Starting phenix.real_space_refine on Tue May 20 15:37:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asc_43812/05_2025/9asc_43812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asc_43812/05_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_43812/05_2025/9asc_43812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asc_43812/05_2025/9asc_43812.map" model { file = "/net/cci-nas-00/data/ceres_data/9asc_43812/05_2025/9asc_43812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asc_43812/05_2025/9asc_43812.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 11.75, per 1000 atoms: 0.58 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: 5.86 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.83 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: 6.96 Time building geometry restraints manager: 6.85 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.560 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: 0.360 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 45.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.003 0.000 TRP A 41 HIS 0.002 0.001 HIS B 81 PHE 0.008 0.001 PHE C 136 TYR 0.009 0.001 TYR B 299 ARG 0.002 0.000 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.14723 ( 584) hydrogen bonds : angle 6.07764 ( 1728) covalent geometry : bond 0.00312 (10256) covalent geometry : angle 0.55552 (13912) *********************** 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 : 1.479 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: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 3.5284 time to fit residues: 680.9459 Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.204646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143314 restraints weight = 31044.978| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.26 r_work: 0.3282 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10256 Z= 0.171 Angle : 0.543 4.472 13912 Z= 0.288 Chirality : 0.042 0.152 1616 Planarity : 0.005 0.040 1760 Dihedral : 9.149 78.027 1528 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.93 % Allowed : 9.07 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1264 helix: 2.36 (0.20), residues: 652 sheet: 0.24 (0.37), residues: 200 loop : -0.82 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 41 HIS 0.002 0.001 HIS C 202 PHE 0.009 0.001 PHE A 121 TYR 0.010 0.002 TYR B 166 ARG 0.004 0.001 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.06954 ( 584) hydrogen bonds : angle 5.08641 ( 1728) covalent geometry : bond 0.00399 (10256) covalent geometry : angle 0.54301 (13912) *********************** 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: 10 poor density : 125 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6720 (ptp) cc_final: 0.6510 (ptp) REVERT: A 218 ILE cc_start: 0.8743 (mt) cc_final: 0.8528 (mm) REVERT: B 156 MET cc_start: 0.6697 (ptm) cc_final: 0.6484 (ptp) REVERT: B 218 ILE cc_start: 0.8710 (mt) cc_final: 0.8489 (mm) REVERT: C 218 ILE cc_start: 0.8761 (mt) cc_final: 0.8560 (mm) REVERT: D 156 MET cc_start: 0.6832 (ptp) cc_final: 0.6575 (ptp) REVERT: D 218 ILE cc_start: 0.8773 (mt) cc_final: 0.8571 (mm) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 3.3233 time to fit residues: 478.5911 Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.199355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143728 restraints weight = 30908.628| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.02 r_work: 0.3335 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2361 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= 0.176 Angle : 0.541 4.756 13912 Z= 0.285 Chirality : 0.042 0.148 1616 Planarity : 0.005 0.045 1760 Dihedral : 8.824 89.875 1528 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.30 % Allowed : 11.02 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1264 helix: 2.17 (0.20), residues: 652 sheet: 0.12 (0.37), residues: 200 loop : -0.99 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 41 HIS 0.003 0.001 HIS B 81 PHE 0.008 0.001 PHE A 214 TYR 0.010 0.002 TYR A 308 ARG 0.004 0.001 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.07294 ( 584) hydrogen bonds : angle 4.92545 ( 1728) covalent geometry : bond 0.00422 (10256) covalent geometry : angle 0.54060 (13912) *********************** 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: 14 poor density : 125 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ILE cc_start: 0.8837 (mt) cc_final: 0.8630 (mm) outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 3.4384 time to fit residues: 491.4149 Evaluate side-chains 135 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.209481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.148444 restraints weight = 30664.012| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.32 r_work: 0.3417 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10256 Z= 0.172 Angle : 0.535 5.228 13912 Z= 0.282 Chirality : 0.042 0.150 1616 Planarity : 0.006 0.046 1760 Dihedral : 7.767 74.385 1528 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.04 % Allowed : 10.74 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1264 helix: 2.05 (0.20), residues: 652 sheet: -0.05 (0.36), residues: 200 loop : -1.13 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 41 HIS 0.003 0.001 HIS B 81 PHE 0.007 0.001 PHE C 136 TYR 0.010 0.002 TYR D 308 ARG 0.004 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.07223 ( 584) hydrogen bonds : angle 4.86134 ( 1728) covalent geometry : bond 0.00409 (10256) covalent geometry : angle 0.53475 (13912) *********************** 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 137 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 MET cc_start: 0.6094 (tpt) cc_final: 0.5718 (tpt) outliers start: 22 outliers final: 14 residues processed: 133 average time/residue: 3.3389 time to fit residues: 470.5554 Evaluate side-chains 120 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 0.0870 chunk 5 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.210922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150925 restraints weight = 30273.259| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.28 r_work: 0.3455 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2864 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= 0.134 Angle : 0.485 4.586 13912 Z= 0.255 Chirality : 0.040 0.141 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.317 79.259 1528 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.57 % Allowed : 11.57 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1264 helix: 2.24 (0.20), residues: 652 sheet: -0.05 (0.37), residues: 200 loop : -1.15 (0.25), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 41 HIS 0.002 0.001 HIS D 81 PHE 0.015 0.001 PHE D 207 TYR 0.007 0.001 TYR D 308 ARG 0.003 0.000 ARG C 303 Details of bonding type rmsd hydrogen bonds : bond 0.06434 ( 584) hydrogen bonds : angle 4.76126 ( 1728) covalent geometry : bond 0.00298 (10256) covalent geometry : angle 0.48450 (13912) *********************** 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 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7621 (mtp) cc_final: 0.7420 (mtp) REVERT: A 122 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: B 122 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: B 215 MET cc_start: 0.6021 (tpt) cc_final: 0.5654 (tpt) REVERT: C 122 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: D 122 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7393 (m-30) outliers start: 17 outliers final: 11 residues processed: 130 average time/residue: 3.5475 time to fit residues: 488.0450 Evaluate side-chains 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 122 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 122 ASP 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 122 ASP 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 122 ASP Chi-restraints excluded: chain D residue 196 THR 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 103 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 118 optimal weight: 0.0770 chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.190286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 138)---------------| | r_work = 0.3546 r_free = 0.3546 target = 0.138053 restraints weight = 31125.188| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.96 r_work: 0.3138 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10256 Z= 0.133 Angle : 0.479 4.385 13912 Z= 0.252 Chirality : 0.040 0.141 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.137 80.159 1528 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.04 % Allowed : 11.76 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1264 helix: 2.28 (0.20), residues: 652 sheet: -0.04 (0.37), residues: 200 loop : -1.16 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 41 HIS 0.002 0.001 HIS C 81 PHE 0.014 0.001 PHE C 207 TYR 0.007 0.001 TYR A 308 ARG 0.002 0.000 ARG B 297 Details of bonding type rmsd hydrogen bonds : bond 0.06333 ( 584) hydrogen bonds : angle 4.68943 ( 1728) covalent geometry : bond 0.00301 (10256) covalent geometry : angle 0.47933 (13912) *********************** 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 138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 MET cc_start: 0.6312 (tpt) cc_final: 0.5933 (tpt) outliers start: 22 outliers final: 12 residues processed: 130 average time/residue: 3.5205 time to fit residues: 484.2105 Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR 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 237 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.197877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142192 restraints weight = 30710.504| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.02 r_work: 0.3157 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10256 Z= 0.118 Angle : 0.462 4.290 13912 Z= 0.243 Chirality : 0.040 0.136 1616 Planarity : 0.005 0.046 1760 Dihedral : 7.016 80.579 1528 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.39 % Allowed : 12.41 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1264 helix: 2.45 (0.20), residues: 652 sheet: -0.07 (0.37), residues: 200 loop : -1.17 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 41 HIS 0.002 0.001 HIS C 81 PHE 0.015 0.001 PHE D 207 TYR 0.006 0.001 TYR D 308 ARG 0.002 0.000 ARG D 303 Details of bonding type rmsd hydrogen bonds : bond 0.05850 ( 584) hydrogen bonds : angle 4.58847 ( 1728) covalent geometry : bond 0.00261 (10256) covalent geometry : angle 0.46203 (13912) *********************** 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 126 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 MET cc_start: 0.6351 (tpt) cc_final: 0.5970 (tpt) outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 3.6875 time to fit residues: 459.1941 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 : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 237 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 116 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.210007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150106 restraints weight = 30267.529| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.29 r_work: 0.3428 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10256 Z= 0.164 Angle : 0.518 5.170 13912 Z= 0.272 Chirality : 0.041 0.146 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.052 78.622 1528 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.39 % Allowed : 12.78 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1264 helix: 2.19 (0.20), residues: 652 sheet: -0.11 (0.37), residues: 200 loop : -1.29 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 41 HIS 0.003 0.001 HIS A 81 PHE 0.005 0.001 PHE A 214 TYR 0.010 0.002 TYR A 308 ARG 0.003 0.000 ARG C 297 Details of bonding type rmsd hydrogen bonds : bond 0.06983 ( 584) hydrogen bonds : angle 4.67945 ( 1728) covalent geometry : bond 0.00392 (10256) covalent geometry : angle 0.51848 (13912) *********************** 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 127 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 MET cc_start: 0.6256 (tpt) cc_final: 0.5830 (tpt) REVERT: C 156 MET cc_start: 0.6788 (ptm) cc_final: 0.6492 (ptp) outliers start: 15 outliers final: 12 residues processed: 120 average time/residue: 3.6018 time to fit residues: 456.9300 Evaluate side-chains 120 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 237 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.212010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152531 restraints weight = 30255.164| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.29 r_work: 0.3455 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10256 Z= 0.119 Angle : 0.466 4.298 13912 Z= 0.245 Chirality : 0.040 0.135 1616 Planarity : 0.005 0.046 1760 Dihedral : 6.949 79.067 1528 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.11 % Allowed : 13.15 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1264 helix: 2.43 (0.20), residues: 652 sheet: -0.12 (0.38), residues: 200 loop : -1.22 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 41 HIS 0.002 0.001 HIS C 201 PHE 0.004 0.001 PHE C 285 TYR 0.007 0.001 TYR A 166 ARG 0.002 0.000 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.05933 ( 584) hydrogen bonds : angle 4.55871 ( 1728) covalent geometry : bond 0.00258 (10256) covalent geometry : angle 0.46626 (13912) *********************** 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 125 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7530 (mtp) cc_final: 0.7289 (mtp) REVERT: A 204 GLU cc_start: 0.7045 (tt0) cc_final: 0.6811 (tm-30) REVERT: B 215 MET cc_start: 0.6178 (tpt) cc_final: 0.5773 (tpt) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 3.6765 time to fit residues: 462.5857 Evaluate side-chains 118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 D residue 36 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 237 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.209788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.150622 restraints weight = 29934.144| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.25 r_work: 0.3438 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10256 Z= 0.169 Angle : 0.525 5.269 13912 Z= 0.275 Chirality : 0.041 0.146 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.004 77.858 1528 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.57 % Allowed : 12.59 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1264 helix: 2.21 (0.20), residues: 652 sheet: -0.16 (0.37), residues: 200 loop : -1.36 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 41 HIS 0.002 0.001 HIS C 81 PHE 0.006 0.001 PHE D 136 TYR 0.010 0.002 TYR B 308 ARG 0.003 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.07037 ( 584) hydrogen bonds : angle 4.65032 ( 1728) covalent geometry : bond 0.00405 (10256) covalent geometry : angle 0.52501 (13912) ********************** 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 122 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.574 Fit side-chains REVERT: A 58 MET cc_start: 0.7524 (mtp) cc_final: 0.7302 (mtp) REVERT: B 215 MET cc_start: 0.6324 (tpt) cc_final: 0.5944 (tpt) REVERT: C 204 GLU cc_start: 0.7024 (tt0) cc_final: 0.6787 (tm-30) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 3.3677 time to fit residues: 415.3069 Evaluate side-chains 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 237 SER Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 237 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 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 = 0.4376 r_free = 0.4376 target = 0.208774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147867 restraints weight = 30209.162| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.32 r_work: 0.3433 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10256 Z= 0.182 Angle : 0.537 5.637 13912 Z= 0.283 Chirality : 0.042 0.146 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.085 77.742 1528 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.57 % Allowed : 12.50 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1264 helix: 2.09 (0.20), residues: 652 sheet: -0.17 (0.37), residues: 200 loop : -1.42 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 41 HIS 0.002 0.001 HIS C 202 PHE 0.007 0.001 PHE C 136 TYR 0.010 0.002 TYR B 308 ARG 0.003 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.07319 ( 584) hydrogen bonds : angle 4.69550 ( 1728) covalent geometry : bond 0.00439 (10256) covalent geometry : angle 0.53718 (13912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14899.34 seconds wall clock time: 255 minutes 7.81 seconds (15307.81 seconds total)