Starting phenix.real_space_refine on Wed Feb 4 04:23:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q1y_72145/02_2026/9q1y_72145.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q1y_72145/02_2026/9q1y_72145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q1y_72145/02_2026/9q1y_72145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q1y_72145/02_2026/9q1y_72145.map" model { file = "/net/cci-nas-00/data/ceres_data/9q1y_72145/02_2026/9q1y_72145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q1y_72145/02_2026/9q1y_72145.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 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 36 5.16 5 C 5682 2.51 5 N 1380 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8632 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2315 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain: "D" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2315 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain: "A" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2001 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 240} Chain: "B" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2001 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 240} Time building chain proxies: 2.17, per 1000 atoms: 0.25 Number of scatterers: 8632 At special positions: 0 Unit cell: (77.39, 90.47, 142.79, 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 36 16.00 O 1534 8.00 N 1380 7.00 C 5682 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: 0.64 Conformation dependent library (CDL) restraints added in 301.8 milliseconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 63.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'C' and resid 38 through 48 Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 96 through 108 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 121 through 136 removed outlier: 4.029A pdb=" N ASN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 169 removed outlier: 4.301A pdb=" N ASN C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.787A pdb=" N ILE C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 233 removed outlier: 5.068A pdb=" N ARG C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 276 through 286 removed outlier: 4.583A pdb=" N THR C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 96 through 108 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 121 through 136 Processing helix chain 'D' and resid 151 through 169 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 253 through 263 Processing helix chain 'D' and resid 276 through 286 Processing helix chain 'A' and resid 1 through 17 removed outlier: 3.658A pdb=" N SER A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 40 removed outlier: 4.481A pdb=" N TYR A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 81 removed outlier: 5.050A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 132 through 162 removed outlier: 3.648A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 186 removed outlier: 4.399A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Proline residue: A 179 - end of helix Proline residue: A 183 - end of helix removed outlier: 4.463A pdb=" N THR A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 202 through 213 removed outlier: 4.242A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 242 Processing helix chain 'B' and resid 1 through 17 removed outlier: 4.617A pdb=" N LEU B 6 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 7 " --> pdb=" O ILE B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 40 removed outlier: 4.511A pdb=" N TYR B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 81 removed outlier: 4.583A pdb=" N VAL B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASP B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 removed outlier: 3.920A pdb=" N TYR B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 126 Processing helix chain 'B' and resid 132 through 162 removed outlier: 3.752A pdb=" N TYR B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 186 removed outlier: 3.616A pdb=" N PHE B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Proline residue: B 179 - end of helix Proline residue: B 183 - end of helix removed outlier: 4.677A pdb=" N THR B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 202 through 210 Processing helix chain 'B' and resid 219 through 244 Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 22 removed outlier: 5.076A pdb=" N VAL C 14 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR C 10 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE C 6 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP C 20 " --> pdb=" O GLU C 4 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU C 4 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP C 22 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LYS C 2 " --> pdb=" O ASP C 22 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 56 " --> pdb=" O GLU C 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 68 removed outlier: 3.612A pdb=" N LEU C 141 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 174 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL C 29 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 28 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL C 191 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C 30 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU C 193 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 32 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 192 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN C 200 " --> pdb=" O PHE C 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 237 through 239 Processing sheet with id=AA4, first strand: chain 'D' and resid 13 through 22 removed outlier: 6.414A pdb=" N LYS D 8 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE D 6 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE D 19 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU D 4 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE D 21 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS D 2 " --> pdb=" O PHE D 21 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 4 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D 56 " --> pdb=" O GLU D 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.564A pdb=" N ILE D 28 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL D 191 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY D 30 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU D 193 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 32 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN D 200 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG D 194 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 238 through 239 534 hydrogen bonds defined for protein. 1539 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: 1.27 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1880 1.33 - 1.46: 2184 1.46 - 1.58: 4674 1.58 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 8808 Sorted by residual: bond pdb=" CA ASP C 201 " pdb=" CB ASP C 201 " ideal model delta sigma weight residual 1.524 1.570 -0.047 1.62e-02 3.81e+03 8.27e+00 bond pdb=" C ARG C 110 " pdb=" N PRO C 111 " ideal model delta sigma weight residual 1.335 1.370 -0.036 1.28e-02 6.10e+03 7.74e+00 bond pdb=" CG1 ILE D 103 " pdb=" CD1 ILE D 103 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.71e+00 bond pdb=" CA ASN D 252 " pdb=" CB ASN D 252 " ideal model delta sigma weight residual 1.531 1.573 -0.042 1.52e-02 4.33e+03 7.61e+00 bond pdb=" C VAL A 178 " pdb=" N PRO A 179 " ideal model delta sigma weight residual 1.335 1.369 -0.035 1.28e-02 6.10e+03 7.31e+00 ... (remaining 8803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 11447 4.60 - 9.20: 364 9.20 - 13.80: 76 13.80 - 18.40: 4 18.40 - 23.00: 3 Bond angle restraints: 11894 Sorted by residual: angle pdb=" C GLN C 286 " pdb=" N ARG C 287 " pdb=" CA ARG C 287 " ideal model delta sigma weight residual 120.28 132.96 -12.68 1.34e+00 5.57e-01 8.95e+01 angle pdb=" CB MET D 43 " pdb=" CG MET D 43 " pdb=" SD MET D 43 " ideal model delta sigma weight residual 112.70 135.70 -23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" N ASN D 285 " pdb=" CA ASN D 285 " pdb=" C ASN D 285 " ideal model delta sigma weight residual 113.28 121.88 -8.60 1.22e+00 6.72e-01 4.97e+01 angle pdb=" CA ASN D 148 " pdb=" CB ASN D 148 " pdb=" CG ASN D 148 " ideal model delta sigma weight residual 112.60 119.28 -6.68 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C MET C 150 " pdb=" CA MET C 150 " pdb=" CB MET C 150 " ideal model delta sigma weight residual 109.33 122.44 -13.11 1.97e+00 2.58e-01 4.43e+01 ... (remaining 11889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4417 17.79 - 35.58: 665 35.58 - 53.37: 151 53.37 - 71.16: 24 71.16 - 88.96: 7 Dihedral angle restraints: 5264 sinusoidal: 2116 harmonic: 3148 Sorted by residual: dihedral pdb=" N ASP C 25 " pdb=" C ASP C 25 " pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " ideal model delta harmonic sigma weight residual 122.80 136.04 -13.24 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" C VAL A 178 " pdb=" N VAL A 178 " pdb=" CA VAL A 178 " pdb=" CB VAL A 178 " ideal model delta harmonic sigma weight residual -122.00 -134.72 12.72 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N MET D 43 " pdb=" C MET D 43 " pdb=" CA MET D 43 " pdb=" CB MET D 43 " ideal model delta harmonic sigma weight residual 122.80 135.10 -12.30 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 965 0.082 - 0.163: 305 0.163 - 0.245: 84 0.245 - 0.327: 27 0.327 - 0.409: 9 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CB ILE B 225 " pdb=" CA ILE B 225 " pdb=" CG1 ILE B 225 " pdb=" CG2 ILE B 225 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA MET D 43 " pdb=" N MET D 43 " pdb=" C MET D 43 " pdb=" CB MET D 43 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.07e+00 ... (remaining 1387 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 148 " -0.025 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C ASN D 148 " 0.086 2.00e-02 2.50e+03 pdb=" O ASN D 148 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY D 149 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 64 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C ILE B 64 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE B 64 " 0.029 2.00e-02 2.50e+03 pdb=" N ILE B 65 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 24 " 0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C GLY C 24 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY C 24 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP C 25 " 0.026 2.00e-02 2.50e+03 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 195 2.66 - 3.22: 7914 3.22 - 3.78: 13627 3.78 - 4.34: 16660 4.34 - 4.90: 27535 Nonbonded interactions: 65931 Sorted by model distance: nonbonded pdb=" NE2 GLN C 89 " pdb=" OD1 ASN A 5 " model vdw 2.102 3.120 nonbonded pdb=" OG1 THR C 212 " pdb=" O ILE C 247 " model vdw 2.208 3.040 nonbonded pdb=" O THR B 75 " pdb=" OG1 THR B 75 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR D 253 " pdb=" OG1 THR D 272 " model vdw 2.245 3.040 nonbonded pdb=" O THR A 75 " pdb=" OG1 THR A 75 " model vdw 2.266 3.040 ... (remaining 65926 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.650 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.009 0.108 8808 Z= 0.427 Angle : 1.919 22.998 11894 Z= 1.042 Chirality : 0.095 0.409 1390 Planarity : 0.009 0.050 1458 Dihedral : 17.345 88.956 3232 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.00 % Favored : 96.81 % Rotamer: Outliers : 1.87 % Allowed : 37.66 % Favored : 60.48 % Cbeta Deviations : 0.89 % 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: 0.95 (0.25), residues: 1066 helix: 1.65 (0.21), residues: 601 sheet: 2.28 (0.60), residues: 79 loop : -1.44 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG D 194 TYR 0.054 0.006 TYR D 82 PHE 0.043 0.003 PHE A 234 TRP 0.032 0.002 TRP A 60 HIS 0.021 0.003 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00861 ( 8808) covalent geometry : angle 1.91879 (11894) hydrogen bonds : bond 0.13909 ( 534) hydrogen bonds : angle 5.92846 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 273 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8434 (t0) REVERT: C 200 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 204 MET cc_start: 0.8151 (ptp) cc_final: 0.7845 (ptp) REVERT: B 166 MET cc_start: 0.8412 (ttm) cc_final: 0.7849 (tmm) REVERT: B 243 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7537 (tptt) outliers start: 18 outliers final: 7 residues processed: 277 average time/residue: 0.0807 time to fit residues: 31.9504 Evaluate side-chains 254 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 246 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 245 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 148 ASN ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN A 80 GLN B 139 ASN B 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.126356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094737 restraints weight = 22775.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.097783 restraints weight = 13342.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099703 restraints weight = 9201.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101079 restraints weight = 7167.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101912 restraints weight = 6003.342| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8808 Z= 0.161 Angle : 0.765 11.208 11894 Z= 0.397 Chirality : 0.048 0.189 1390 Planarity : 0.004 0.038 1458 Dihedral : 5.823 76.465 1163 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.29 % Allowed : 28.32 % Favored : 66.39 % 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: 0.92 (0.25), residues: 1066 helix: 1.52 (0.20), residues: 613 sheet: 2.45 (0.61), residues: 78 loop : -1.39 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 2 TYR 0.045 0.002 TYR B 9 PHE 0.012 0.001 PHE D 222 TRP 0.018 0.001 TRP A 60 HIS 0.004 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8808) covalent geometry : angle 0.76535 (11894) hydrogen bonds : bond 0.05275 ( 534) hydrogen bonds : angle 5.07055 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 266 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 LEU cc_start: 0.9039 (tt) cc_final: 0.8794 (tt) REVERT: C 68 LEU cc_start: 0.8677 (tt) cc_final: 0.8468 (tt) REVERT: C 89 GLN cc_start: 0.8698 (tp40) cc_final: 0.8440 (tp-100) REVERT: C 153 ASP cc_start: 0.8414 (t70) cc_final: 0.8146 (t0) REVERT: C 200 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7416 (tm-30) REVERT: C 250 GLN cc_start: 0.7685 (mm110) cc_final: 0.7394 (mm110) REVERT: C 286 GLN cc_start: 0.8525 (tp-100) cc_final: 0.7914 (tp40) REVERT: D 89 GLN cc_start: 0.9143 (mm110) cc_final: 0.8793 (mm-40) REVERT: A 87 MET cc_start: 0.9065 (mmm) cc_final: 0.8718 (mmm) REVERT: B 59 LYS cc_start: 0.9038 (tttt) cc_final: 0.8802 (tttt) REVERT: B 87 MET cc_start: 0.8234 (mmp) cc_final: 0.7878 (mmp) REVERT: B 166 MET cc_start: 0.8456 (ttm) cc_final: 0.7907 (tmm) REVERT: B 243 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7413 (tptt) outliers start: 51 outliers final: 33 residues processed: 291 average time/residue: 0.0737 time to fit residues: 31.0039 Evaluate side-chains 273 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 196 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN B 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.120258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088528 restraints weight = 23063.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091433 restraints weight = 13471.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.093379 restraints weight = 9324.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094656 restraints weight = 7201.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.095590 restraints weight = 6049.125| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8808 Z= 0.216 Angle : 0.774 11.670 11894 Z= 0.401 Chirality : 0.047 0.199 1390 Planarity : 0.004 0.037 1458 Dihedral : 5.459 72.374 1150 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 7.99 % Allowed : 26.14 % Favored : 65.87 % 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: 0.69 (0.25), residues: 1066 helix: 1.31 (0.20), residues: 610 sheet: 2.50 (0.65), residues: 75 loop : -1.43 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 2 TYR 0.052 0.003 TYR B 9 PHE 0.018 0.002 PHE B 234 TRP 0.006 0.001 TRP A 60 HIS 0.007 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8808) covalent geometry : angle 0.77409 (11894) hydrogen bonds : bond 0.05139 ( 534) hydrogen bonds : angle 4.92009 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 248 time to evaluate : 0.368 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: C 150 MET cc_start: 0.8377 (ttp) cc_final: 0.6981 (tmm) REVERT: C 153 ASP cc_start: 0.8426 (t70) cc_final: 0.8156 (t0) REVERT: C 171 MET cc_start: 0.8757 (mmm) cc_final: 0.8427 (mmm) REVERT: C 250 GLN cc_start: 0.7860 (mm110) cc_final: 0.7564 (mm110) REVERT: C 286 GLN cc_start: 0.8551 (tp-100) cc_final: 0.7634 (tp-100) REVERT: D 43 MET cc_start: 0.9112 (mpp) cc_final: 0.8812 (mpp) REVERT: A 87 MET cc_start: 0.9261 (mmm) cc_final: 0.8625 (mmm) REVERT: B 10 ASP cc_start: 0.8405 (m-30) cc_final: 0.8031 (m-30) REVERT: B 12 TYR cc_start: 0.7259 (m-80) cc_final: 0.6906 (m-80) REVERT: B 87 MET cc_start: 0.8447 (mmp) cc_final: 0.8022 (mmp) REVERT: B 166 MET cc_start: 0.8584 (ttm) cc_final: 0.8027 (tmm) outliers start: 77 outliers final: 54 residues processed: 287 average time/residue: 0.0728 time to fit residues: 30.3661 Evaluate side-chains 290 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.089419 restraints weight = 23099.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092396 restraints weight = 13419.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094417 restraints weight = 9251.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.095697 restraints weight = 7088.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096683 restraints weight = 5930.403| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8808 Z= 0.154 Angle : 0.723 13.210 11894 Z= 0.364 Chirality : 0.045 0.174 1390 Planarity : 0.004 0.038 1458 Dihedral : 5.104 69.154 1146 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.95 % Allowed : 28.94 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1066 helix: 1.44 (0.20), residues: 608 sheet: 2.51 (0.67), residues: 75 loop : -1.47 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 2 TYR 0.045 0.002 TYR B 9 PHE 0.011 0.001 PHE B 234 TRP 0.005 0.001 TRP A 221 HIS 0.004 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8808) covalent geometry : angle 0.72346 (11894) hydrogen bonds : bond 0.04736 ( 534) hydrogen bonds : angle 4.75366 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 GLN cc_start: 0.8797 (tp40) cc_final: 0.8367 (tp-100) REVERT: C 153 ASP cc_start: 0.8283 (t70) cc_final: 0.7992 (t0) REVERT: C 171 MET cc_start: 0.8572 (mmm) cc_final: 0.8267 (mmm) REVERT: C 250 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7685 (mm110) REVERT: D 54 ASP cc_start: 0.8503 (t70) cc_final: 0.8217 (t0) REVERT: D 113 ILE cc_start: 0.9032 (tp) cc_final: 0.8530 (mt) REVERT: D 171 MET cc_start: 0.8135 (mpp) cc_final: 0.7813 (pmm) REVERT: D 184 GLU cc_start: 0.8917 (pt0) cc_final: 0.8473 (pt0) REVERT: A 87 MET cc_start: 0.9258 (mmm) cc_final: 0.8578 (mmm) REVERT: A 245 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: B 10 ASP cc_start: 0.8443 (m-30) cc_final: 0.7958 (m-30) REVERT: B 12 TYR cc_start: 0.7271 (m-80) cc_final: 0.6900 (m-80) REVERT: B 87 MET cc_start: 0.8445 (mmp) cc_final: 0.8039 (mmp) REVERT: B 166 MET cc_start: 0.8555 (ttm) cc_final: 0.7984 (tmm) outliers start: 67 outliers final: 55 residues processed: 275 average time/residue: 0.0609 time to fit residues: 24.5571 Evaluate side-chains 288 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 9 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 212 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS C 286 GLN D 47 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.121162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.089484 restraints weight = 22819.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.092490 restraints weight = 13227.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.094480 restraints weight = 9042.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095738 restraints weight = 6957.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.096707 restraints weight = 5824.941| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8808 Z= 0.147 Angle : 0.719 12.430 11894 Z= 0.361 Chirality : 0.045 0.194 1390 Planarity : 0.003 0.036 1458 Dihedral : 4.997 65.789 1146 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 7.26 % Allowed : 28.01 % Favored : 64.73 % 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: 0.78 (0.25), residues: 1066 helix: 1.48 (0.20), residues: 608 sheet: 2.52 (0.68), residues: 75 loop : -1.55 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 194 TYR 0.045 0.002 TYR B 9 PHE 0.012 0.001 PHE B 234 TRP 0.004 0.000 TRP A 221 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8808) covalent geometry : angle 0.71901 (11894) hydrogen bonds : bond 0.04554 ( 534) hydrogen bonds : angle 4.71365 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 245 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 ARG cc_start: 0.7970 (mmp80) cc_final: 0.7619 (mmp-170) REVERT: C 150 MET cc_start: 0.8182 (ttp) cc_final: 0.7815 (tmm) REVERT: C 153 ASP cc_start: 0.8260 (t70) cc_final: 0.7960 (t0) REVERT: C 171 MET cc_start: 0.8449 (mmm) cc_final: 0.8187 (mmm) REVERT: C 194 ARG cc_start: 0.8409 (tmm-80) cc_final: 0.8111 (tmm-80) REVERT: C 250 GLN cc_start: 0.8082 (mm110) cc_final: 0.7821 (mm110) REVERT: C 286 GLN cc_start: 0.8202 (tp40) cc_final: 0.7936 (tp-100) REVERT: D 54 ASP cc_start: 0.8523 (t70) cc_final: 0.8303 (t70) REVERT: D 171 MET cc_start: 0.8324 (mpp) cc_final: 0.8013 (pmm) REVERT: D 184 GLU cc_start: 0.9013 (pt0) cc_final: 0.8468 (pt0) REVERT: A 78 PHE cc_start: 0.8613 (m-80) cc_final: 0.8277 (m-80) REVERT: A 87 MET cc_start: 0.9260 (mmm) cc_final: 0.8551 (mmm) REVERT: A 245 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: B 10 ASP cc_start: 0.8268 (m-30) cc_final: 0.7764 (m-30) REVERT: B 12 TYR cc_start: 0.7331 (m-80) cc_final: 0.6968 (m-80) REVERT: B 87 MET cc_start: 0.8415 (mmp) cc_final: 0.7990 (mmp) REVERT: B 166 MET cc_start: 0.8544 (ttm) cc_final: 0.8001 (tmm) outliers start: 70 outliers final: 53 residues processed: 284 average time/residue: 0.0737 time to fit residues: 30.3136 Evaluate side-chains 286 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 226 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS D 47 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.122116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090788 restraints weight = 22915.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093748 restraints weight = 13408.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095742 restraints weight = 9240.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097107 restraints weight = 7111.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097960 restraints weight = 5927.993| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8808 Z= 0.142 Angle : 0.722 12.269 11894 Z= 0.359 Chirality : 0.044 0.204 1390 Planarity : 0.003 0.035 1458 Dihedral : 4.925 61.948 1146 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 7.05 % Allowed : 29.67 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1066 helix: 1.55 (0.20), residues: 604 sheet: 2.40 (0.69), residues: 75 loop : -1.57 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 224 TYR 0.020 0.002 TYR B 206 PHE 0.011 0.001 PHE B 234 TRP 0.009 0.001 TRP B 223 HIS 0.004 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8808) covalent geometry : angle 0.72161 (11894) hydrogen bonds : bond 0.04381 ( 534) hydrogen bonds : angle 4.64787 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 SER cc_start: 0.9441 (t) cc_final: 0.9152 (p) REVERT: C 150 MET cc_start: 0.8248 (ttp) cc_final: 0.7848 (tmm) REVERT: C 153 ASP cc_start: 0.8238 (t70) cc_final: 0.7941 (t0) REVERT: C 194 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.8186 (tmm-80) REVERT: C 250 GLN cc_start: 0.7994 (mm110) cc_final: 0.7729 (mm110) REVERT: C 286 GLN cc_start: 0.8321 (tp40) cc_final: 0.8085 (tp-100) REVERT: D 54 ASP cc_start: 0.8377 (t70) cc_final: 0.8128 (t70) REVERT: D 73 LYS cc_start: 0.9054 (mttp) cc_final: 0.8810 (mttm) REVERT: D 113 ILE cc_start: 0.9006 (tp) cc_final: 0.8500 (mt) REVERT: D 171 MET cc_start: 0.8381 (mpp) cc_final: 0.8051 (pmm) REVERT: D 184 GLU cc_start: 0.8970 (pt0) cc_final: 0.8600 (pt0) REVERT: D 197 HIS cc_start: 0.7447 (p-80) cc_final: 0.7004 (p90) REVERT: A 78 PHE cc_start: 0.8621 (m-80) cc_final: 0.8293 (m-80) REVERT: A 87 MET cc_start: 0.9287 (mmm) cc_final: 0.8564 (mmm) REVERT: A 245 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: B 10 ASP cc_start: 0.8279 (m-30) cc_final: 0.7780 (m-30) REVERT: B 12 TYR cc_start: 0.7300 (m-80) cc_final: 0.6940 (m-80) REVERT: B 87 MET cc_start: 0.8367 (mmp) cc_final: 0.7938 (mmp) REVERT: B 166 MET cc_start: 0.8540 (ttm) cc_final: 0.8009 (tmm) outliers start: 68 outliers final: 56 residues processed: 286 average time/residue: 0.0834 time to fit residues: 34.3922 Evaluate side-chains 293 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 212 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.122536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.091302 restraints weight = 23035.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094316 restraints weight = 13436.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.096354 restraints weight = 9218.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.097625 restraints weight = 7057.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.098607 restraints weight = 5916.404| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.003 0.056 8808 Z= 0.142 Angle : 0.741 11.476 11894 Z= 0.367 Chirality : 0.045 0.216 1390 Planarity : 0.004 0.037 1458 Dihedral : 4.877 57.511 1146 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.54 % Allowed : 31.95 % Favored : 61.51 % 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: 0.81 (0.25), residues: 1066 helix: 1.56 (0.20), residues: 608 sheet: 2.41 (0.69), residues: 73 loop : -1.60 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 27 TYR 0.029 0.002 TYR A 206 PHE 0.010 0.001 PHE B 234 TRP 0.005 0.000 TRP A 221 HIS 0.003 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8808) covalent geometry : angle 0.74088 (11894) hydrogen bonds : bond 0.04299 ( 534) hydrogen bonds : angle 4.66707 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 244 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 133 SER cc_start: 0.9352 (t) cc_final: 0.9078 (p) REVERT: C 150 MET cc_start: 0.8253 (ttp) cc_final: 0.7936 (tmm) REVERT: C 153 ASP cc_start: 0.8231 (t70) cc_final: 0.7928 (t0) REVERT: C 171 MET cc_start: 0.8855 (mmm) cc_final: 0.8638 (mmm) REVERT: C 194 ARG cc_start: 0.8376 (tmm-80) cc_final: 0.8147 (tmm-80) REVERT: C 250 GLN cc_start: 0.8049 (mm110) cc_final: 0.7772 (mm110) REVERT: C 286 GLN cc_start: 0.8341 (tp40) cc_final: 0.8079 (tp-100) REVERT: D 54 ASP cc_start: 0.8380 (t70) cc_final: 0.8125 (t70) REVERT: D 73 LYS cc_start: 0.9022 (mttp) cc_final: 0.8774 (mttm) REVERT: D 113 ILE cc_start: 0.9116 (tp) cc_final: 0.8611 (mt) REVERT: D 184 GLU cc_start: 0.8944 (pt0) cc_final: 0.8539 (pt0) REVERT: D 197 HIS cc_start: 0.7482 (p-80) cc_final: 0.7054 (p90) REVERT: A 78 PHE cc_start: 0.8629 (m-80) cc_final: 0.8285 (m-80) REVERT: A 87 MET cc_start: 0.9290 (mmm) cc_final: 0.8555 (mmm) REVERT: A 245 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: B 10 ASP cc_start: 0.8406 (m-30) cc_final: 0.7905 (m-30) REVERT: B 12 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: B 87 MET cc_start: 0.8260 (mmp) cc_final: 0.7845 (mmp) REVERT: B 91 LYS cc_start: 0.7378 (ptmt) cc_final: 0.6717 (tptt) REVERT: B 166 MET cc_start: 0.8537 (ttm) cc_final: 0.8007 (tmm) outliers start: 63 outliers final: 52 residues processed: 277 average time/residue: 0.0850 time to fit residues: 33.8769 Evaluate side-chains 290 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 12 TYR Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 250 GLN D 47 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.119358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.088194 restraints weight = 23207.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.090954 restraints weight = 13805.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092838 restraints weight = 9666.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094126 restraints weight = 7530.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094930 restraints weight = 6323.903| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8808 Z= 0.201 Angle : 0.776 10.787 11894 Z= 0.395 Chirality : 0.047 0.240 1390 Planarity : 0.004 0.040 1458 Dihedral : 4.962 51.905 1146 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.64 % Allowed : 32.68 % Favored : 60.68 % 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: 0.66 (0.25), residues: 1066 helix: 1.45 (0.20), residues: 608 sheet: 2.21 (0.68), residues: 79 loop : -1.71 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 27 TYR 0.026 0.002 TYR B 9 PHE 0.018 0.001 PHE B 234 TRP 0.005 0.001 TRP A 221 HIS 0.005 0.001 HIS A 1 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8808) covalent geometry : angle 0.77551 (11894) hydrogen bonds : bond 0.04664 ( 534) hydrogen bonds : angle 4.77785 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 ASP cc_start: 0.8351 (t70) cc_final: 0.8033 (t0) REVERT: C 171 MET cc_start: 0.8834 (mmm) cc_final: 0.8600 (mmm) REVERT: C 194 ARG cc_start: 0.8425 (tmm-80) cc_final: 0.8181 (tmm-80) REVERT: C 286 GLN cc_start: 0.8367 (tp40) cc_final: 0.8048 (tp-100) REVERT: D 54 ASP cc_start: 0.8351 (t70) cc_final: 0.8095 (t70) REVERT: D 73 LYS cc_start: 0.9081 (mttp) cc_final: 0.8734 (mttm) REVERT: D 113 ILE cc_start: 0.9117 (tp) cc_final: 0.8630 (mt) REVERT: D 184 GLU cc_start: 0.9031 (pt0) cc_final: 0.8584 (pt0) REVERT: D 197 HIS cc_start: 0.7487 (p-80) cc_final: 0.7104 (p90) REVERT: A 87 MET cc_start: 0.9411 (mmm) cc_final: 0.8722 (mmm) REVERT: A 245 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7238 (m-30) REVERT: B 10 ASP cc_start: 0.8297 (m-30) cc_final: 0.7702 (m-30) REVERT: B 12 TYR cc_start: 0.7528 (m-80) cc_final: 0.7009 (m-80) REVERT: B 87 MET cc_start: 0.8252 (mmp) cc_final: 0.7822 (mmp) REVERT: B 166 MET cc_start: 0.8539 (ttm) cc_final: 0.8053 (tmm) outliers start: 64 outliers final: 50 residues processed: 259 average time/residue: 0.0813 time to fit residues: 30.5019 Evaluate side-chains 262 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 212 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 17 optimal weight: 0.0570 chunk 52 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.119826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.088581 restraints weight = 23007.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091430 restraints weight = 13543.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093360 restraints weight = 9404.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094670 restraints weight = 7291.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095485 restraints weight = 6116.228| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8808 Z= 0.164 Angle : 0.779 12.335 11894 Z= 0.388 Chirality : 0.047 0.271 1390 Planarity : 0.004 0.037 1458 Dihedral : 4.947 48.490 1146 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.91 % Allowed : 34.54 % Favored : 59.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.25), residues: 1066 helix: 1.47 (0.20), residues: 607 sheet: 2.11 (0.67), residues: 78 loop : -1.65 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 27 TYR 0.026 0.002 TYR A 206 PHE 0.015 0.001 PHE B 234 TRP 0.005 0.001 TRP A 221 HIS 0.003 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8808) covalent geometry : angle 0.77860 (11894) hydrogen bonds : bond 0.04579 ( 534) hydrogen bonds : angle 4.73329 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 MET cc_start: 0.8287 (ttp) cc_final: 0.7889 (tmm) REVERT: C 153 ASP cc_start: 0.8251 (t70) cc_final: 0.7959 (t0) REVERT: C 181 GLU cc_start: 0.8787 (pm20) cc_final: 0.8532 (pm20) REVERT: C 194 ARG cc_start: 0.8372 (tmm-80) cc_final: 0.8122 (tmm-80) REVERT: C 269 TYR cc_start: 0.8969 (t80) cc_final: 0.8763 (t80) REVERT: C 286 GLN cc_start: 0.8332 (tp40) cc_final: 0.8018 (tp-100) REVERT: D 54 ASP cc_start: 0.8317 (t70) cc_final: 0.8048 (t70) REVERT: D 73 LYS cc_start: 0.9107 (mttp) cc_final: 0.8621 (mttm) REVERT: D 113 ILE cc_start: 0.9105 (tp) cc_final: 0.8613 (mt) REVERT: D 184 GLU cc_start: 0.9015 (pt0) cc_final: 0.8561 (pt0) REVERT: D 195 ASP cc_start: 0.7771 (t0) cc_final: 0.7568 (t0) REVERT: D 197 HIS cc_start: 0.7512 (p-80) cc_final: 0.7106 (p90) REVERT: A 87 MET cc_start: 0.9405 (mmm) cc_final: 0.8685 (mmm) REVERT: A 176 LEU cc_start: 0.8818 (mp) cc_final: 0.8598 (tt) REVERT: A 245 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7252 (m-30) REVERT: B 10 ASP cc_start: 0.8261 (m-30) cc_final: 0.7839 (m-30) REVERT: B 12 TYR cc_start: 0.7436 (m-80) cc_final: 0.6956 (m-80) REVERT: B 38 MET cc_start: 0.8457 (ppp) cc_final: 0.7168 (mmt) REVERT: B 87 MET cc_start: 0.8204 (mmp) cc_final: 0.7772 (mmp) REVERT: B 166 MET cc_start: 0.8539 (ttm) cc_final: 0.7995 (tmm) outliers start: 57 outliers final: 48 residues processed: 253 average time/residue: 0.0778 time to fit residues: 28.4083 Evaluate side-chains 267 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 176 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 94 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 40.0000 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.118977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087669 restraints weight = 23241.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.090517 restraints weight = 13613.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092441 restraints weight = 9447.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093733 restraints weight = 7317.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094487 restraints weight = 6138.468| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8808 Z= 0.181 Angle : 0.807 11.979 11894 Z= 0.400 Chirality : 0.047 0.282 1390 Planarity : 0.004 0.035 1458 Dihedral : 4.939 44.998 1146 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.50 % Allowed : 34.96 % Favored : 59.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1066 helix: 1.47 (0.20), residues: 608 sheet: 1.74 (0.66), residues: 80 loop : -1.65 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 27 TYR 0.030 0.002 TYR B 9 PHE 0.017 0.001 PHE B 234 TRP 0.005 0.001 TRP A 221 HIS 0.004 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8808) covalent geometry : angle 0.80679 (11894) hydrogen bonds : bond 0.04573 ( 534) hydrogen bonds : angle 4.75228 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 MET cc_start: 0.8278 (ttp) cc_final: 0.7917 (tmm) REVERT: C 153 ASP cc_start: 0.8258 (t70) cc_final: 0.7964 (t0) REVERT: C 181 GLU cc_start: 0.8826 (pm20) cc_final: 0.8538 (pm20) REVERT: C 286 GLN cc_start: 0.8196 (tp40) cc_final: 0.7923 (tp-100) REVERT: D 1 MET cc_start: 0.7976 (tpp) cc_final: 0.7606 (tpp) REVERT: D 54 ASP cc_start: 0.8325 (t70) cc_final: 0.8064 (t70) REVERT: D 73 LYS cc_start: 0.9114 (mttp) cc_final: 0.8739 (mttm) REVERT: D 197 HIS cc_start: 0.7523 (p-80) cc_final: 0.7107 (p90) REVERT: A 87 MET cc_start: 0.9447 (mmm) cc_final: 0.8720 (mmm) REVERT: A 176 LEU cc_start: 0.8825 (mp) cc_final: 0.8621 (tt) REVERT: B 10 ASP cc_start: 0.8312 (m-30) cc_final: 0.7899 (m-30) REVERT: B 12 TYR cc_start: 0.7487 (m-80) cc_final: 0.7257 (m-80) REVERT: B 38 MET cc_start: 0.8487 (ppp) cc_final: 0.7240 (mmt) REVERT: B 87 MET cc_start: 0.8207 (mmp) cc_final: 0.7780 (mmp) REVERT: B 166 MET cc_start: 0.8505 (ttm) cc_final: 0.7964 (tmm) outliers start: 53 outliers final: 49 residues processed: 249 average time/residue: 0.0810 time to fit residues: 29.0938 Evaluate side-chains 265 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 218 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 59 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.119183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088119 restraints weight = 23143.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090954 restraints weight = 13483.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092860 restraints weight = 9321.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094189 restraints weight = 7229.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.095025 restraints weight = 6044.121| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8808 Z= 0.170 Angle : 0.802 12.099 11894 Z= 0.398 Chirality : 0.047 0.278 1390 Planarity : 0.004 0.037 1458 Dihedral : 4.960 44.953 1146 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.29 % Allowed : 35.17 % Favored : 59.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1066 helix: 1.48 (0.20), residues: 608 sheet: 1.82 (0.68), residues: 75 loop : -1.60 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 27 TYR 0.031 0.002 TYR B 9 PHE 0.015 0.001 PHE B 234 TRP 0.006 0.001 TRP A 221 HIS 0.004 0.001 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8808) covalent geometry : angle 0.80193 (11894) hydrogen bonds : bond 0.04482 ( 534) hydrogen bonds : angle 4.73701 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1634.34 seconds wall clock time: 29 minutes 5.76 seconds (1745.76 seconds total)