 652 sheet: -0.25 (0.37), residues: 200 loop : -1.46 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 303 TYR 0.008 0.001 TYR A 308 PHE 0.005 0.001 PHE D 136 TRP 0.003 0.001 TRP C 41 HIS 0.002 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00344 (10256) covalent geometry : angle 0.50197 (13912) hydrogen bonds : bond 0.06618 ( 584) hydrogen bonds : angle 4.60182 ( 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 113 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.700 Fit side-chains REVERT: A 85 MET cc_start: 0.9080 (mmt) cc_final: 0.8553 (mmt) REVERT: B 85 MET cc_start: 0.9075 (mmt) cc_final: 0.8611 (mmt) REVERT: B 156 MET cc_start: 0.6691 (ptm) cc_final: 0.6475 (ptp) REVERT: B 215 MET cc_start: 0.6267 (tpt) cc_final: 0.5873 (tpt) REVERT: C 204 GLU cc_start: 0.7067 (tt0) cc_final: 0.6855 (tm-30) REVERT: C 265 TRP cc_start: 0.5299 (OUTLIER) cc_final: 0.4701 (m-90) outliers start: 5 outliers final: 4 residues processed: 108 average time/residue: 1.9881 time to fit residues: 225.9309 Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 93 optimal weight: 7.9990 chunk 81 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.212300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153900 restraints weight = 30298.031| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.21 r_work: 0.3478 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10256 Z= 0.110 Angle : 0.460 4.300 13912 Z= 0.241 Chirality : 0.039 0.131 1616 Planarity : 0.005 0.045 1760 Dihedral : 6.873 79.073 1528 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.65 % Allowed : 14.07 % Favored : 85.28 % 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 aren not related in a simple way. whole: 1.35 (0.24), residues: 1264 helix: 2.57 (0.20), residues: 652 sheet: -0.25 (0.38), residues: 200 loop : -1.34 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.006 0.001 TYR D 166 PHE 0.004 0.001 PHE D 285 TRP 0.002 0.000 TRP B 41 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00235 (10256) covalent geometry : angle 0.45963 (13912) hydrogen bonds : bond 0.05493 ( 584) hydrogen bonds : angle 4.45927 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7191.49 seconds wall clock time: 122 minutes 5.53 seconds (7325.53 seconds total)