Starting phenix.real_space_refine on Thu Oct 22 23:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tg8_55893/10_2026/9tg8_55893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tg8_55893/10_2026/9tg8_55893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tg8_55893/10_2026/9tg8_55893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tg8_55893/10_2026/9tg8_55893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tg8_55893/10_2026/9tg8_55893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tg8_55893/10_2026/9tg8_55893.map" } resolution = 2.37 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= 0.001 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 4041 2.51 5 N 1105 2.21 5 O 1505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6701 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 594 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "B" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2893 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2893 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "D" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Residues with excluded nonbonded symmetry interactions: 1045 residue: pdb=" N LYS A 165 " occ=0.88 ... (7 atoms not shown) pdb=" NZ LYS A 165 " occ=0.88 residue: pdb=" N THR A 166 " occ=0.64 ... (5 atoms not shown) pdb=" CG2 THR A 166 " occ=0.64 residue: pdb=" N ASP A 167 " occ=0.80 ... (6 atoms not shown) pdb=" OD2 ASP A 167 " occ=0.80 residue: pdb=" N ALA A 168 " occ=0.73 ... (3 atoms not shown) pdb=" CB ALA A 168 " occ=0.73 residue: pdb=" N ALA A 169 " occ=0.90 ... (3 atoms not shown) pdb=" CB ALA A 169 " occ=0.90 residue: pdb=" N VAL A 170 " occ=0.77 ... (5 atoms not shown) pdb=" CG2 VAL A 170 " occ=0.77 residue: pdb=" N GLU A 171 " occ=0.62 ... (7 atoms not shown) pdb=" OE2 GLU A 171 " occ=0.62 residue: pdb=" N MET A 172 " occ=0.82 ... (6 atoms not shown) pdb=" CE MET A 172 " occ=0.82 residue: pdb=" N LYS A 173 " occ=0.78 ... (7 atoms not shown) pdb=" NZ LYS A 173 " occ=0.78 residue: pdb=" N ARG A 174 " occ=0.72 ... (9 atoms not shown) pdb=" NH2 ARG A 174 " occ=0.72 residue: pdb=" N ILE A 175 " occ=0.93 ... (6 atoms not shown) pdb=" CD1 ILE A 175 " occ=0.93 residue: pdb=" N ASN A 176 " occ=0.84 ... (6 atoms not shown) pdb=" ND2 ASN A 176 " occ=0.84 ... (remaining 1033 not shown) Time building chain proxies: 1.67, per 1000 atoms: 0.25 Number of scatterers: 6701 At special positions: 0 Unit cell: (83.79, 62.377, 136.857, 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) S 44 16.00 P 4 15.00 Mg 2 11.99 O 1505 8.00 N 1105 7.00 C 4041 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: 0.54 Conformation dependent library (CDL) restraints added in 400.1 milliseconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 55.7% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 229 removed outlier: 4.141A pdb=" N PHE A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.041A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.521A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.701A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.145A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.869A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.542A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.868A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.071A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.292A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 353 removed outlier: 3.521A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 353' Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.539A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.744A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.363A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.594A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.713A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.351A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 241 364 hydrogen bonds defined for protein. 930 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: 1.11 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2124 1.34 - 1.46: 1046 1.46 - 1.57: 3314 1.57 - 1.69: 6 1.69 - 1.81: 78 Bond restraints: 6568 Sorted by residual: bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" N VAL D 163 " pdb=" CA VAL D 163 " ideal model delta sigma weight residual 1.454 1.461 -0.007 7.70e-03 1.69e+04 7.78e-01 bond pdb=" C2' ADP D 401 " pdb=" C3' ADP D 401 " ideal model delta sigma weight residual 1.524 1.507 0.017 2.00e-02 2.50e+03 7.56e-01 bond pdb=" C2' ADP B 401 " pdb=" C3' ADP B 401 " ideal model delta sigma weight residual 1.524 1.508 0.016 2.00e-02 2.50e+03 6.25e-01 ... (remaining 6563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 8740 1.79 - 3.59: 113 3.59 - 5.38: 24 5.38 - 7.17: 8 7.17 - 8.97: 3 Bond angle restraints: 8888 Sorted by residual: angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.53 110.23 3.30 9.80e-01 1.04e+00 1.14e+01 angle pdb=" C1' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C3' ADP D 401 " ideal model delta sigma weight residual 111.00 102.03 8.97 3.00e+00 1.11e-01 8.93e+00 angle pdb=" C1' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C3' ADP B 401 " ideal model delta sigma weight residual 111.00 102.40 8.60 3.00e+00 1.11e-01 8.21e+00 angle pdb=" N GLY D 55 " pdb=" CA GLY D 55 " pdb=" C GLY D 55 " ideal model delta sigma weight residual 110.86 115.53 -4.67 1.84e+00 2.95e-01 6.45e+00 angle pdb=" CA VAL B 201 " pdb=" C VAL B 201 " pdb=" N THR B 202 " ideal model delta sigma weight residual 117.65 120.37 -2.72 1.10e+00 8.26e-01 6.10e+00 ... (remaining 8883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.47: 3850 32.47 - 64.94: 121 64.94 - 97.41: 11 97.41 - 129.88: 1 129.88 - 162.35: 3 Dihedral angle restraints: 3986 sinusoidal: 1653 harmonic: 2333 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.35 -162.35 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 78.39 -138.39 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 74.62 -134.62 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 3983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 720 0.043 - 0.086: 180 0.086 - 0.129: 65 0.129 - 0.172: 2 0.172 - 0.215: 2 Chirality restraints: 969 Sorted by residual: chirality pdb=" C3' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C4' ADP D 401 " pdb=" O3' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA ILE D 165 " pdb=" N ILE D 165 " pdb=" C ILE D 165 " pdb=" CB ILE D 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 966 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 306 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO D 307 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 307 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 307 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 344 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C SER B 344 " -0.025 2.00e-02 2.50e+03 pdb=" O SER B 344 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 345 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 321 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B 322 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " 0.019 5.00e-02 4.00e+02 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 2 2.52 - 3.12: 4880 3.12 - 3.71: 10775 3.71 - 4.31: 16482 4.31 - 4.90: 25945 Nonbonded interactions: 58084 Sorted by model distance: nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.930 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.951 2.170 nonbonded pdb=" O2A ADP B 401 " pdb="MG MG B 402 " model vdw 2.540 2.170 nonbonded pdb=" O2' ADP B 401 " pdb=" O3' ADP B 401 " model vdw 2.608 2.432 nonbonded pdb=" O2' ADP D 401 " pdb=" O3' ADP D 401 " model vdw 2.616 2.432 ... (remaining 58079 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: 0.00 Found NCS groups: 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=0.07 max=1.00 mean=0.76 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: 2.990 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 8.090 Find NCS groups from input model: 0.090 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6568 Z= 0.138 Angle : 0.573 8.967 8888 Z= 0.282 Chirality : 0.043 0.215 969 Planarity : 0.004 0.040 1146 Dihedral : 16.171 162.351 2488 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.15 % Allowed : 9.20 % Favored : 90.66 % 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: 1.48 (0.31), residues: 793 helix: 0.90 (0.29), residues: 370 sheet: 0.57 (0.42), residues: 132 loop : 1.64 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.012 0.001 TYR B 218 PHE 0.008 0.001 PHE D 31 TRP 0.010 0.002 TRP D 340 HIS 0.005 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6568) covalent geometry : angle 0.57334 / 0.28 ( 8888) hydrogen bonds : bond 0.13369 / 8.53 ( 358) hydrogen bonds : angle 6.02574 / 4.42 ( 930) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 360 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8406 (tp-100) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.8410 time to fit residues: 96.3228 Evaluate side-chains 83 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.0040 chunk 74 optimal weight: 0.7980 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 49 GLN B 128 ASN D 128 ASN D 246 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.063530 restraints weight = 11478.390| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.31 r_work: 0.2749 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (19 function evaluations) r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6568 Z= 0.133 Angle : 0.593 7.767 8888 Z= 0.287 Chirality : 0.042 0.169 969 Planarity : 0.004 0.034 1146 Dihedral : 10.997 176.206 910 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.17 % Allowed : 13.43 % Favored : 85.40 % 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: 1.82 (0.31), residues: 793 helix: 1.28 (0.29), residues: 370 sheet: 0.65 (0.43), residues: 132 loop : 1.71 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 210 TYR 0.018 0.001 TYR A 225 PHE 0.007 0.001 PHE B 31 TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6568) covalent geometry : angle 0.59325 / 0.29 ( 8888) hydrogen bonds : bond 0.03558 / 2.32 ( 358) hydrogen bonds : angle 4.67638 / 3.42 ( 930) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 182 GLU cc_start: 0.8557 (tt0) cc_final: 0.8193 (pp20) REVERT: A 185 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.7903 (pttm) REVERT: A 197 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7930 (mmtm) REVERT: A 200 LEU cc_start: 0.9107 (tp) cc_final: 0.8852 (tt) REVERT: B 360 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8423 (tp-100) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.7858 time to fit residues: 72.6216 Evaluate side-chains 82 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain B residue 354 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [4, 62, 31, 26, 35, 20, 23, 57, 29, 5, 10] chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN A 216 GLN ** D 371 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 = 0.3049 r_free = 0.3049 target = 0.073742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.060042 restraints weight = 11582.538| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.31 r_work: 0.2693 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6568 Z= 0.140 Angle : 0.593 7.137 8888 Z= 0.286 Chirality : 0.043 0.164 969 Planarity : 0.004 0.028 1146 Dihedral : 10.178 155.451 910 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.46 % Allowed : 12.99 % Favored : 85.55 % 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: 1.86 (0.31), residues: 793 helix: 1.30 (0.29), residues: 370 sheet: 0.72 (0.43), residues: 132 loop : 1.71 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 226 TYR 0.021 0.001 TYR A 225 PHE 0.007 0.001 PHE B 31 TRP 0.012 0.002 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6568) covalent geometry : angle 0.59279 / 0.29 ( 8888) hydrogen bonds : bond 0.03525 / 2.31 ( 358) hydrogen bonds : angle 4.50936 / 3.27 ( 930) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: A 200 LEU cc_start: 0.9020 (tp) cc_final: 0.8816 (tt) REVERT: A 204 LEU cc_start: 0.8631 (mt) cc_final: 0.8424 (pp) REVERT: B 326 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8735 (tttm) REVERT: B 360 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8311 (tm-30) outliers start: 10 outliers final: 4 residues processed: 87 average time/residue: 0.7240 time to fit residues: 65.5249 Evaluate side-chains 86 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [67, 73, 57, 76, 9, 66, 41, 40, 64, 45, 43] chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 0.0020 chunk 43 optimal weight: 4.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN A 216 GLN ** D 371 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 = 0.3071 r_free = 0.3071 target = 0.074857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.060688 restraints weight = 11662.814| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.36 r_work: 0.2709 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6568 Z= 0.105 Angle : 0.561 6.745 8888 Z= 0.269 Chirality : 0.042 0.151 969 Planarity : 0.003 0.027 1146 Dihedral : 9.554 141.872 910 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.61 % Allowed : 12.99 % Favored : 85.40 % 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: 1.93 (0.31), residues: 793 helix: 1.36 (0.28), residues: 370 sheet: 0.74 (0.43), residues: 132 loop : 1.77 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 226 TYR 0.022 0.001 TYR A 225 PHE 0.007 0.001 PHE B 31 TRP 0.011 0.002 TRP B 79 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 6568) covalent geometry : angle 0.56106 / 0.27 ( 8888) hydrogen bonds : bond 0.03078 / 2.00 ( 358) hydrogen bonds : angle 4.34815 / 3.14 ( 930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7971 (mmtm) REVERT: A 200 LEU cc_start: 0.9030 (tp) cc_final: 0.8802 (tt) REVERT: B 326 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8746 (tttm) REVERT: B 360 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8280 (tm-30) outliers start: 11 outliers final: 3 residues processed: 88 average time/residue: 0.7276 time to fit residues: 66.4983 Evaluate side-chains 83 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 354 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [78, 15, 52, 8, 20, 21, 65, 75, 70, 9, 31] chunk 78 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 12 ASN D 92 ASN ** D 371 HIS ** 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 = 0.3060 r_free = 0.3060 target = 0.074215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.060036 restraints weight = 11795.354| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.39 r_work: 0.2696 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6568 Z= 0.126 Angle : 0.582 8.463 8888 Z= 0.279 Chirality : 0.043 0.151 969 Planarity : 0.003 0.026 1146 Dihedral : 9.253 148.360 910 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.46 % Allowed : 13.14 % Favored : 85.40 % 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: 1.98 (0.31), residues: 793 helix: 1.43 (0.28), residues: 370 sheet: 0.72 (0.43), residues: 132 loop : 1.77 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.006 0.001 TYR D 240 PHE 0.006 0.001 PHE B 31 TRP 0.011 0.002 TRP B 79 HIS 0.002 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6568) covalent geometry : angle 0.58163 / 0.28 ( 8888) hydrogen bonds : bond 0.03258 / 2.13 ( 358) hydrogen bonds : angle 4.32048 / 3.12 ( 930) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 197 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8037 (mmtm) REVERT: A 200 LEU cc_start: 0.9068 (tp) cc_final: 0.8815 (tt) REVERT: B 147 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8546 (mtp85) REVERT: B 326 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8752 (tttm) REVERT: B 360 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 360 GLN cc_start: 0.9146 (pp30) cc_final: 0.8749 (pm20) outliers start: 10 outliers final: 2 residues processed: 87 average time/residue: 0.7698 time to fit residues: 69.5385 Evaluate side-chains 84 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 326 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [26, 56, 3, 58, 79, 2, 9, 76, 16, 11, 34] chunk 26 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** D 371 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 = 0.3060 r_free = 0.3060 target = 0.074134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.059929 restraints weight = 11757.198| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.39 r_work: 0.2695 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6568 Z= 0.132 Angle : 0.594 12.085 8888 Z= 0.283 Chirality : 0.043 0.154 969 Planarity : 0.003 0.026 1146 Dihedral : 8.985 153.602 910 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.31 % Allowed : 14.01 % Favored : 84.67 % 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: 1.98 (0.31), residues: 793 helix: 1.45 (0.28), residues: 370 sheet: 0.71 (0.43), residues: 132 loop : 1.75 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.025 0.001 TYR A 225 PHE 0.006 0.001 PHE D 255 TRP 0.012 0.002 TRP A 181 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6568) covalent geometry : angle 0.59409 / 0.28 ( 8888) hydrogen bonds : bond 0.03288 / 2.16 ( 358) hydrogen bonds : angle 4.29433 / 3.09 ( 930) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 185 LYS cc_start: 0.9266 (pttm) cc_final: 0.8995 (pttm) REVERT: A 186 LYS cc_start: 0.8373 (mmtm) cc_final: 0.7694 (mmtm) REVERT: A 200 LEU cc_start: 0.9083 (tp) cc_final: 0.8831 (tt) REVERT: A 223 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8044 (mtm-85) REVERT: B 147 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8578 (mtp85) REVERT: B 326 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8755 (tttm) REVERT: B 360 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 360 GLN cc_start: 0.9191 (pp30) cc_final: 0.8735 (pm20) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 0.7204 time to fit residues: 68.2378 Evaluate side-chains 86 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 326 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [51, 59, 5, 37, 77, 50, 4, 26, 19, 28, 10] chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 225 ASN ** D 371 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 = 0.3085 r_free = 0.3085 target = 0.075219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.061540 restraints weight = 11780.184| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.37 r_work: 0.2742 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6568 Z= 0.109 Angle : 0.585 11.226 8888 Z= 0.279 Chirality : 0.043 0.147 969 Planarity : 0.003 0.025 1146 Dihedral : 8.654 157.594 910 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.31 % Allowed : 14.01 % Favored : 84.67 % 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: 1.98 (0.31), residues: 793 helix: 1.45 (0.28), residues: 370 sheet: 0.70 (0.43), residues: 132 loop : 1.75 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.006 0.001 TYR D 240 PHE 0.006 0.001 PHE B 31 TRP 0.011 0.002 TRP A 181 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6568) covalent geometry : angle 0.58451 / 0.28 ( 8888) hydrogen bonds : bond 0.03059 / 2.02 ( 358) hydrogen bonds : angle 4.22665 / 3.04 ( 930) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 185 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8943 (pttm) REVERT: A 186 LYS cc_start: 0.8419 (mmtm) cc_final: 0.7866 (mmtm) REVERT: A 200 LEU cc_start: 0.9090 (tp) cc_final: 0.8814 (tt) REVERT: A 223 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8028 (mtm-85) REVERT: B 147 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8633 (ptm160) REVERT: B 326 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8762 (tttm) REVERT: B 360 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8255 (tm-30) REVERT: D 360 GLN cc_start: 0.9188 (pp30) cc_final: 0.8738 (pm20) outliers start: 9 outliers final: 1 residues processed: 85 average time/residue: 0.7451 time to fit residues: 65.8112 Evaluate side-chains 86 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 326 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [1, 43, 37, 63, 5, 14, 7, 15, 54, 41, 62] chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** D 371 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 = 0.3072 r_free = 0.3072 target = 0.074664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.060752 restraints weight = 11823.032| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.38 r_work: 0.2725 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6568 Z= 0.129 Angle : 0.608 10.504 8888 Z= 0.290 Chirality : 0.043 0.151 969 Planarity : 0.003 0.026 1146 Dihedral : 8.544 158.871 910 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.17 % Allowed : 14.31 % Favored : 84.53 % 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: 1.97 (0.31), residues: 793 helix: 1.45 (0.28), residues: 370 sheet: 0.70 (0.43), residues: 132 loop : 1.74 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.007 0.001 TYR D 240 PHE 0.006 0.001 PHE D 255 TRP 0.012 0.002 TRP A 181 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6568) covalent geometry : angle 0.60754 / 0.29 ( 8888) hydrogen bonds : bond 0.03234 / 2.13 ( 358) hydrogen bonds : angle 4.26638 / 3.07 ( 930) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 185 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8957 (pttm) REVERT: A 186 LYS cc_start: 0.8429 (mmtm) cc_final: 0.7842 (mmtm) REVERT: A 200 LEU cc_start: 0.9079 (tp) cc_final: 0.8792 (tt) REVERT: A 223 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8090 (mtm-85) REVERT: B 147 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8645 (ptm160) REVERT: B 326 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8752 (tttm) REVERT: B 360 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 360 GLN cc_start: 0.9197 (pp30) cc_final: 0.8742 (pm20) outliers start: 8 outliers final: 1 residues processed: 85 average time/residue: 0.7746 time to fit residues: 68.4890 Evaluate side-chains 86 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 326 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [74, 16, 10, 35, 73, 76, 45, 37, 61, 3, 15] chunk 74 optimal weight: 0.9980 chunk 16 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** D 371 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 = 0.3078 r_free = 0.3078 target = 0.074931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061359 restraints weight = 12004.857| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.35 r_work: 0.2740 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6568 Z= 0.117 Angle : 0.619 13.595 8888 Z= 0.295 Chirality : 0.043 0.145 969 Planarity : 0.003 0.026 1146 Dihedral : 8.314 160.370 910 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.17 % Allowed : 14.89 % Favored : 83.94 % 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: 1.97 (0.31), residues: 793 helix: 1.42 (0.28), residues: 370 sheet: 0.71 (0.43), residues: 132 loop : 1.77 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.011 0.001 TYR A 225 PHE 0.006 0.001 PHE D 255 TRP 0.011 0.002 TRP A 181 HIS 0.002 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6568) covalent geometry : angle 0.61930 / 0.30 ( 8888) hydrogen bonds : bond 0.03101 / 2.05 ( 358) hydrogen bonds : angle 4.23839 / 3.04 ( 930) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7640 (mtmm) REVERT: A 179 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 185 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8956 (pttm) REVERT: A 186 LYS cc_start: 0.8418 (mmtm) cc_final: 0.7819 (mmtm) REVERT: A 197 LYS cc_start: 0.8685 (mppt) cc_final: 0.8384 (mmpt) REVERT: A 200 LEU cc_start: 0.9114 (tp) cc_final: 0.8827 (tt) REVERT: A 204 LEU cc_start: 0.8576 (pp) cc_final: 0.8369 (mt) REVERT: A 223 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8108 (mtm-85) REVERT: B 147 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8639 (ptm160) REVERT: B 326 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8753 (tttm) REVERT: B 360 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 360 GLN cc_start: 0.9197 (pp30) cc_final: 0.8703 (pm20) outliers start: 8 outliers final: 1 residues processed: 83 average time/residue: 0.7423 time to fit residues: 64.2254 Evaluate side-chains 84 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 326 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [65, 70, 9, 31, 20, 69, 64, 18, 11, 51, 42] chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** D 371 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 = 0.3083 r_free = 0.3083 target = 0.075068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.061646 restraints weight = 12014.056| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.35 r_work: 0.2747 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6568 Z= 0.112 Angle : 0.623 12.770 8888 Z= 0.295 Chirality : 0.043 0.140 969 Planarity : 0.003 0.026 1146 Dihedral : 8.068 160.133 910 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.88 % Allowed : 15.18 % Favored : 83.94 % 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: 1.98 (0.31), residues: 793 helix: 1.41 (0.28), residues: 370 sheet: 0.71 (0.43), residues: 132 loop : 1.81 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.048 0.001 TYR A 225 PHE 0.006 0.001 PHE B 31 TRP 0.011 0.002 TRP B 79 HIS 0.002 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6568) covalent geometry : angle 0.62297 / 0.30 ( 8888) hydrogen bonds : bond 0.03019 / 1.99 ( 358) hydrogen bonds : angle 4.19610 / 3.01 ( 930) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8307 (mmmt) cc_final: 0.7868 (mtmm) REVERT: A 179 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 185 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8913 (pttm) REVERT: A 186 LYS cc_start: 0.8428 (mmtm) cc_final: 0.7885 (mmtm) REVERT: A 197 LYS cc_start: 0.8677 (mppt) cc_final: 0.8352 (mmtm) REVERT: A 200 LEU cc_start: 0.9109 (tp) cc_final: 0.8812 (tt) REVERT: A 204 LEU cc_start: 0.8585 (pp) cc_final: 0.8382 (mt) REVERT: A 223 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8119 (mtm-85) REVERT: B 326 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8725 (tttm) REVERT: B 360 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8229 (tm-30) REVERT: D 360 GLN cc_start: 0.9182 (pp30) cc_final: 0.8675 (pm20) outliers start: 6 outliers final: 1 residues processed: 83 average time/residue: 0.7563 time to fit residues: 65.2740 Evaluate side-chains 83 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 326 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [74, 44, 25, 30, 47, 66, 8, 57, 11, 56, 65] chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN ** D 371 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 = 0.3068 r_free = 0.3068 target = 0.074357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.060816 restraints weight = 11965.535| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.34 r_work: 0.2728 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6568 Z= 0.134 Angle : 0.628 12.583 8888 Z= 0.302 Chirality : 0.044 0.148 969 Planarity : 0.003 0.026 1146 Dihedral : 8.058 157.360 910 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.73 % Allowed : 15.04 % Favored : 84.23 % 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: 1.96 (0.31), residues: 793 helix: 1.39 (0.28), residues: 370 sheet: 0.72 (0.43), residues: 132 loop : 1.79 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 147 TYR 0.012 0.001 TYR A 225 PHE 0.007 0.001 PHE D 255 TRP 0.010 0.002 TRP B 79 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6568) covalent geometry : angle 0.62787 / 0.30 ( 8888) hydrogen bonds : bond 0.03262 / 2.15 ( 358) hydrogen bonds : angle 4.26187 / 3.06 ( 930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.98 seconds wall clock time: 47 minutes 32.14 seconds (2852.14 seconds total)