Starting phenix.real_space_refine on Fri Jul 3 15:47:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vxi_65409/07_2026/9vxi_65409.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vxi_65409/07_2026/9vxi_65409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vxi_65409/07_2026/9vxi_65409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vxi_65409/07_2026/9vxi_65409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vxi_65409/07_2026/9vxi_65409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vxi_65409/07_2026/9vxi_65409.map" } resolution = 2.47 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= -0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8021 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Co 4 6.85 5 P 4 5.49 5 S 32 5.16 5 C 5182 2.51 5 N 1364 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8190 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2508 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 318} Chain: "B" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1556 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 190} Chain: "C" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2508 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 318} Chain: "D" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1556 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 190} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Ad-hoc single atom residues: {' CO': 2} Unusual residues: {'GGS': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Ad-hoc single atom residues: {' CO': 2} Unusual residues: {'GGS': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 2.01, per 1000 atoms: 0.25 Number of scatterers: 8190 At special positions: 0 Unit cell: (97.572, 106.568, 94.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 4 26.99 S 32 16.00 P 4 15.00 O 1604 8.00 N 1364 7.00 C 5182 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: 0.74 Conformation dependent library (CDL) restraints added in 439.7 milliseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 66.1% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.704A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 135 through 153 Processing helix chain 'A' and resid 158 through 182 removed outlier: 3.562A pdb=" N GLN A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 199 through 222 removed outlier: 3.898A pdb=" N GLU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 247 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.757A pdb=" N ILE A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 313 removed outlier: 4.180A pdb=" N PHE A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.583A pdb=" N LYS A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.543A pdb=" N ARG A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'B' and resid 83 through 96 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 107 through 124 Processing helix chain 'B' and resid 129 through 132 removed outlier: 3.773A pdb=" N ASP B 132 " --> pdb=" O GLU B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 132' Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 234 through 243 Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.685A pdb=" N LEU C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 135 through 153 Processing helix chain 'C' and resid 158 through 182 removed outlier: 3.564A pdb=" N GLN C 162 " --> pdb=" O THR C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.898A pdb=" N GLU C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 247 Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 266 through 282 removed outlier: 3.759A pdb=" N ILE C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 313 removed outlier: 4.086A pdb=" N PHE C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 removed outlier: 3.614A pdb=" N LYS C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 370 through 390 removed outlier: 3.543A pdb=" N ARG C 374 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 396 through 412 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 107 through 124 Processing helix chain 'D' and resid 129 through 132 removed outlier: 4.043A pdb=" N ASP D 132 " --> pdb=" O GLU D 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 132' Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 224 through 232 Processing helix chain 'D' and resid 234 through 243 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.711A pdb=" N LYS A 191 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 147 removed outlier: 5.313A pdb=" N PHE B 170 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N TYR B 146 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 14.002A pdb=" N GLY B 168 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU B 167 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER B 188 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 169 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER B 204 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU B 217 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS B 206 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 215 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N THR B 208 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL B 213 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU B 271 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU B 144 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 187 through 188 removed outlier: 3.707A pdb=" N LYS C 191 " --> pdb=" O ARG C 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 142 through 147 removed outlier: 5.304A pdb=" N PHE D 170 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N TYR D 146 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 14.007A pdb=" N GLY D 168 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU D 167 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER D 188 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 169 " --> pdb=" O LYS D 186 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER D 204 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU D 217 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS D 206 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE D 215 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE D 250 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG D 261 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU D 271 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU D 144 " --> pdb=" O GLU D 271 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1572 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: 1.30 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3214 1.38 - 1.56: 5022 1.56 - 1.74: 6 1.74 - 1.91: 52 1.91 - 2.09: 2 Bond restraints: 8296 Sorted by residual: bond pdb=" O3A GGS A 501 " pdb=" PB GGS A 501 " ideal model delta sigma weight residual 1.760 1.617 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" O3A GGS C 501 " pdb=" PB GGS C 501 " ideal model delta sigma weight residual 1.760 1.618 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" PA GGS C 501 " pdb=" S1 GGS C 501 " ideal model delta sigma weight residual 2.170 2.092 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" PA GGS A 501 " pdb=" S1 GGS A 501 " ideal model delta sigma weight residual 2.170 2.092 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CG LEU A 106 " pdb=" CD1 LEU A 106 " ideal model delta sigma weight residual 1.521 1.401 0.120 3.30e-02 9.18e+02 1.32e+01 ... (remaining 8291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 10617 2.24 - 4.48: 493 4.48 - 6.72: 61 6.72 - 8.96: 27 8.96 - 11.20: 6 Bond angle restraints: 11204 Sorted by residual: angle pdb=" C VAL C 114 " pdb=" N GLY C 115 " pdb=" CA GLY C 115 " ideal model delta sigma weight residual 121.41 113.46 7.95 1.96e+00 2.60e-01 1.65e+01 angle pdb=" C VAL A 114 " pdb=" N GLY A 115 " pdb=" CA GLY A 115 " ideal model delta sigma weight residual 121.41 113.71 7.70 1.96e+00 2.60e-01 1.54e+01 angle pdb=" O1A GGS C 501 " pdb=" PA GGS C 501 " pdb=" S1 GGS C 501 " ideal model delta sigma weight residual 101.12 112.32 -11.20 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O1A GGS A 501 " pdb=" PA GGS A 501 " pdb=" S1 GGS A 501 " ideal model delta sigma weight residual 101.12 112.32 -11.20 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CA TYR B 252 " pdb=" CB TYR B 252 " pdb=" CG TYR B 252 " ideal model delta sigma weight residual 113.90 107.71 6.19 1.80e+00 3.09e-01 1.18e+01 ... (remaining 11199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.87: 4909 30.87 - 61.74: 166 61.74 - 92.61: 15 92.61 - 123.48: 0 123.48 - 154.36: 4 Dihedral angle restraints: 5094 sinusoidal: 2062 harmonic: 3032 Sorted by residual: dihedral pdb=" O1A GGS C 501 " pdb=" O3A GGS C 501 " pdb=" PA GGS C 501 " pdb=" PB GGS C 501 " ideal model delta sinusoidal sigma weight residual -135.55 18.81 -154.36 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" O1A GGS A 501 " pdb=" O3A GGS A 501 " pdb=" PA GGS A 501 " pdb=" PB GGS A 501 " ideal model delta sinusoidal sigma weight residual -135.55 18.77 -154.32 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA GLU D 129 " pdb=" C GLU D 129 " pdb=" N PRO D 130 " pdb=" CA PRO D 130 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 739 0.056 - 0.113: 450 0.113 - 0.169: 91 0.169 - 0.225: 26 0.225 - 0.281: 6 Chirality restraints: 1312 Sorted by residual: chirality pdb=" CG LEU A 269 " pdb=" CB LEU A 269 " pdb=" CD1 LEU A 269 " pdb=" CD2 LEU A 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CG LEU C 269 " pdb=" CB LEU C 269 " pdb=" CD1 LEU C 269 " pdb=" CD2 LEU C 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A 335 " pdb=" CA VAL A 335 " pdb=" CG1 VAL A 335 " pdb=" CG2 VAL A 335 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1309 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 294 " 0.041 2.00e-02 2.50e+03 2.15e-02 9.21e+00 pdb=" CG TYR A 294 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 294 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 294 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 294 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 294 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 294 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 294 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 294 " 0.041 2.00e-02 2.50e+03 2.14e-02 9.12e+00 pdb=" CG TYR C 294 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 294 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR C 294 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 294 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 294 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 294 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 294 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 146 " -0.028 2.00e-02 2.50e+03 1.42e-02 4.06e+00 pdb=" CG TYR D 146 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 146 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 146 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR D 146 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 146 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 146 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 146 " -0.012 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 23 2.28 - 2.94: 3772 2.94 - 3.59: 12604 3.59 - 4.25: 21233 4.25 - 4.90: 35139 Nonbonded interactions: 72771 Sorted by model distance: nonbonded pdb=" O1B GGS A 501 " pdb="CO CO A 503 " model vdw 1.626 2.960 nonbonded pdb=" O1B GGS C 501 " pdb="CO CO C 502 " model vdw 1.627 2.960 nonbonded pdb=" O1A GGS C 501 " pdb="CO CO C 503 " model vdw 1.839 2.960 nonbonded pdb=" O1A GGS A 501 " pdb="CO CO A 502 " model vdw 1.842 2.960 nonbonded pdb=" OH TYR C 258 " pdb=" OD2 ASP C 307 " model vdw 1.920 3.040 ... (remaining 72766 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.019 0.143 8296 Z= 0.807 Angle : 1.123 11.203 11204 Z= 0.588 Chirality : 0.071 0.281 1312 Planarity : 0.005 0.040 1438 Dihedral : 15.782 154.355 3126 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -3.22 (0.23), residues: 1036 helix: -1.83 (0.16), residues: 654 sheet: -2.75 (0.36), residues: 148 loop : -1.75 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 296 TYR 0.041 0.006 TYR A 294 PHE 0.026 0.004 PHE A 129 TRP 0.013 0.004 TRP C 216 HIS 0.008 0.003 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.01895 / 0.81 ( 8296) covalent geometry : angle 1.12286 / 0.59 (11204) hydrogen bonds : bond 0.13067 / 8.54 ( 532) hydrogen bonds : angle 7.02360 / 5.11 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.354 Fit side-chains REVERT: A 373 LYS cc_start: 0.7138 (mmtm) cc_final: 0.6783 (ttpt) REVERT: B 122 GLU cc_start: 0.7453 (pp20) cc_final: 0.7037 (pp20) REVERT: B 139 ASP cc_start: 0.7622 (t0) cc_final: 0.7213 (t70) REVERT: B 163 ASP cc_start: 0.7183 (p0) cc_final: 0.6963 (t0) REVERT: B 175 ASP cc_start: 0.8019 (t70) cc_final: 0.7287 (t0) REVERT: C 222 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 373 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6766 (ttpt) REVERT: D 99 MET cc_start: 0.8105 (mmp) cc_final: 0.7750 (mmm) REVERT: D 122 GLU cc_start: 0.7401 (pp20) cc_final: 0.6889 (pp20) REVERT: D 139 ASP cc_start: 0.7783 (t0) cc_final: 0.7286 (t70) REVERT: D 163 ASP cc_start: 0.7212 (p0) cc_final: 0.6990 (t0) REVERT: D 175 ASP cc_start: 0.7933 (t70) cc_final: 0.7401 (t0) REVERT: D 249 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7810 (tm-30) REVERT: D 277 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7310 (mm-30) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.7086 time to fit residues: 111.5900 Evaluate side-chains 118 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 213 GLN B 266 ASN C 127 GLN C 213 GLN D 266 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.189649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136060 restraints weight = 8586.023| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.06 r_work: 0.3414 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8296 Z= 0.154 Angle : 0.553 5.086 11204 Z= 0.298 Chirality : 0.041 0.136 1312 Planarity : 0.004 0.034 1438 Dihedral : 11.557 119.741 1164 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.90 % Allowed : 14.04 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.84 (0.25), residues: 1036 helix: 0.24 (0.19), residues: 660 sheet: -2.32 (0.40), residues: 146 loop : -1.21 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 380 TYR 0.012 0.002 TYR C 294 PHE 0.010 0.001 PHE B 170 TRP 0.009 0.002 TRP D 247 HIS 0.006 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8296) covalent geometry : angle 0.55300 / 0.30 (11204) hydrogen bonds : bond 0.04633 / 3.13 ( 532) hydrogen bonds : angle 5.04082 / 3.72 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.365 Fit side-chains REVERT: A 160 GLU cc_start: 0.8140 (mp0) cc_final: 0.7831 (mt-10) REVERT: A 189 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8106 (mtt180) REVERT: A 328 LYS cc_start: 0.8072 (ttpp) cc_final: 0.7643 (ttmm) REVERT: A 373 LYS cc_start: 0.6930 (mmtm) cc_final: 0.6445 (ttpt) REVERT: B 99 MET cc_start: 0.8009 (mmp) cc_final: 0.7649 (mmm) REVERT: B 122 GLU cc_start: 0.7123 (pp20) cc_final: 0.6579 (pp20) REVERT: B 139 ASP cc_start: 0.7326 (t0) cc_final: 0.6966 (t70) REVERT: B 141 CYS cc_start: 0.7538 (t) cc_final: 0.7310 (t) REVERT: B 163 ASP cc_start: 0.7474 (p0) cc_final: 0.6869 (t0) REVERT: B 254 ASP cc_start: 0.7709 (t0) cc_final: 0.7292 (t0) REVERT: C 160 GLU cc_start: 0.8147 (mp0) cc_final: 0.7841 (mt-10) REVERT: C 328 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7652 (ttmm) REVERT: C 373 LYS cc_start: 0.6915 (mmtm) cc_final: 0.6429 (ttpt) REVERT: D 122 GLU cc_start: 0.7191 (pp20) cc_final: 0.6430 (pp20) REVERT: D 139 ASP cc_start: 0.7424 (t0) cc_final: 0.7215 (t70) REVERT: D 163 ASP cc_start: 0.7455 (p0) cc_final: 0.6864 (t0) REVERT: D 178 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7875 (mp0) REVERT: D 249 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7516 (tm-30) outliers start: 8 outliers final: 3 residues processed: 146 average time/residue: 0.5952 time to fit residues: 92.1418 Evaluate side-chains 132 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain D residue 176 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 36 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.191520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137397 restraints weight = 8653.193| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.13 r_work: 0.3437 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8296 Z= 0.136 Angle : 0.512 5.214 11204 Z= 0.274 Chirality : 0.040 0.130 1312 Planarity : 0.003 0.029 1438 Dihedral : 10.666 103.153 1164 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.80 % Allowed : 14.61 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.33 (0.26), residues: 1036 helix: 1.20 (0.20), residues: 660 sheet: -1.90 (0.41), residues: 142 loop : -0.99 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 380 TYR 0.013 0.002 TYR C 294 PHE 0.011 0.001 PHE B 170 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 8296) covalent geometry : angle 0.51190 / 0.27 (11204) hydrogen bonds : bond 0.04168 / 2.80 ( 532) hydrogen bonds : angle 4.68294 / 3.47 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.335 Fit side-chains REVERT: A 117 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7954 (mm-30) REVERT: A 160 GLU cc_start: 0.8439 (mp0) cc_final: 0.8156 (mt-10) REVERT: A 373 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6760 (ttpt) REVERT: A 390 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8035 (tp) REVERT: B 99 MET cc_start: 0.8044 (mmp) cc_final: 0.7665 (mmm) REVERT: B 122 GLU cc_start: 0.7136 (pp20) cc_final: 0.6624 (pp20) REVERT: B 141 CYS cc_start: 0.7751 (t) cc_final: 0.7521 (t) REVERT: B 163 ASP cc_start: 0.7493 (p0) cc_final: 0.6917 (t0) REVERT: B 254 ASP cc_start: 0.7750 (t0) cc_final: 0.7391 (t0) REVERT: C 160 GLU cc_start: 0.8425 (mp0) cc_final: 0.8152 (mt-10) REVERT: C 189 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8271 (mtt180) REVERT: C 373 LYS cc_start: 0.7197 (mmtm) cc_final: 0.6738 (ttpt) REVERT: C 390 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8048 (tp) REVERT: D 122 GLU cc_start: 0.7141 (pp20) cc_final: 0.6492 (pp20) REVERT: D 154 LYS cc_start: 0.8199 (tttt) cc_final: 0.7974 (ttmm) REVERT: D 163 ASP cc_start: 0.7496 (p0) cc_final: 0.6932 (t0) REVERT: D 249 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7577 (tm-30) outliers start: 16 outliers final: 2 residues processed: 153 average time/residue: 0.5680 time to fit residues: 92.4343 Evaluate side-chains 133 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 176 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 63 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.192299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139244 restraints weight = 8742.139| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.03 r_work: 0.3449 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8296 Z= 0.120 Angle : 0.471 5.191 11204 Z= 0.251 Chirality : 0.040 0.184 1312 Planarity : 0.003 0.027 1438 Dihedral : 9.556 83.825 1164 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.25 % Allowed : 15.62 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.97 (0.27), residues: 1036 helix: 1.70 (0.20), residues: 662 sheet: -1.57 (0.42), residues: 142 loop : -0.85 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 380 TYR 0.011 0.001 TYR C 294 PHE 0.010 0.001 PHE B 170 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8296) covalent geometry : angle 0.47091 / 0.25 (11204) hydrogen bonds : bond 0.03860 / 2.60 ( 532) hydrogen bonds : angle 4.42417 / 3.29 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.354 Fit side-chains REVERT: A 117 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7804 (mm-30) REVERT: A 160 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: A 189 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8121 (mtt180) REVERT: A 257 ASP cc_start: 0.7832 (t0) cc_final: 0.7632 (t70) REVERT: A 328 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7498 (ttmm) REVERT: A 373 LYS cc_start: 0.6821 (mmtm) cc_final: 0.6336 (ttpt) REVERT: B 99 MET cc_start: 0.7855 (mmp) cc_final: 0.7506 (mmm) REVERT: B 122 GLU cc_start: 0.6988 (pp20) cc_final: 0.6374 (pp20) REVERT: B 141 CYS cc_start: 0.7482 (t) cc_final: 0.7244 (t) REVERT: B 163 ASP cc_start: 0.7398 (p0) cc_final: 0.6767 (t0) REVERT: B 178 GLU cc_start: 0.8494 (mp0) cc_final: 0.8279 (pm20) REVERT: B 254 ASP cc_start: 0.7536 (t0) cc_final: 0.6790 (t0) REVERT: C 117 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7744 (mm-30) REVERT: C 160 GLU cc_start: 0.8125 (mp0) cc_final: 0.7809 (mt-10) REVERT: C 162 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7051 (mm-40) REVERT: C 257 ASP cc_start: 0.7824 (t0) cc_final: 0.7623 (t70) REVERT: C 328 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7506 (ttmm) REVERT: C 364 GLU cc_start: 0.7678 (tp30) cc_final: 0.7459 (mt-10) REVERT: C 373 LYS cc_start: 0.6816 (mmtm) cc_final: 0.6336 (ttpt) REVERT: D 99 MET cc_start: 0.7984 (mmp) cc_final: 0.7452 (mmm) REVERT: D 122 GLU cc_start: 0.7044 (pp20) cc_final: 0.6289 (pp20) REVERT: D 163 ASP cc_start: 0.7355 (p0) cc_final: 0.6747 (t0) REVERT: D 177 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8113 (mmtm) REVERT: D 178 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7874 (mp0) REVERT: D 249 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7387 (tm-30) outliers start: 20 outliers final: 5 residues processed: 159 average time/residue: 0.6002 time to fit residues: 101.0882 Evaluate side-chains 141 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 239 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.193117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139338 restraints weight = 8723.083| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.13 r_work: 0.3459 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8296 Z= 0.126 Angle : 0.479 5.346 11204 Z= 0.254 Chirality : 0.040 0.148 1312 Planarity : 0.003 0.025 1438 Dihedral : 9.039 83.803 1164 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.13 % Allowed : 17.87 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.21 (0.27), residues: 1036 helix: 1.89 (0.20), residues: 662 sheet: -1.49 (0.42), residues: 142 loop : -0.74 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.011 0.002 TYR C 294 PHE 0.010 0.001 PHE B 170 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8296) covalent geometry : angle 0.47852 / 0.25 (11204) hydrogen bonds : bond 0.03776 / 2.54 ( 532) hydrogen bonds : angle 4.32674 / 3.21 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.411 Fit side-chains REVERT: A 117 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7947 (mm-30) REVERT: A 160 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: A 189 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8084 (mtt180) REVERT: A 191 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7205 (mmpt) REVERT: A 328 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7669 (ttmm) REVERT: A 373 LYS cc_start: 0.7212 (mmtm) cc_final: 0.6716 (ttpt) REVERT: A 380 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7195 (mtp85) REVERT: A 390 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7405 (mp) REVERT: B 99 MET cc_start: 0.7967 (mmp) cc_final: 0.7632 (mmm) REVERT: B 122 GLU cc_start: 0.7145 (pp20) cc_final: 0.6504 (pp20) REVERT: B 141 CYS cc_start: 0.7699 (t) cc_final: 0.7451 (t) REVERT: B 163 ASP cc_start: 0.7401 (p0) cc_final: 0.6878 (t0) REVERT: C 117 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7895 (mm-30) REVERT: C 160 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: C 162 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7405 (mm110) REVERT: C 328 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7744 (ttmm) REVERT: C 373 LYS cc_start: 0.7209 (mmtm) cc_final: 0.6713 (ttpt) REVERT: D 99 MET cc_start: 0.8109 (mmp) cc_final: 0.7556 (mmm) REVERT: D 122 GLU cc_start: 0.7190 (pp20) cc_final: 0.6499 (pp20) REVERT: D 163 ASP cc_start: 0.7409 (p0) cc_final: 0.6914 (t0) REVERT: D 177 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8087 (mmtm) REVERT: D 249 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7549 (tm-30) outliers start: 19 outliers final: 5 residues processed: 149 average time/residue: 0.5572 time to fit residues: 87.9752 Evaluate side-chains 138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.191493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138164 restraints weight = 8589.161| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.01 r_work: 0.3433 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8296 Z= 0.150 Angle : 0.512 8.024 11204 Z= 0.268 Chirality : 0.040 0.175 1312 Planarity : 0.003 0.025 1438 Dihedral : 8.722 83.578 1164 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.81 % Allowed : 17.53 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.17 (0.27), residues: 1036 helix: 1.86 (0.20), residues: 662 sheet: -1.65 (0.40), residues: 146 loop : -0.64 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.012 0.002 TYR C 294 PHE 0.012 0.001 PHE B 170 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8296) covalent geometry : angle 0.51187 / 0.27 (11204) hydrogen bonds : bond 0.03989 / 2.68 ( 532) hydrogen bonds : angle 4.36299 / 3.24 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.334 Fit side-chains REVERT: A 95 LEU cc_start: 0.7822 (mt) cc_final: 0.7512 (tp) REVERT: A 117 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7854 (mm-30) REVERT: A 160 GLU cc_start: 0.8171 (mp0) cc_final: 0.7845 (mt-10) REVERT: A 162 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7231 (mm110) REVERT: A 189 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8056 (mtt180) REVERT: A 191 LYS cc_start: 0.7519 (mtpp) cc_final: 0.6898 (mmpt) REVERT: A 328 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7523 (ttmm) REVERT: A 373 LYS cc_start: 0.6825 (mmtm) cc_final: 0.6305 (ttpt) REVERT: A 380 ARG cc_start: 0.7424 (ttm110) cc_final: 0.6796 (mtp85) REVERT: A 390 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7212 (mp) REVERT: A 405 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.6101 (mtm) REVERT: B 122 GLU cc_start: 0.7077 (pp20) cc_final: 0.6430 (pp20) REVERT: B 141 CYS cc_start: 0.7464 (t) cc_final: 0.7223 (t) REVERT: B 163 ASP cc_start: 0.7275 (p0) cc_final: 0.6713 (t0) REVERT: C 117 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7757 (mm-30) REVERT: C 160 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: C 162 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7077 (mm-40) REVERT: C 191 LYS cc_start: 0.7487 (mtpp) cc_final: 0.6861 (mmpt) REVERT: C 328 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7566 (ttmm) REVERT: C 373 LYS cc_start: 0.6832 (mmtm) cc_final: 0.6320 (ttpt) REVERT: C 390 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7148 (mp) REVERT: D 122 GLU cc_start: 0.7114 (pp20) cc_final: 0.6436 (pp20) REVERT: D 163 ASP cc_start: 0.7302 (p0) cc_final: 0.6738 (t0) REVERT: D 249 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7380 (tm-30) REVERT: D 277 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7194 (mm-30) outliers start: 25 outliers final: 7 residues processed: 150 average time/residue: 0.6345 time to fit residues: 100.7192 Evaluate side-chains 141 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 0.0040 chunk 88 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139365 restraints weight = 8832.172| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.02 r_work: 0.3450 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8296 Z= 0.131 Angle : 0.492 5.835 11204 Z= 0.260 Chirality : 0.040 0.204 1312 Planarity : 0.003 0.024 1438 Dihedral : 8.487 83.409 1164 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.25 % Allowed : 18.88 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.32 (0.27), residues: 1036 helix: 1.98 (0.20), residues: 662 sheet: -1.51 (0.41), residues: 142 loop : -0.69 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 189 TYR 0.010 0.001 TYR C 294 PHE 0.011 0.001 PHE D 170 TRP 0.007 0.001 TRP B 247 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8296) covalent geometry : angle 0.49203 / 0.26 (11204) hydrogen bonds : bond 0.03756 / 2.53 ( 532) hydrogen bonds : angle 4.30624 / 3.19 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.349 Fit side-chains REVERT: A 117 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7766 (mm-30) REVERT: A 160 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: A 162 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7172 (mm110) REVERT: A 328 LYS cc_start: 0.7972 (ttpp) cc_final: 0.7510 (ttmm) REVERT: A 373 LYS cc_start: 0.6826 (mmtm) cc_final: 0.6328 (ttpt) REVERT: A 380 ARG cc_start: 0.7419 (ttm110) cc_final: 0.6801 (mtp85) REVERT: A 388 GLN cc_start: 0.7163 (mm110) cc_final: 0.6357 (tp-100) REVERT: B 122 GLU cc_start: 0.7066 (pp20) cc_final: 0.6401 (pp20) REVERT: B 141 CYS cc_start: 0.7439 (t) cc_final: 0.7183 (t) REVERT: B 163 ASP cc_start: 0.7203 (p0) cc_final: 0.6659 (t0) REVERT: B 177 LYS cc_start: 0.9050 (mttp) cc_final: 0.8686 (mmtm) REVERT: B 266 ASN cc_start: 0.7824 (m-40) cc_final: 0.7361 (t0) REVERT: C 117 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7784 (mm-30) REVERT: C 160 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: C 162 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7163 (mm110) REVERT: C 189 ARG cc_start: 0.8381 (mtp180) cc_final: 0.8016 (mtp85) REVERT: C 243 LYS cc_start: 0.7482 (tttp) cc_final: 0.7272 (tttp) REVERT: C 328 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7538 (ttmm) REVERT: C 373 LYS cc_start: 0.6804 (mmtm) cc_final: 0.6307 (ttpt) REVERT: C 388 GLN cc_start: 0.7189 (mm110) cc_final: 0.6385 (tp-100) REVERT: D 122 GLU cc_start: 0.7112 (pp20) cc_final: 0.6425 (pp20) REVERT: D 163 ASP cc_start: 0.7300 (p0) cc_final: 0.6739 (t0) REVERT: D 177 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7746 (mtmt) REVERT: D 178 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7462 (mp0) REVERT: D 249 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7342 (tm-30) REVERT: D 277 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7167 (mt-10) outliers start: 20 outliers final: 8 residues processed: 151 average time/residue: 0.5845 time to fit residues: 93.5352 Evaluate side-chains 137 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 0.0170 chunk 91 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN D 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.192141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139172 restraints weight = 8720.027| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.02 r_work: 0.3448 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8296 Z= 0.140 Angle : 0.516 7.270 11204 Z= 0.270 Chirality : 0.041 0.258 1312 Planarity : 0.003 0.024 1438 Dihedral : 8.314 82.871 1164 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.47 % Allowed : 19.55 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.26 (0.27), residues: 1036 helix: 1.94 (0.20), residues: 664 sheet: -1.58 (0.40), residues: 142 loop : -0.72 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.011 0.002 TYR C 294 PHE 0.012 0.001 PHE B 170 TRP 0.007 0.001 TRP B 247 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 8296) covalent geometry : angle 0.51598 / 0.27 (11204) hydrogen bonds : bond 0.03833 / 2.58 ( 532) hydrogen bonds : angle 4.33153 / 3.21 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7790 (mm-30) REVERT: A 159 THR cc_start: 0.7456 (m) cc_final: 0.7237 (t) REVERT: A 160 GLU cc_start: 0.8152 (mp0) cc_final: 0.7812 (mt-10) REVERT: A 162 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7202 (mm110) REVERT: A 328 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7531 (ttmm) REVERT: A 373 LYS cc_start: 0.6829 (mmtm) cc_final: 0.6319 (ttpt) REVERT: A 380 ARG cc_start: 0.7422 (ttm110) cc_final: 0.6809 (mtp85) REVERT: A 388 GLN cc_start: 0.7183 (mm110) cc_final: 0.6380 (tp-100) REVERT: B 122 GLU cc_start: 0.7053 (pp20) cc_final: 0.6390 (pp20) REVERT: B 141 CYS cc_start: 0.7439 (t) cc_final: 0.7170 (t) REVERT: B 163 ASP cc_start: 0.7205 (p0) cc_final: 0.6663 (t0) REVERT: B 177 LYS cc_start: 0.8973 (mttp) cc_final: 0.8610 (mmtm) REVERT: C 117 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7786 (mm-30) REVERT: C 160 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: C 162 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7173 (mm110) REVERT: C 189 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8053 (mtp85) REVERT: C 243 LYS cc_start: 0.7488 (tttp) cc_final: 0.7269 (tttm) REVERT: C 257 ASP cc_start: 0.8157 (t70) cc_final: 0.7853 (t70) REVERT: C 328 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7538 (ttmm) REVERT: C 373 LYS cc_start: 0.6820 (mmtm) cc_final: 0.6316 (ttpt) REVERT: C 388 GLN cc_start: 0.7202 (mm110) cc_final: 0.6400 (tp-100) REVERT: D 122 GLU cc_start: 0.7117 (pp20) cc_final: 0.6432 (pp20) REVERT: D 163 ASP cc_start: 0.7220 (p0) cc_final: 0.6685 (t0) REVERT: D 249 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7315 (tm-30) REVERT: D 266 ASN cc_start: 0.7975 (m-40) cc_final: 0.7566 (t0) REVERT: D 277 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7159 (mt-10) outliers start: 22 outliers final: 10 residues processed: 143 average time/residue: 0.5711 time to fit residues: 86.7529 Evaluate side-chains 143 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.192071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142188 restraints weight = 8707.245| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.81 r_work: 0.3464 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8296 Z= 0.129 Angle : 0.503 8.162 11204 Z= 0.263 Chirality : 0.040 0.260 1312 Planarity : 0.003 0.024 1438 Dihedral : 8.200 82.556 1164 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.80 % Allowed : 20.79 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.31 (0.27), residues: 1036 helix: 2.02 (0.20), residues: 662 sheet: -1.66 (0.40), residues: 142 loop : -0.75 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.010 0.001 TYR C 294 PHE 0.011 0.001 PHE D 170 TRP 0.007 0.001 TRP B 247 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8296) covalent geometry : angle 0.50298 / 0.26 (11204) hydrogen bonds : bond 0.03675 / 2.48 ( 532) hydrogen bonds : angle 4.29915 / 3.19 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8439 (mp0) cc_final: 0.8150 (mt-10) REVERT: A 162 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7657 (mm110) REVERT: A 328 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7769 (ttmm) REVERT: A 373 LYS cc_start: 0.7272 (mmtm) cc_final: 0.6825 (ttpt) REVERT: A 380 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7258 (mtp85) REVERT: A 388 GLN cc_start: 0.7443 (mm110) cc_final: 0.6716 (tp-100) REVERT: B 122 GLU cc_start: 0.7201 (pp20) cc_final: 0.6530 (pp20) REVERT: B 163 ASP cc_start: 0.7331 (p0) cc_final: 0.6903 (t0) REVERT: B 173 MET cc_start: 0.7404 (mpt) cc_final: 0.7196 (mpt) REVERT: B 177 LYS cc_start: 0.8934 (mttp) cc_final: 0.8587 (mmtm) REVERT: C 160 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: C 162 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7640 (mm110) REVERT: C 189 ARG cc_start: 0.8521 (mtp180) cc_final: 0.8190 (mtp85) REVERT: C 257 ASP cc_start: 0.8400 (t70) cc_final: 0.8103 (t70) REVERT: C 328 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7745 (ttmm) REVERT: C 373 LYS cc_start: 0.7261 (mmtm) cc_final: 0.6802 (ttpt) REVERT: C 380 ARG cc_start: 0.7758 (ttm110) cc_final: 0.7271 (mtp85) REVERT: C 388 GLN cc_start: 0.7452 (mm110) cc_final: 0.6720 (tp-100) REVERT: D 122 GLU cc_start: 0.7244 (pp20) cc_final: 0.6555 (pp20) REVERT: D 163 ASP cc_start: 0.7348 (p0) cc_final: 0.6928 (t0) REVERT: D 249 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7510 (tm-30) REVERT: D 266 ASN cc_start: 0.8245 (m-40) cc_final: 0.7798 (t0) outliers start: 16 outliers final: 9 residues processed: 143 average time/residue: 0.5914 time to fit residues: 89.6398 Evaluate side-chains 138 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 37 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.192602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143243 restraints weight = 8665.094| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.92 r_work: 0.3459 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8296 Z= 0.129 Angle : 0.509 8.195 11204 Z= 0.264 Chirality : 0.040 0.234 1312 Planarity : 0.003 0.024 1438 Dihedral : 8.113 82.244 1164 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.57 % Allowed : 21.12 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.34 (0.27), residues: 1036 helix: 2.04 (0.20), residues: 662 sheet: -1.49 (0.40), residues: 138 loop : -0.87 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.010 0.001 TYR C 294 PHE 0.011 0.001 PHE B 170 TRP 0.007 0.001 TRP B 247 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8296) covalent geometry : angle 0.50852 / 0.26 (11204) hydrogen bonds : bond 0.03655 / 2.47 ( 532) hydrogen bonds : angle 4.28824 / 3.18 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: A 162 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7674 (mm110) REVERT: A 328 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7775 (ttmm) REVERT: A 373 LYS cc_start: 0.7280 (mmtm) cc_final: 0.6812 (ttpt) REVERT: A 380 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7269 (mtp85) REVERT: A 388 GLN cc_start: 0.7445 (mm110) cc_final: 0.6720 (tp-100) REVERT: B 122 GLU cc_start: 0.7182 (pp20) cc_final: 0.6506 (pp20) REVERT: B 163 ASP cc_start: 0.7330 (p0) cc_final: 0.6893 (t0) REVERT: B 173 MET cc_start: 0.7347 (mpt) cc_final: 0.7137 (mpt) REVERT: B 177 LYS cc_start: 0.8936 (mttp) cc_final: 0.8579 (mmtm) REVERT: C 160 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: C 162 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7637 (mm110) REVERT: C 189 ARG cc_start: 0.8534 (mtp180) cc_final: 0.8202 (mtp85) REVERT: C 257 ASP cc_start: 0.8379 (t70) cc_final: 0.8157 (t70) REVERT: C 328 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7747 (ttmm) REVERT: C 373 LYS cc_start: 0.7229 (mmtm) cc_final: 0.6757 (ttpt) REVERT: C 380 ARG cc_start: 0.7769 (ttm110) cc_final: 0.7294 (mtp85) REVERT: C 388 GLN cc_start: 0.7451 (mm110) cc_final: 0.6726 (tp-100) REVERT: D 122 GLU cc_start: 0.7223 (pp20) cc_final: 0.6526 (pp20) REVERT: D 163 ASP cc_start: 0.7376 (p0) cc_final: 0.6947 (t0) REVERT: D 249 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7500 (tm-30) REVERT: D 266 ASN cc_start: 0.8199 (m-40) cc_final: 0.7796 (t0) outliers start: 14 outliers final: 8 residues processed: 135 average time/residue: 0.5723 time to fit residues: 82.2923 Evaluate side-chains 135 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 176 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.191803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138411 restraints weight = 8733.317| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.03 r_work: 0.3433 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8296 Z= 0.155 Angle : 0.537 7.968 11204 Z= 0.281 Chirality : 0.041 0.223 1312 Planarity : 0.003 0.024 1438 Dihedral : 8.104 81.839 1164 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.35 % Allowed : 21.35 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.23 (0.27), residues: 1036 helix: 1.93 (0.20), residues: 662 sheet: -1.46 (0.41), residues: 138 loop : -0.86 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 162 TYR 0.012 0.002 TYR C 294 PHE 0.013 0.001 PHE D 170 TRP 0.008 0.001 TRP B 247 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 8296) covalent geometry : angle 0.53735 / 0.28 (11204) hydrogen bonds : bond 0.03922 / 2.64 ( 532) hydrogen bonds : angle 4.36721 / 3.24 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4421.90 seconds wall clock time: 75 minutes 58.10 seconds (4558.10 seconds total)