Starting phenix.real_space_refine on Wed Sep 17 15:49:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gvk_51637/09_2025/9gvk_51637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gvk_51637/09_2025/9gvk_51637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gvk_51637/09_2025/9gvk_51637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gvk_51637/09_2025/9gvk_51637.map" model { file = "/net/cci-nas-00/data/ceres_data/9gvk_51637/09_2025/9gvk_51637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gvk_51637/09_2025/9gvk_51637.cif" } resolution = 3.5 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= 0.004 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 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6134 2.51 5 N 1705 2.21 5 O 1775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9673 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2978 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3172 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 14, 'TRANS': 396} Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1729 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.27, per 1000 atoms: 0.23 Number of scatterers: 9673 At special positions: 0 Unit cell: (95.316, 137.904, 122.694, 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 51 16.00 P 6 15.00 Mg 2 11.99 O 1775 8.00 N 1705 7.00 C 6134 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 342.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 48.1% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C' and resid 4 through 14 Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.718A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.316A pdb=" N VAL C 85 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 230 through 235 removed outlier: 4.303A pdb=" N ASP C 233 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 253 through 293 removed outlier: 3.773A pdb=" N LYS C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.848A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 339 removed outlier: 3.600A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 365 removed outlier: 4.005A pdb=" N GLN C 364 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 390 removed outlier: 3.837A pdb=" N THR C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix removed outlier: 3.896A pdb=" N THR C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 24 through 59 removed outlier: 3.556A pdb=" N GLY E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 242 removed outlier: 4.275A pdb=" N LEU E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 258 through 298 removed outlier: 3.688A pdb=" N ASN E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE E 287 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR E 290 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 Processing helix chain 'E' and resid 311 through 344 removed outlier: 4.037A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 395 Processing helix chain 'E' and resid 396 through 404 Processing helix chain 'E' and resid 406 through 412 removed outlier: 3.531A pdb=" N VAL E 410 " --> pdb=" O ASP E 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 77 through 88 removed outlier: 4.244A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.603A pdb=" N ALA D 139 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 147 through 161 removed outlier: 3.565A pdb=" N GLN D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 196 Processing helix chain 'D' and resid 205 through 211 removed outlier: 3.505A pdb=" N LYS D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 103 through 115 Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 118 through 133 removed outlier: 3.808A pdb=" N ASN F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.586A pdb=" N ARG F 138 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 139 " --> pdb=" O ASP F 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 135 through 139' Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 147 through 161 Processing helix chain 'F' and resid 177 through 196 Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.726A pdb=" N ARG F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.628A pdb=" N ILE C 67 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96 removed outlier: 4.461A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 113 removed outlier: 8.890A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 160 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 93 through 94 removed outlier: 3.738A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 168 removed outlier: 7.623A pdb=" N ALA E 204 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN E 114 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE E 206 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYS E 116 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 150 through 151 removed outlier: 5.917A pdb=" N ILE E 150 " --> pdb=" O LEU E 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 33 removed outlier: 6.163A pdb=" N VAL D 28 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP D 9 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE D 30 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN D 7 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 32 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 9 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP D 65 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.754A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP D 170 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE D 92 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 202 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 169 " --> pdb=" O VAL D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 31 through 32 removed outlier: 3.653A pdb=" N ASP F 65 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 92 removed outlier: 6.786A pdb=" N GLY F 90 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ASP F 170 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE F 92 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N MET F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 217 " --> pdb=" O THR F 224 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2110 1.33 - 1.45: 1942 1.45 - 1.57: 5676 1.57 - 1.69: 10 1.69 - 1.81: 96 Bond restraints: 9834 Sorted by residual: bond pdb=" CA ALA D 82 " pdb=" CB ALA D 82 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.55e-02 4.16e+03 9.47e+00 bond pdb=" N ASP F 101 " pdb=" CA ASP F 101 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.33e-02 5.65e+03 7.13e+00 bond pdb=" N GLU C 138 " pdb=" CA GLU C 138 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.41e-02 5.03e+03 6.25e+00 bond pdb=" C LEU D 84 " pdb=" O LEU D 84 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.15e-02 7.56e+03 6.11e+00 bond pdb=" C ALA D 82 " pdb=" O ALA D 82 " ideal model delta sigma weight residual 1.236 1.209 0.028 1.15e-02 7.56e+03 5.74e+00 ... (remaining 9829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 13093 2.35 - 4.71: 191 4.71 - 7.06: 37 7.06 - 9.41: 6 9.41 - 11.77: 3 Bond angle restraints: 13330 Sorted by residual: angle pdb=" N LEU D 84 " pdb=" CA LEU D 84 " pdb=" C LEU D 84 " ideal model delta sigma weight residual 111.07 104.93 6.14 1.07e+00 8.73e-01 3.29e+01 angle pdb=" N LYS D 81 " pdb=" CA LYS D 81 " pdb=" C LYS D 81 " ideal model delta sigma weight residual 111.28 105.34 5.94 1.09e+00 8.42e-01 2.97e+01 angle pdb=" C LYS D 81 " pdb=" CA LYS D 81 " pdb=" CB LYS D 81 " ideal model delta sigma weight residual 110.79 104.18 6.61 1.66e+00 3.63e-01 1.58e+01 angle pdb=" CB MET E 205 " pdb=" CG MET E 205 " pdb=" SD MET E 205 " ideal model delta sigma weight residual 112.70 124.47 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ASP F 220 " pdb=" C ASP F 220 " pdb=" O ASP F 220 " ideal model delta sigma weight residual 122.03 117.56 4.47 1.17e+00 7.31e-01 1.46e+01 ... (remaining 13325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4954 17.53 - 35.06: 737 35.06 - 52.58: 239 52.58 - 70.11: 43 70.11 - 87.64: 13 Dihedral angle restraints: 5986 sinusoidal: 2418 harmonic: 3568 Sorted by residual: dihedral pdb=" CA GLU C 361 " pdb=" C GLU C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta harmonic sigma weight residual 180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C LYS D 81 " pdb=" N LYS D 81 " pdb=" CA LYS D 81 " pdb=" CB LYS D 81 " ideal model delta harmonic sigma weight residual -122.60 -112.58 -10.02 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" CA THR E 346 " pdb=" C THR E 346 " pdb=" N PRO E 347 " pdb=" CA PRO E 347 " ideal model delta harmonic sigma weight residual 180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1291 0.058 - 0.116: 224 0.116 - 0.174: 34 0.174 - 0.232: 1 0.232 - 0.291: 3 Chirality restraints: 1553 Sorted by residual: chirality pdb=" CB ILE D 40 " pdb=" CA ILE D 40 " pdb=" CG1 ILE D 40 " pdb=" CG2 ILE D 40 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA LEU D 84 " pdb=" N LEU D 84 " pdb=" C LEU D 84 " pdb=" CB LEU D 84 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LYS D 81 " pdb=" N LYS D 81 " pdb=" C LYS D 81 " pdb=" CB LYS D 81 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1550 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 190 " 0.019 2.00e-02 2.50e+03 2.12e-02 7.85e+00 pdb=" CG PHE C 190 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 190 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE C 190 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 190 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 190 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 190 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 80 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO C 81 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 76 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 77 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 77 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 77 " -0.032 5.00e-02 4.00e+02 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 70 2.60 - 3.18: 8085 3.18 - 3.75: 15343 3.75 - 4.33: 19872 4.33 - 4.90: 33256 Nonbonded interactions: 76626 Sorted by model distance: nonbonded pdb=" OE1 GLN F 94 " pdb="MG MG F 603 " model vdw 2.026 2.170 nonbonded pdb=" OE1 GLN D 94 " pdb="MG MG D 301 " model vdw 2.040 2.170 nonbonded pdb="MG MG D 301 " pdb=" O2B ATP F 601 " model vdw 2.043 2.170 nonbonded pdb=" OD1 ASP C 123 " pdb=" OG1 THR C 126 " model vdw 2.203 3.040 nonbonded pdb=" O PRO C 167 " pdb=" OG SER C 170 " model vdw 2.292 3.040 ... (remaining 76621 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 'D' and ((resid 3 and (name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or resid 4 through 228)) selection = (chain 'F' and resid 3 through 228) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.500 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.004 0.048 9835 Z= 0.175 Angle : 0.713 11.766 13330 Z= 0.379 Chirality : 0.047 0.291 1553 Planarity : 0.005 0.060 1703 Dihedral : 18.624 87.638 3692 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.39 % Allowed : 37.21 % Favored : 62.40 % 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 aren not related in a simple way. whole: -0.64 (0.24), residues: 1246 helix: 1.09 (0.22), residues: 553 sheet: -0.66 (0.40), residues: 180 loop : -2.07 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 219 TYR 0.016 0.001 TYR C 2 PHE 0.048 0.002 PHE C 190 TRP 0.008 0.001 TRP C 249 HIS 0.005 0.001 HIS F 26 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9834) covalent geometry : angle 0.71345 (13330) hydrogen bonds : bond 0.17404 ( 443) hydrogen bonds : angle 6.36398 ( 1260) Misc. bond : bond 0.00363 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.363 Fit side-chains REVERT: C 149 GLN cc_start: 0.8812 (tp40) cc_final: 0.8338 (tp-100) REVERT: C 175 MET cc_start: 0.4918 (pmm) cc_final: 0.4585 (tmm) REVERT: F 36 GLU cc_start: 0.8046 (mp0) cc_final: 0.7806 (mp0) outliers start: 4 outliers final: 0 residues processed: 186 average time/residue: 0.0996 time to fit residues: 25.2392 Evaluate side-chains 169 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.147349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097347 restraints weight = 15693.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100693 restraints weight = 7851.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.102821 restraints weight = 5264.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104133 restraints weight = 4193.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104750 restraints weight = 3668.388| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9835 Z= 0.176 Angle : 0.590 7.295 13330 Z= 0.306 Chirality : 0.044 0.192 1553 Planarity : 0.005 0.047 1703 Dihedral : 6.973 71.355 1412 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.20 % Allowed : 33.91 % Favored : 62.89 % 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 aren not related in a simple way. whole: -0.33 (0.25), residues: 1246 helix: 1.45 (0.23), residues: 569 sheet: -0.71 (0.41), residues: 174 loop : -2.07 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 219 TYR 0.010 0.001 TYR C 128 PHE 0.022 0.002 PHE C 190 TRP 0.006 0.001 TRP C 249 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9834) covalent geometry : angle 0.58974 (13330) hydrogen bonds : bond 0.04655 ( 443) hydrogen bonds : angle 4.85958 ( 1260) Misc. bond : bond 0.00554 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.266 Fit side-chains REVERT: C 149 GLN cc_start: 0.8824 (tp40) cc_final: 0.8326 (tp-100) REVERT: C 175 MET cc_start: 0.4634 (pmm) cc_final: 0.4384 (tmm) REVERT: C 201 MET cc_start: 0.8283 (ppp) cc_final: 0.7838 (ppp) REVERT: E 51 PHE cc_start: 0.8297 (t80) cc_final: 0.8088 (t80) REVERT: D 83 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7594 (tm-30) REVERT: D 190 GLU cc_start: 0.7501 (tp30) cc_final: 0.6853 (tp30) outliers start: 33 outliers final: 15 residues processed: 201 average time/residue: 0.0900 time to fit residues: 25.2364 Evaluate side-chains 179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 222 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 87 optimal weight: 0.0770 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 ASN D 215 GLN F 21 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.149030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099806 restraints weight = 15701.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103181 restraints weight = 7784.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105333 restraints weight = 5183.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106564 restraints weight = 4108.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107389 restraints weight = 3590.492| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9835 Z= 0.119 Angle : 0.538 6.521 13330 Z= 0.279 Chirality : 0.042 0.157 1553 Planarity : 0.004 0.046 1703 Dihedral : 6.597 71.472 1412 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.00 % Allowed : 34.21 % Favored : 62.79 % 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 aren not related in a simple way. whole: -0.12 (0.25), residues: 1246 helix: 1.70 (0.23), residues: 570 sheet: -0.66 (0.41), residues: 173 loop : -2.05 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 219 TYR 0.011 0.001 TYR E 214 PHE 0.018 0.001 PHE E 319 TRP 0.005 0.001 TRP C 249 HIS 0.002 0.000 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9834) covalent geometry : angle 0.53778 (13330) hydrogen bonds : bond 0.03764 ( 443) hydrogen bonds : angle 4.57717 ( 1260) Misc. bond : bond 0.00366 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: C 149 GLN cc_start: 0.8817 (tp40) cc_final: 0.8302 (tp-100) REVERT: C 201 MET cc_start: 0.8328 (ppp) cc_final: 0.7681 (ppp) REVERT: C 272 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8605 (p) REVERT: C 293 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8484 (ptpp) REVERT: C 381 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7836 (tt) REVERT: E 51 PHE cc_start: 0.8141 (t80) cc_final: 0.7878 (t80) REVERT: D 83 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7630 (tm-30) REVERT: D 147 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8666 (p) REVERT: D 166 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9238 (tp) REVERT: D 190 GLU cc_start: 0.7590 (tp30) cc_final: 0.7267 (tp30) REVERT: D 193 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.7251 (ttp-110) outliers start: 31 outliers final: 20 residues processed: 210 average time/residue: 0.0907 time to fit residues: 26.5039 Evaluate side-chains 190 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 222 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 91 ASN E 99 ASN D 10 ASN D 192 ASN D 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093188 restraints weight = 15877.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096363 restraints weight = 7893.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098456 restraints weight = 5306.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099600 restraints weight = 4215.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100438 restraints weight = 3714.089| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 9835 Z= 0.293 Angle : 0.673 7.446 13330 Z= 0.350 Chirality : 0.048 0.202 1553 Planarity : 0.005 0.047 1703 Dihedral : 6.961 80.650 1412 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 6.40 % Allowed : 31.78 % Favored : 61.82 % 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 aren not related in a simple way. whole: -0.65 (0.25), residues: 1246 helix: 1.07 (0.22), residues: 571 sheet: -0.86 (0.42), residues: 168 loop : -2.09 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 19 TYR 0.011 0.002 TYR F 15 PHE 0.027 0.002 PHE E 319 TRP 0.008 0.001 TRP E 377 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 9834) covalent geometry : angle 0.67254 (13330) hydrogen bonds : bond 0.05289 ( 443) hydrogen bonds : angle 4.82663 ( 1260) Misc. bond : bond 0.00972 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 159 time to evaluate : 0.253 Fit side-chains REVERT: C 28 TRP cc_start: 0.6503 (m100) cc_final: 0.6192 (m-10) REVERT: C 149 GLN cc_start: 0.8868 (tp40) cc_final: 0.8381 (tp-100) REVERT: C 201 MET cc_start: 0.8474 (ppp) cc_final: 0.8203 (ppp) REVERT: C 293 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8553 (ptpp) REVERT: C 381 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7979 (tt) REVERT: E 99 ASN cc_start: 0.6745 (OUTLIER) cc_final: 0.6464 (m-40) REVERT: D 166 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9322 (tp) REVERT: D 190 GLU cc_start: 0.7556 (tp30) cc_final: 0.7294 (tp30) REVERT: F 81 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8224 (ttmt) outliers start: 66 outliers final: 39 residues processed: 214 average time/residue: 0.0898 time to fit residues: 27.0586 Evaluate side-chains 189 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS D 10 ASN D 215 GLN F 21 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097895 restraints weight = 15774.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101218 restraints weight = 7812.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103342 restraints weight = 5220.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104666 restraints weight = 4126.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105139 restraints weight = 3602.818| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9835 Z= 0.131 Angle : 0.565 7.711 13330 Z= 0.292 Chirality : 0.043 0.167 1553 Planarity : 0.004 0.047 1703 Dihedral : 6.683 80.434 1412 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.07 % Allowed : 33.53 % Favored : 62.40 % 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 aren not related in a simple way. whole: -0.31 (0.25), residues: 1246 helix: 1.52 (0.23), residues: 570 sheet: -0.84 (0.43), residues: 160 loop : -2.06 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 193 TYR 0.011 0.001 TYR E 97 PHE 0.032 0.002 PHE C 190 TRP 0.019 0.001 TRP E 78 HIS 0.002 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9834) covalent geometry : angle 0.56470 (13330) hydrogen bonds : bond 0.03959 ( 443) hydrogen bonds : angle 4.56951 ( 1260) Misc. bond : bond 0.00474 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: C 149 GLN cc_start: 0.8827 (tp40) cc_final: 0.8321 (tp-100) REVERT: C 201 MET cc_start: 0.8448 (ppp) cc_final: 0.8108 (ppp) REVERT: C 293 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8499 (ptpp) REVERT: C 381 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7868 (tt) REVERT: E 392 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8397 (mp) REVERT: D 166 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9280 (tp) REVERT: D 190 GLU cc_start: 0.7335 (tp30) cc_final: 0.6858 (tp30) REVERT: F 17 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6324 (pt0) outliers start: 42 outliers final: 26 residues processed: 206 average time/residue: 0.0897 time to fit residues: 26.1593 Evaluate side-chains 198 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 101 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 107 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 ASN D 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.147951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098822 restraints weight = 15641.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102122 restraints weight = 7749.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104288 restraints weight = 5173.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105602 restraints weight = 4085.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106262 restraints weight = 3561.588| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9835 Z= 0.120 Angle : 0.553 7.971 13330 Z= 0.284 Chirality : 0.042 0.160 1553 Planarity : 0.004 0.045 1703 Dihedral : 6.458 80.566 1412 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.55 % Allowed : 33.04 % Favored : 62.40 % 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 aren not related in a simple way. whole: -0.11 (0.25), residues: 1246 helix: 1.74 (0.23), residues: 571 sheet: -0.82 (0.44), residues: 157 loop : -2.00 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 179 TYR 0.009 0.001 TYR E 214 PHE 0.023 0.001 PHE C 190 TRP 0.017 0.001 TRP E 78 HIS 0.002 0.000 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9834) covalent geometry : angle 0.55346 (13330) hydrogen bonds : bond 0.03647 ( 443) hydrogen bonds : angle 4.45980 ( 1260) Misc. bond : bond 0.00395 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: C 65 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: C 149 GLN cc_start: 0.8833 (tp40) cc_final: 0.8318 (tp-100) REVERT: C 201 MET cc_start: 0.8438 (ppp) cc_final: 0.8024 (ppp) REVERT: C 293 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8544 (ptpp) REVERT: C 381 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7889 (tt) REVERT: E 392 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8409 (mp) REVERT: D 166 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9243 (tp) REVERT: D 190 GLU cc_start: 0.7566 (tp30) cc_final: 0.7148 (tp30) REVERT: D 193 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7245 (ttp-110) REVERT: F 17 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6325 (pt0) REVERT: F 129 MET cc_start: 0.8913 (tpp) cc_final: 0.8618 (mmt) REVERT: F 195 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7961 (mt0) outliers start: 47 outliers final: 31 residues processed: 220 average time/residue: 0.0916 time to fit residues: 28.4369 Evaluate side-chains 209 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 195 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 26 HIS D 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091374 restraints weight = 15830.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094479 restraints weight = 7995.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096492 restraints weight = 5398.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097739 restraints weight = 4318.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098356 restraints weight = 3791.843| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 9835 Z= 0.350 Angle : 0.741 9.626 13330 Z= 0.383 Chirality : 0.050 0.216 1553 Planarity : 0.005 0.048 1703 Dihedral : 7.054 85.941 1412 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 6.20 % Allowed : 32.66 % Favored : 61.14 % 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 aren not related in a simple way. whole: -0.80 (0.24), residues: 1246 helix: 0.92 (0.22), residues: 571 sheet: -0.90 (0.43), residues: 169 loop : -2.13 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 179 TYR 0.011 0.002 TYR C 128 PHE 0.029 0.003 PHE E 319 TRP 0.014 0.002 TRP E 78 HIS 0.006 0.002 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00827 ( 9834) covalent geometry : angle 0.74121 (13330) hydrogen bonds : bond 0.05608 ( 443) hydrogen bonds : angle 4.88283 ( 1260) Misc. bond : bond 0.01250 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: C 28 TRP cc_start: 0.6563 (m100) cc_final: 0.6240 (m-10) REVERT: C 65 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: C 201 MET cc_start: 0.8478 (ppp) cc_final: 0.8257 (ppp) REVERT: C 381 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8031 (tt) REVERT: E 392 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 166 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9337 (tp) REVERT: F 17 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6358 (pt0) REVERT: F 195 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8082 (mt0) outliers start: 64 outliers final: 43 residues processed: 209 average time/residue: 0.0966 time to fit residues: 28.3012 Evaluate side-chains 195 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 146 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 246 TRP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 224 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS D 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095959 restraints weight = 15644.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099307 restraints weight = 7757.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101451 restraints weight = 5158.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102730 restraints weight = 4104.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103528 restraints weight = 3587.321| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9835 Z= 0.149 Angle : 0.592 9.309 13330 Z= 0.304 Chirality : 0.044 0.224 1553 Planarity : 0.004 0.050 1703 Dihedral : 6.691 83.516 1412 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.84 % Allowed : 34.01 % Favored : 61.14 % 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 aren not related in a simple way. whole: -0.42 (0.25), residues: 1246 helix: 1.45 (0.23), residues: 569 sheet: -0.78 (0.43), residues: 163 loop : -2.18 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 179 TYR 0.008 0.001 TYR E 214 PHE 0.020 0.002 PHE C 190 TRP 0.013 0.001 TRP E 78 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9834) covalent geometry : angle 0.59248 (13330) hydrogen bonds : bond 0.04085 ( 443) hydrogen bonds : angle 4.59243 ( 1260) Misc. bond : bond 0.00524 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.376 Fit side-chains REVERT: C 65 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: C 201 MET cc_start: 0.8473 (ppp) cc_final: 0.8117 (ppp) REVERT: C 293 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8572 (ptpp) REVERT: C 381 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7938 (tt) REVERT: E 392 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8420 (mp) REVERT: D 166 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9307 (tp) REVERT: D 190 GLU cc_start: 0.7452 (tp30) cc_final: 0.6920 (tp30) REVERT: D 193 ARG cc_start: 0.7531 (ttp-110) cc_final: 0.7081 (ttp-110) REVERT: F 17 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6368 (pt0) REVERT: F 195 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8036 (mt0) outliers start: 50 outliers final: 38 residues processed: 209 average time/residue: 0.0946 time to fit residues: 27.7419 Evaluate side-chains 208 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 246 TRP Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 222 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 0.0050 chunk 48 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN D 10 ASN D 207 GLN D 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.148583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099284 restraints weight = 15655.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102639 restraints weight = 7677.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104880 restraints weight = 5114.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.106242 restraints weight = 4025.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106884 restraints weight = 3509.489| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9835 Z= 0.114 Angle : 0.587 10.005 13330 Z= 0.295 Chirality : 0.043 0.240 1553 Planarity : 0.004 0.050 1703 Dihedral : 6.388 80.501 1412 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.78 % Allowed : 34.88 % Favored : 61.34 % 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 aren not related in a simple way. whole: -0.03 (0.25), residues: 1246 helix: 1.94 (0.23), residues: 563 sheet: -0.82 (0.42), residues: 171 loop : -2.07 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 179 TYR 0.010 0.001 TYR C 142 PHE 0.016 0.001 PHE C 190 TRP 0.013 0.001 TRP E 78 HIS 0.001 0.000 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9834) covalent geometry : angle 0.58684 (13330) hydrogen bonds : bond 0.03404 ( 443) hydrogen bonds : angle 4.42611 ( 1260) Misc. bond : bond 0.00314 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.366 Fit side-chains REVERT: C 65 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: C 149 GLN cc_start: 0.8847 (tp40) cc_final: 0.8319 (tp-100) REVERT: C 201 MET cc_start: 0.8456 (ppp) cc_final: 0.8044 (ppp) REVERT: C 293 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8476 (ptpp) REVERT: E 274 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7989 (tp) REVERT: E 392 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8417 (mp) REVERT: D 190 GLU cc_start: 0.7469 (tp30) cc_final: 0.6611 (tp30) REVERT: D 193 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.6932 (ttp-110) REVERT: F 195 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.7992 (mt0) outliers start: 39 outliers final: 29 residues processed: 211 average time/residue: 0.0989 time to fit residues: 28.9350 Evaluate side-chains 199 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 195 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 ASN D 10 ASN D 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096555 restraints weight = 15684.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099862 restraints weight = 7733.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102012 restraints weight = 5144.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103395 restraints weight = 4068.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104020 restraints weight = 3537.343| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9835 Z= 0.185 Angle : 0.634 10.700 13330 Z= 0.321 Chirality : 0.045 0.248 1553 Planarity : 0.004 0.051 1703 Dihedral : 6.537 81.467 1412 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.17 % Allowed : 34.59 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.25), residues: 1246 helix: 1.62 (0.23), residues: 570 sheet: -0.75 (0.44), residues: 163 loop : -2.13 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 179 TYR 0.008 0.001 TYR E 214 PHE 0.024 0.002 PHE E 319 TRP 0.013 0.001 TRP E 78 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9834) covalent geometry : angle 0.63356 (13330) hydrogen bonds : bond 0.04165 ( 443) hydrogen bonds : angle 4.51800 ( 1260) Misc. bond : bond 0.00612 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.316 Fit side-chains REVERT: C 65 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: C 149 GLN cc_start: 0.8854 (tp40) cc_final: 0.8328 (tp-100) REVERT: C 201 MET cc_start: 0.8438 (ppp) cc_final: 0.8173 (ppp) REVERT: C 293 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8489 (ptpp) REVERT: C 381 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7878 (tt) REVERT: E 392 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8465 (mp) REVERT: D 166 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9296 (tp) REVERT: D 190 GLU cc_start: 0.7506 (tp30) cc_final: 0.6873 (tp30) REVERT: D 193 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7047 (ttp-110) REVERT: F 195 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8029 (mt0) outliers start: 43 outliers final: 36 residues processed: 200 average time/residue: 0.0920 time to fit residues: 25.7356 Evaluate side-chains 203 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 246 TRP Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 195 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 12 optimal weight: 0.0020 chunk 113 optimal weight: 0.0980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 ASN D 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.149208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100048 restraints weight = 15455.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103451 restraints weight = 7610.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105694 restraints weight = 5046.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107004 restraints weight = 3977.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107743 restraints weight = 3460.174| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9835 Z= 0.114 Angle : 0.599 9.734 13330 Z= 0.300 Chirality : 0.043 0.239 1553 Planarity : 0.004 0.049 1703 Dihedral : 6.323 79.158 1412 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.17 % Allowed : 34.50 % Favored : 61.34 % 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 aren not related in a simple way. whole: 0.02 (0.25), residues: 1246 helix: 2.01 (0.23), residues: 562 sheet: -0.82 (0.42), residues: 171 loop : -2.07 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 179 TYR 0.008 0.001 TYR E 214 PHE 0.022 0.001 PHE C 190 TRP 0.013 0.001 TRP E 78 HIS 0.002 0.000 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9834) covalent geometry : angle 0.59881 (13330) hydrogen bonds : bond 0.03332 ( 443) hydrogen bonds : angle 4.38539 ( 1260) Misc. bond : bond 0.00288 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.17 seconds wall clock time: 31 minutes 41.29 seconds (1901.29 seconds total)