Starting phenix.real_space_refine on Tue Mar 3 13:43:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a01_15044/03_2026/8a01_15044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a01_15044/03_2026/8a01_15044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a01_15044/03_2026/8a01_15044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a01_15044/03_2026/8a01_15044.map" model { file = "/net/cci-nas-00/data/ceres_data/8a01_15044/03_2026/8a01_15044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a01_15044/03_2026/8a01_15044.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "B" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "A" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Time building chain proxies: 1.40, per 1000 atoms: 0.25 Number of scatterers: 5511 At special positions: 0 Unit cell: (104.16, 97.96, 71.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 885 7.00 C 3495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 277.1 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 17 sheets defined 10.2% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 60 through 68 removed outlier: 3.514A pdb=" N SER C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.652A pdb=" N LEU B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.638A pdb=" N SER B 67 " --> pdb=" O PHE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.617A pdb=" N LEU A 35 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 178 through 188 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 7 removed outlier: 5.422A pdb=" N LYS C 2 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 119 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 23 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 17 removed outlier: 3.557A pdb=" N SER C 101 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE C 40 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN C 56 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 42 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 128 through 136 removed outlier: 5.664A pdb=" N ASN C 230 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 153 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 147 removed outlier: 6.570A pdb=" N GLN C 168 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 219 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER C 166 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE C 221 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP C 164 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS C 223 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 162 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 7 removed outlier: 6.711A pdb=" N LEU B 117 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR B 5 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR B 115 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG B 114 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N SER B 28 " --> pdb=" O ARG B 114 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP B 116 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU B 26 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS B 118 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 24 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 120 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 17 removed outlier: 7.237A pdb=" N ILE B 40 " --> pdb=" O ASN B 56 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN B 56 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 42 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 5.260A pdb=" N SER B 93 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 137 removed outlier: 5.983A pdb=" N ASN B 230 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 157 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 153 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 143 through 146 removed outlier: 6.457A pdb=" N GLN B 168 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 219 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 166 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 221 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 164 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LYS B 223 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 162 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AB3, first strand: chain 'A' and resid 2 through 6 removed outlier: 5.584A pdb=" N LYS A 2 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 119 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 4 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 27 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 15 through 17 removed outlier: 7.006A pdb=" N ILE A 40 " --> pdb=" O ASN A 56 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN A 56 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 42 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 93 through 94 removed outlier: 5.757A pdb=" N SER A 93 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 128 through 137 removed outlier: 5.535A pdb=" N ASN A 230 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 153 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.525A pdb=" N GLN A 168 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A 219 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER A 166 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE A 221 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 164 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS A 223 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 162 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 194 through 195 201 hydrogen bonds defined for protein. 531 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: 0.71 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1818 1.34 - 1.46: 1045 1.46 - 1.58: 2684 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.18e-01 bond pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " ideal model delta sigma weight residual 1.536 1.553 -0.017 2.08e-02 2.31e+03 6.77e-01 bond pdb=" CB ASP C 29 " pdb=" CG ASP C 29 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.77e-01 bond pdb=" CA ASN B 143 " pdb=" CB ASN B 143 " ideal model delta sigma weight residual 1.534 1.546 -0.012 1.76e-02 3.23e+03 4.52e-01 bond pdb=" CB ASN B 143 " pdb=" CG ASN B 143 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.19e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 7178 0.86 - 1.72: 297 1.72 - 2.58: 46 2.58 - 3.44: 20 3.44 - 4.30: 7 Bond angle restraints: 7548 Sorted by residual: angle pdb=" N LYS C 223 " pdb=" CA LYS C 223 " pdb=" C LYS C 223 " ideal model delta sigma weight residual 108.34 111.92 -3.58 1.31e+00 5.83e-01 7.46e+00 angle pdb=" C ALA C 138 " pdb=" N SER C 139 " pdb=" CA SER C 139 " ideal model delta sigma weight residual 121.54 125.84 -4.30 1.91e+00 2.74e-01 5.07e+00 angle pdb=" CA ASN C 143 " pdb=" CB ASN C 143 " pdb=" CG ASN C 143 " ideal model delta sigma weight residual 112.60 114.26 -1.66 1.00e+00 1.00e+00 2.75e+00 angle pdb=" C ILE C 3 " pdb=" N ALA C 4 " pdb=" CA ALA C 4 " ideal model delta sigma weight residual 121.62 118.94 2.68 1.83e+00 2.99e-01 2.14e+00 angle pdb=" CA TYR B 167 " pdb=" CB TYR B 167 " pdb=" CG TYR B 167 " ideal model delta sigma weight residual 113.90 116.48 -2.58 1.80e+00 3.09e-01 2.05e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3068 17.43 - 34.86: 270 34.86 - 52.29: 60 52.29 - 69.73: 13 69.73 - 87.16: 9 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CB LYS A 57 " pdb=" CG LYS A 57 " pdb=" CD LYS A 57 " pdb=" CE LYS A 57 " ideal model delta sinusoidal sigma weight residual -180.00 -126.25 -53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CB LYS B 200 " pdb=" CG LYS B 200 " pdb=" CD LYS B 200 " pdb=" CE LYS B 200 " ideal model delta sinusoidal sigma weight residual 60.00 112.52 -52.52 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" CB GLU B 141 " pdb=" CG GLU B 141 " pdb=" CD GLU B 141 " pdb=" OE1 GLU B 141 " ideal model delta sinusoidal sigma weight residual 0.00 80.58 -80.58 1 3.00e+01 1.11e-03 8.92e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 564 0.027 - 0.054: 188 0.054 - 0.081: 71 0.081 - 0.109: 72 0.109 - 0.136: 41 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE C 155 " pdb=" N ILE C 155 " pdb=" C ILE C 155 " pdb=" CB ILE C 155 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE C 42 " pdb=" N ILE C 42 " pdb=" C ILE C 42 " pdb=" CB ILE C 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE C 221 " pdb=" N ILE C 221 " pdb=" C ILE C 221 " pdb=" CB ILE C 221 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 178 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.03e-01 pdb=" N PRO B 179 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 178 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO C 179 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 211 " -0.013 5.00e-02 4.00e+02 2.04e-02 6.67e-01 pdb=" N PRO A 212 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.011 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1470 2.81 - 3.33: 4379 3.33 - 3.86: 8347 3.86 - 4.38: 9858 4.38 - 4.90: 18283 Nonbonded interactions: 42337 Sorted by model distance: nonbonded pdb=" OG SER C 163 " pdb=" O ASN C 222 " model vdw 2.289 3.040 nonbonded pdb=" O ILE A 64 " pdb=" OG1 THR A 68 " model vdw 2.297 3.040 nonbonded pdb=" NE2 GLN B 183 " pdb=" OD2 ASP A 77 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASN B 128 " pdb=" OG1 THR B 238 " model vdw 2.335 3.040 nonbonded pdb=" OD1 ASP C 98 " pdb=" N LYS C 99 " model vdw 2.375 3.120 ... (remaining 42332 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.500 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.640 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.002 0.021 5571 Z= 0.088 Angle : 0.437 4.302 7548 Z= 0.240 Chirality : 0.046 0.136 936 Planarity : 0.002 0.024 960 Dihedral : 14.812 87.157 2064 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.31), residues: 711 helix: 1.53 (0.67), residues: 63 sheet: 0.94 (0.31), residues: 282 loop : -1.06 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 114 TYR 0.010 0.001 TYR C 43 PHE 0.006 0.001 PHE A 231 HIS 0.001 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 5571) covalent geometry : angle 0.43730 ( 7548) hydrogen bonds : bond 0.09871 ( 201) hydrogen bonds : angle 5.31474 ( 531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.213 Fit side-chains REVERT: C 171 ASN cc_start: 0.8580 (p0) cc_final: 0.8301 (p0) REVERT: A 149 GLN cc_start: 0.7674 (tt0) cc_final: 0.7445 (tt0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0704 time to fit residues: 11.0396 Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 203 GLN B 149 GLN B 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.097623 restraints weight = 7559.923| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.79 r_work: 0.2904 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5571 Z= 0.210 Angle : 0.552 4.381 7548 Z= 0.298 Chirality : 0.050 0.153 936 Planarity : 0.003 0.024 960 Dihedral : 4.436 17.091 750 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.59 % Allowed : 8.10 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.31), residues: 711 helix: 1.11 (0.66), residues: 63 sheet: 0.72 (0.31), residues: 291 loop : -1.09 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 187 TYR 0.014 0.002 TYR C 43 PHE 0.011 0.002 PHE B 231 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 5571) covalent geometry : angle 0.55227 ( 7548) hydrogen bonds : bond 0.04296 ( 201) hydrogen bonds : angle 4.91063 ( 531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.235 Fit side-chains REVERT: C 100 GLU cc_start: 0.8267 (mp0) cc_final: 0.7973 (mp0) REVERT: B 87 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: B 156 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (ptm) REVERT: A 149 GLN cc_start: 0.8216 (tt0) cc_final: 0.7963 (tt0) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.0797 time to fit residues: 10.1910 Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN B 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.107589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.095455 restraints weight = 7550.802| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.79 r_work: 0.2867 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 5571 Z= 0.272 Angle : 0.610 4.561 7548 Z= 0.327 Chirality : 0.051 0.151 936 Planarity : 0.004 0.028 960 Dihedral : 4.871 18.374 750 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.06 % Allowed : 12.70 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.30), residues: 711 helix: 0.96 (0.66), residues: 63 sheet: 0.49 (0.31), residues: 291 loop : -1.26 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 114 TYR 0.015 0.002 TYR B 43 PHE 0.011 0.002 PHE B 231 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 5571) covalent geometry : angle 0.61034 ( 7548) hydrogen bonds : bond 0.04779 ( 201) hydrogen bonds : angle 5.08096 ( 531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.251 Fit side-chains REVERT: B 87 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6916 (pm20) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.0784 time to fit residues: 10.3000 Evaluate side-chains 89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.108396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.096184 restraints weight = 7499.422| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.80 r_work: 0.2877 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5571 Z= 0.205 Angle : 0.542 4.185 7548 Z= 0.295 Chirality : 0.049 0.149 936 Planarity : 0.003 0.029 960 Dihedral : 4.687 18.311 750 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.06 % Allowed : 14.92 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.31), residues: 711 helix: 1.04 (0.67), residues: 63 sheet: 0.38 (0.31), residues: 291 loop : -1.26 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 114 TYR 0.015 0.001 TYR B 43 PHE 0.010 0.001 PHE B 231 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 5571) covalent geometry : angle 0.54242 ( 7548) hydrogen bonds : bond 0.04254 ( 201) hydrogen bonds : angle 5.02132 ( 531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.188 Fit side-chains REVERT: C 100 GLU cc_start: 0.8415 (mp0) cc_final: 0.8064 (mp0) REVERT: B 87 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: B 156 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8681 (ptm) REVERT: A 48 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8475 (m110) REVERT: A 100 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8352 (mp0) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.0791 time to fit residues: 9.4218 Evaluate side-chains 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097278 restraints weight = 7579.468| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.81 r_work: 0.2893 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5571 Z= 0.161 Angle : 0.497 4.060 7548 Z= 0.273 Chirality : 0.048 0.146 936 Planarity : 0.003 0.029 960 Dihedral : 4.450 17.298 750 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.38 % Allowed : 16.35 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.31), residues: 711 helix: 1.21 (0.67), residues: 63 sheet: 0.36 (0.31), residues: 291 loop : -1.19 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.015 0.001 TYR B 43 PHE 0.009 0.001 PHE B 231 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5571) covalent geometry : angle 0.49662 ( 7548) hydrogen bonds : bond 0.03878 ( 201) hydrogen bonds : angle 4.92058 ( 531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.211 Fit side-chains REVERT: B 87 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: B 156 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8659 (ptm) REVERT: A 100 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8284 (mp0) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.0757 time to fit residues: 9.2873 Evaluate side-chains 93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.108015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.095821 restraints weight = 7503.089| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.79 r_work: 0.2872 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 5571 Z= 0.230 Angle : 0.567 4.488 7548 Z= 0.307 Chirality : 0.050 0.146 936 Planarity : 0.003 0.030 960 Dihedral : 4.715 18.902 750 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.17 % Allowed : 16.83 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.30), residues: 711 helix: 1.07 (0.67), residues: 63 sheet: 0.23 (0.31), residues: 291 loop : -1.28 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 114 TYR 0.016 0.002 TYR B 43 PHE 0.009 0.002 PHE B 231 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00573 ( 5571) covalent geometry : angle 0.56703 ( 7548) hydrogen bonds : bond 0.04455 ( 201) hydrogen bonds : angle 5.04714 ( 531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.214 Fit side-chains REVERT: C 100 GLU cc_start: 0.8385 (mp0) cc_final: 0.8048 (mp0) REVERT: B 87 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: A 48 ASN cc_start: 0.9180 (OUTLIER) cc_final: 0.8479 (m110) REVERT: A 100 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8334 (mp0) outliers start: 20 outliers final: 14 residues processed: 97 average time/residue: 0.0739 time to fit residues: 9.5749 Evaluate side-chains 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.0770 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN A 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.113015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.100740 restraints weight = 7450.643| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.81 r_work: 0.2944 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5571 Z= 0.082 Angle : 0.425 3.706 7548 Z= 0.236 Chirality : 0.046 0.132 936 Planarity : 0.003 0.030 960 Dihedral : 3.926 12.744 750 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.90 % Allowed : 17.94 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.31), residues: 711 helix: 1.50 (0.68), residues: 63 sheet: 0.64 (0.31), residues: 276 loop : -1.16 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.014 0.001 TYR B 43 PHE 0.007 0.001 PHE C 231 HIS 0.001 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 5571) covalent geometry : angle 0.42517 ( 7548) hydrogen bonds : bond 0.03059 ( 201) hydrogen bonds : angle 4.71664 ( 531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.224 Fit side-chains REVERT: C 100 GLU cc_start: 0.8134 (mp0) cc_final: 0.7825 (mp0) REVERT: C 141 GLU cc_start: 0.8228 (pt0) cc_final: 0.7986 (pt0) REVERT: B 87 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6876 (pm20) outliers start: 12 outliers final: 6 residues processed: 95 average time/residue: 0.0739 time to fit residues: 9.4153 Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.109219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.096886 restraints weight = 7487.497| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.82 r_work: 0.2888 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 5571 Z= 0.188 Angle : 0.527 4.101 7548 Z= 0.286 Chirality : 0.049 0.145 936 Planarity : 0.003 0.029 960 Dihedral : 4.418 16.321 750 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.54 % Allowed : 17.94 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.31), residues: 711 helix: 1.28 (0.68), residues: 63 sheet: 0.57 (0.32), residues: 276 loop : -1.21 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 234 TYR 0.015 0.001 TYR B 43 PHE 0.009 0.001 PHE B 231 HIS 0.002 0.000 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 5571) covalent geometry : angle 0.52685 ( 7548) hydrogen bonds : bond 0.04043 ( 201) hydrogen bonds : angle 4.87646 ( 531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.209 Fit side-chains REVERT: C 100 GLU cc_start: 0.8254 (mp0) cc_final: 0.7860 (mp0) REVERT: C 141 GLU cc_start: 0.8302 (pt0) cc_final: 0.8076 (pt0) REVERT: B 87 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: B 156 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8657 (ptm) REVERT: A 48 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8518 (m110) outliers start: 16 outliers final: 11 residues processed: 92 average time/residue: 0.0798 time to fit residues: 9.6154 Evaluate side-chains 94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 136 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.100534 restraints weight = 7450.410| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.81 r_work: 0.2943 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5571 Z= 0.084 Angle : 0.430 3.697 7548 Z= 0.238 Chirality : 0.046 0.133 936 Planarity : 0.003 0.029 960 Dihedral : 3.899 13.050 750 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.59 % Allowed : 19.37 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.31), residues: 711 helix: 1.48 (0.68), residues: 63 sheet: 0.69 (0.32), residues: 276 loop : -1.10 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 114 TYR 0.013 0.001 TYR B 43 PHE 0.006 0.001 PHE A 63 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 5571) covalent geometry : angle 0.42962 ( 7548) hydrogen bonds : bond 0.03082 ( 201) hydrogen bonds : angle 4.66063 ( 531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.216 Fit side-chains REVERT: C 100 GLU cc_start: 0.8068 (mp0) cc_final: 0.7707 (mp0) REVERT: C 141 GLU cc_start: 0.8220 (pt0) cc_final: 0.7969 (pt0) REVERT: B 87 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6832 (pm20) REVERT: B 156 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8533 (ptm) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.0747 time to fit residues: 9.2039 Evaluate side-chains 99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096078 restraints weight = 7552.023| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.81 r_work: 0.2878 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 5571 Z= 0.221 Angle : 0.553 4.187 7548 Z= 0.300 Chirality : 0.050 0.147 936 Planarity : 0.003 0.029 960 Dihedral : 4.537 16.879 750 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.59 % Allowed : 19.05 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.31), residues: 711 helix: 1.22 (0.67), residues: 63 sheet: 0.43 (0.31), residues: 288 loop : -1.15 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 114 TYR 0.016 0.002 TYR B 43 PHE 0.009 0.002 PHE B 231 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 5571) covalent geometry : angle 0.55320 ( 7548) hydrogen bonds : bond 0.04295 ( 201) hydrogen bonds : angle 4.92698 ( 531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.156 Fit side-chains REVERT: C 100 GLU cc_start: 0.8272 (mp0) cc_final: 0.7853 (mp0) REVERT: C 141 GLU cc_start: 0.8306 (pt0) cc_final: 0.8078 (pt0) REVERT: B 87 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: B 156 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8678 (ptm) REVERT: A 98 ASP cc_start: 0.7060 (p0) cc_final: 0.6840 (p0) REVERT: A 100 GLU cc_start: 0.8490 (mp0) cc_final: 0.8252 (mp0) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.0787 time to fit residues: 9.0061 Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain A residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.107032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.094798 restraints weight = 7584.850| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.81 r_work: 0.2860 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 5571 Z= 0.272 Angle : 0.609 4.689 7548 Z= 0.327 Chirality : 0.051 0.147 936 Planarity : 0.004 0.030 960 Dihedral : 4.853 18.226 750 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.90 % Allowed : 19.05 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.31), residues: 711 helix: 0.98 (0.67), residues: 63 sheet: 0.21 (0.31), residues: 288 loop : -1.32 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 114 TYR 0.016 0.002 TYR B 43 PHE 0.011 0.002 PHE B 231 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00680 ( 5571) covalent geometry : angle 0.60881 ( 7548) hydrogen bonds : bond 0.04726 ( 201) hydrogen bonds : angle 5.08663 ( 531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1293.36 seconds wall clock time: 22 minutes 51.17 seconds (1371.17 seconds total)