Starting phenix.real_space_refine on Tue Jun 17 16:21:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asc_43812/06_2025/9asc_43812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asc_43812/06_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_43812/06_2025/9asc_43812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asc_43812/06_2025/9asc_43812.map" model { file = "/net/cci-nas-00/data/ceres_data/9asc_43812/06_2025/9asc_43812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asc_43812/06_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-5710/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: 11.47, per 1000 atoms: 0.57 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: 5.35 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: 1.23 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: 8.03 Time building geometry restraints manager: 6.40 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: 0.09 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: 1.760 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: 0.340 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 45.540 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.420 ------------------------------------------------------------------------------- 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 : 1.442 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: 3.7897 time to fit residues: 733.4696 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 : 2.770 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.205709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144198 restraints weight = 31045.911| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.28 r_work: 0.3297 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1801 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= 0.170 Angle : 0.531 4.536 13912 Z= 0.282 Chirality : 0.042 0.153 1616 Planarity : 0.005 0.039 1760 Dihedral : 9.223 77.358 1528 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.93 % Allowed : 9.63 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.62 (0.23), residues: 1264 helix: 2.45 (0.20), residues: 652 sheet: 0.30 (0.38), residues: 200 loop : -0.82 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 41 HIS 0.002 0.001 HIS D 81 PHE 0.008 0.001 PHE C 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 0.06889 ( 584) hydrogen bonds : angle 5.13070 ( 1728) covalent geometry : bond 0.00390 (10256) covalent geometry : angle 0.53051 (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 129 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.620 Fit side-chains REVERT: A 156 MET cc_start: 0.6719 (ptp) cc_final: 0.6499 (ptp) REVERT: A 218 ILE cc_start: 0.8706 (mt) cc_final: 0.8490 (mm) REVERT: B 156 MET cc_start: 0.6647 (ptm) cc_final: 0.6421 (ptp) REVERT: C 156 MET cc_start: 0.6789 (ptp) cc_final: 0.6584 (ptp) REVERT: C 218 ILE cc_start: 0.8715 (mt) cc_final: 0.8513 (mm) REVERT: D 156 MET cc_start: 0.6841 (ptp) cc_final: 0.6577 (ptp) REVERT: D 218 ILE cc_start: 0.8743 (mt) cc_final: 0.8540 (mm) outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 3.8691 time to fit residues: 531.3285 Evaluate side-chains 118 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 2.141 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.198114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.141114 restraints weight = 30779.789| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.12 r_work: 0.3333 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10256 Z= 0.196 Angle : 0.572 5.207 13912 Z= 0.302 Chirality : 0.043 0.152 1616 Planarity : 0.006 0.044 1760 Dihedral : 8.926 85.679 1528 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.04 % Allowed : 10.83 % Favored : 87.13 % 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: 1.12 (0.23), residues: 1264 helix: 2.03 (0.20), residues: 652 sheet: 0.07 (0.37), residues: 200 loop : -1.02 (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 0.012 0.002 PHE B 121 TYR 0.011 0.002 TYR A 308 ARG 0.005 0.001 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.07733 ( 584) hydrogen bonds : angle 4.98183 ( 1728) covalent geometry : bond 0.00477 (10256) covalent geometry : angle 0.57168 (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 143 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 ILE cc_start: 0.8852 (mt) cc_final: 0.8649 (mm) outliers start: 22 outliers final: 16 residues processed: 139 average time/residue: 4.5560 time to fit residues: 680.7587 Evaluate side-chains 136 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 2.290 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 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 = 0.4373 r_free = 0.4373 target = 0.208842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148201 restraints weight = 30545.929| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.34 r_work: 0.3415 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10256 Z= 0.187 Angle : 0.555 5.681 13912 Z= 0.292 Chirality : 0.042 0.151 1616 Planarity : 0.006 0.047 1760 Dihedral : 8.041 78.505 1528 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.04 % Allowed : 11.85 % 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 (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: 0.89 (0.23), residues: 1264 helix: 1.93 (0.20), residues: 652 sheet: -0.20 (0.36), residues: 200 loop : -1.20 (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 0.012 0.001 PHE B 121 TYR 0.010 0.002 TYR D 308 ARG 0.004 0.000 ARG C 297 Details of bonding type rmsd hydrogen bonds : bond 0.07548 ( 584) hydrogen bonds : angle 4.90216 ( 1728) covalent geometry : bond 0.00451 (10256) covalent geometry : angle 0.55546 (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 142 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 3.650 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: A 265 TRP cc_start: 0.5382 (m-90) cc_final: 0.4508 (p90) REVERT: B 215 MET cc_start: 0.6124 (tpt) cc_final: 0.5739 (tpt) REVERT: B 265 TRP cc_start: 0.5467 (m-90) cc_final: 0.4558 (p90) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 4.0480 time to fit residues: 596.6321 Evaluate side-chains 123 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 211 LYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 211 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 211 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 0.0470 chunk 42 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- 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 = 0.212032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155894 restraints weight = 30335.165| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.50 r_work: 0.3574 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2886 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= 0.121 Angle : 0.470 4.321 13912 Z= 0.248 Chirality : 0.040 0.142 1616 Planarity : 0.005 0.046 1760 Dihedral : 7.307 79.184 1528 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % 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: 1.25 (0.23), residues: 1264 helix: 2.33 (0.20), residues: 652 sheet: -0.22 (0.36), residues: 200 loop : -1.12 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 41 HIS 0.002 0.001 HIS C 81 PHE 0.017 0.001 PHE D 207 TYR 0.006 0.001 TYR B 166 ARG 0.002 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.05990 ( 584) hydrogen bonds : angle 4.71750 ( 1728) covalent geometry : bond 0.00259 (10256) covalent geometry : angle 0.47025 (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 138 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: A 265 TRP cc_start: 0.5417 (m-90) cc_final: 0.4612 (p90) REVERT: B 122 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: B 215 MET cc_start: 0.5967 (tpt) cc_final: 0.5604 (tpt) REVERT: B 265 TRP cc_start: 0.5486 (m-90) cc_final: 0.4663 (p90) REVERT: C 122 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: D 122 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7279 (m-30) outliers start: 17 outliers final: 8 residues processed: 132 average time/residue: 4.4259 time to fit residues: 624.1366 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 : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 237 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: 0.7980 chunk 46 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.209038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148014 restraints weight = 30359.810| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.33 r_work: 0.3424 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3110 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= 0.173 Angle : 0.533 5.447 13912 Z= 0.281 Chirality : 0.042 0.148 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.202 78.441 1528 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.85 % Allowed : 12.50 % 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 (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: 0.96 (0.23), residues: 1264 helix: 2.06 (0.20), residues: 652 sheet: -0.21 (0.37), residues: 200 loop : -1.28 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 41 HIS 0.002 0.001 HIS A 81 PHE 0.014 0.001 PHE C 207 TYR 0.010 0.002 TYR D 308 ARG 0.003 0.000 ARG B 297 Details of bonding type rmsd hydrogen bonds : bond 0.07308 ( 584) hydrogen bonds : angle 4.77189 ( 1728) covalent geometry : bond 0.00413 (10256) covalent geometry : angle 0.53276 (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 130 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.430 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 265 TRP cc_start: 0.5527 (m-90) cc_final: 0.4681 (p90) REVERT: B 215 MET cc_start: 0.6251 (tpt) cc_final: 0.5873 (tpt) REVERT: B 265 TRP cc_start: 0.5559 (m-90) cc_final: 0.4723 (p90) outliers start: 20 outliers final: 13 residues processed: 123 average time/residue: 3.6669 time to fit residues: 477.0487 Evaluate side-chains 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 237 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 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 36 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.192622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140563 restraints weight = 30915.857| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.17 r_work: 0.3173 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10256 Z= 0.130 Angle : 0.479 4.341 13912 Z= 0.252 Chirality : 0.040 0.138 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.076 79.582 1528 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.48 % Allowed : 13.24 % 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 (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: 1.12 (0.23), residues: 1264 helix: 2.27 (0.20), residues: 652 sheet: -0.32 (0.37), residues: 200 loop : -1.24 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 41 HIS 0.002 0.001 HIS A 81 PHE 0.005 0.001 PHE C 285 TYR 0.007 0.001 TYR A 308 ARG 0.002 0.000 ARG C 303 Details of bonding type rmsd hydrogen bonds : bond 0.06285 ( 584) hydrogen bonds : angle 4.65361 ( 1728) covalent geometry : bond 0.00291 (10256) covalent geometry : angle 0.47902 (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 131 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 MET cc_start: 0.6244 (tpt) cc_final: 0.5878 (tpt) outliers start: 16 outliers final: 8 residues processed: 123 average time/residue: 3.5463 time to fit residues: 460.8383 Evaluate side-chains 121 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 5.9990 chunk 116 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.189802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 133)---------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137491 restraints weight = 31116.762| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.20 r_work: 0.3090 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3284 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 : 0.515 5.201 13912 Z= 0.271 Chirality : 0.041 0.144 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.069 78.410 1528 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.39 % Allowed : 12.87 % 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: 0.94 (0.23), residues: 1264 helix: 2.12 (0.20), residues: 652 sheet: -0.29 (0.37), residues: 200 loop : -1.38 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 41 HIS 0.002 0.001 HIS D 201 PHE 0.014 0.001 PHE D 207 TYR 0.010 0.002 TYR A 308 ARG 0.003 0.000 ARG C 297 Details of bonding type rmsd hydrogen bonds : bond 0.06989 ( 584) hydrogen bonds : angle 4.68060 ( 1728) covalent geometry : bond 0.00389 (10256) covalent geometry : angle 0.51505 (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 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 215 MET cc_start: 0.6496 (tpt) cc_final: 0.6130 (tpt) outliers start: 15 outliers final: 12 residues processed: 117 average time/residue: 3.5842 time to fit residues: 442.7409 Evaluate side-chains 119 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 237 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 196 THR Chi-restraints excluded: chain D residue 211 LYS 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: 0.9980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.188458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 152)---------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139340 restraints weight = 31011.584| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.81 r_work: 0.3219 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10256 Z= 0.141 Angle : 0.490 4.710 13912 Z= 0.258 Chirality : 0.040 0.140 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.013 78.406 1528 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.11 % Allowed : 13.06 % 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: 1.03 (0.23), residues: 1264 helix: 2.22 (0.20), residues: 652 sheet: -0.31 (0.37), residues: 200 loop : -1.36 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 41 HIS 0.002 0.001 HIS C 81 PHE 0.015 0.001 PHE A 207 TYR 0.008 0.001 TYR B 308 ARG 0.002 0.000 ARG C 303 Details of bonding type rmsd hydrogen bonds : bond 0.06528 ( 584) hydrogen bonds : angle 4.61938 ( 1728) covalent geometry : bond 0.00324 (10256) covalent geometry : angle 0.49019 (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 122 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.516 Fit side-chains REVERT: B 215 MET cc_start: 0.6444 (tpt) cc_final: 0.6043 (tpt) outliers start: 12 outliers final: 8 residues processed: 114 average time/residue: 3.5943 time to fit residues: 434.8618 Evaluate side-chains 117 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 116 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.183593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119952 restraints weight = 30956.695| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.21 r_work: 0.3051 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10256 Z= 0.198 Angle : 0.559 5.943 13912 Z= 0.294 Chirality : 0.042 0.149 1616 Planarity : 0.006 0.048 1760 Dihedral : 7.110 77.239 1528 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.39 % Allowed : 13.33 % 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 (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: 0.74 (0.23), residues: 1264 helix: 1.97 (0.20), residues: 652 sheet: -0.37 (0.36), residues: 200 loop : -1.52 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 41 HIS 0.003 0.001 HIS A 202 PHE 0.008 0.001 PHE D 136 TYR 0.012 0.002 TYR D 308 ARG 0.004 0.000 ARG D 297 Details of bonding type rmsd hydrogen bonds : bond 0.07657 ( 584) hydrogen bonds : angle 4.73019 ( 1728) covalent geometry : bond 0.00485 (10256) covalent geometry : angle 0.55880 (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 124 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 GLU cc_start: 0.7160 (tt0) cc_final: 0.6873 (tm-30) REVERT: B 215 MET cc_start: 0.6425 (tpt) cc_final: 0.6063 (tpt) outliers start: 15 outliers final: 10 residues processed: 117 average time/residue: 3.5257 time to fit residues: 436.6247 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 : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR 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 237 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 127 VAL 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 77 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.189161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134634 restraints weight = 31118.513| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.01 r_work: 0.3151 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10256 Z= 0.142 Angle : 0.498 4.920 13912 Z= 0.261 Chirality : 0.040 0.139 1616 Planarity : 0.005 0.047 1760 Dihedral : 7.042 77.886 1528 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.11 % Allowed : 13.61 % 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 (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: 2.18 (0.20), residues: 652 sheet: -0.35 (0.37), residues: 200 loop : -1.47 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 41 HIS 0.002 0.001 HIS D 81 PHE 0.006 0.001 PHE D 136 TYR 0.008 0.001 TYR A 308 ARG 0.003 0.000 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.06644 ( 584) hydrogen bonds : angle 4.63718 ( 1728) covalent geometry : bond 0.00325 (10256) covalent geometry : angle 0.49782 (13912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17084.33 seconds wall clock time: 299 minutes 42.13 seconds (17982.13 seconds total)