Starting phenix.real_space_refine on Thu Feb 13 23:32:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gvk_51637/02_2025/9gvk_51637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gvk_51637/02_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_51637/02_2025/9gvk_51637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gvk_51637/02_2025/9gvk_51637.map" model { file = "/net/cci-nas-00/data/ceres_data/9gvk_51637/02_2025/9gvk_51637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gvk_51637/02_2025/9gvk_51637.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.10, per 1000 atoms: 0.63 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.97 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: 2.63 Time building geometry restraints manager: 3.22 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.860 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- 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 9834 Z= 0.228 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 249 HIS 0.005 0.001 HIS F 26 PHE 0.048 0.002 PHE C 190 TYR 0.016 0.001 TYR C 2 ARG 0.007 0.000 ARG D 219 *********************** 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 : 1.184 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: 0.2460 time to fit residues: 61.8946 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 : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.149431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100316 restraints weight = 15649.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103645 restraints weight = 7811.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105782 restraints weight = 5229.342| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9834 Z= 0.183 Angle : 0.555 7.421 13330 Z= 0.287 Chirality : 0.043 0.196 1553 Planarity : 0.004 0.048 1703 Dihedral : 6.856 68.081 1412 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.62 % Allowed : 34.21 % Favored : 63.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1246 helix: 1.62 (0.23), residues: 569 sheet: -0.62 (0.41), residues: 174 loop : -2.06 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 222 HIS 0.003 0.001 HIS D 137 PHE 0.021 0.001 PHE C 190 TYR 0.011 0.001 TYR E 214 ARG 0.003 0.000 ARG D 219 *********************** 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: 27 poor density : 181 time to evaluate : 1.136 Fit side-chains REVERT: C 175 MET cc_start: 0.4483 (pmm) cc_final: 0.4241 (tmm) REVERT: C 201 MET cc_start: 0.8168 (ppp) cc_final: 0.7635 (ppp) REVERT: C 293 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8389 (ptpp) REVERT: E 51 PHE cc_start: 0.8176 (t80) cc_final: 0.7969 (t80) REVERT: D 83 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7475 (tm-30) REVERT: D 190 GLU cc_start: 0.7503 (tp30) cc_final: 0.6664 (tp30) outliers start: 27 outliers final: 9 residues processed: 201 average time/residue: 0.2344 time to fit residues: 65.2047 Evaluate side-chains 173 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 154 LEU Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE 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 32 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 7 optimal weight: 9.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- 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 71 GLN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN F 21 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094184 restraints weight = 15924.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097345 restraints weight = 7928.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099484 restraints weight = 5352.158| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 9834 Z= 0.415 Angle : 0.660 7.732 13330 Z= 0.343 Chirality : 0.047 0.202 1553 Planarity : 0.005 0.046 1703 Dihedral : 6.921 75.037 1412 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.94 % Allowed : 32.75 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1246 helix: 1.16 (0.22), residues: 571 sheet: -0.70 (0.42), residues: 169 loop : -2.08 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 377 HIS 0.005 0.001 HIS D 96 PHE 0.026 0.002 PHE E 319 TYR 0.010 0.002 TYR E 322 ARG 0.003 0.000 ARG D 219 *********************** 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 213 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: C 175 MET cc_start: 0.4859 (pmm) cc_final: 0.4655 (tmm) REVERT: C 201 MET cc_start: 0.8447 (ppp) cc_final: 0.7894 (ppp) REVERT: C 381 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7972 (tt) REVERT: E 99 ASN cc_start: 0.6764 (OUTLIER) cc_final: 0.6513 (m-40) REVERT: D 118 LYS cc_start: 0.8617 (tmtt) cc_final: 0.8392 (tmtt) REVERT: D 166 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9299 (tp) REVERT: F 81 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8151 (ttmt) outliers start: 51 outliers final: 34 residues processed: 206 average time/residue: 0.2364 time to fit residues: 66.4218 Evaluate side-chains 191 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 154 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 SER 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 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 99 ASN 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 293 MET 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 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 96 HIS Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 220 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 35 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 192 ASN D 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099352 restraints weight = 15596.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102698 restraints weight = 7730.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104862 restraints weight = 5157.594| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9834 Z= 0.161 Angle : 0.553 7.212 13330 Z= 0.287 Chirality : 0.042 0.169 1553 Planarity : 0.004 0.046 1703 Dihedral : 6.581 75.142 1412 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.49 % Allowed : 34.21 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1246 helix: 1.67 (0.23), residues: 565 sheet: -0.97 (0.42), residues: 163 loop : -1.99 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 78 HIS 0.005 0.001 HIS C 72 PHE 0.027 0.001 PHE C 190 TYR 0.016 0.001 TYR E 97 ARG 0.003 0.000 ARG F 193 *********************** 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 206 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.964 Fit side-chains REVERT: C 201 MET cc_start: 0.8445 (ppp) cc_final: 0.8093 (ppp) REVERT: C 293 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8481 (ptpp) REVERT: C 381 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7963 (tt) REVERT: D 83 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7761 (tm-30) outliers start: 36 outliers final: 16 residues processed: 200 average time/residue: 0.2320 time to fit residues: 64.0053 Evaluate side-chains 187 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 272 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 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 292 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain F residue 8 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 chunk 46 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN C 72 HIS D 10 ASN D 215 GLN F 21 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.146807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098335 restraints weight = 15583.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101606 restraints weight = 7719.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103692 restraints weight = 5165.342| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9834 Z= 0.258 Angle : 0.583 8.540 13330 Z= 0.300 Chirality : 0.044 0.175 1553 Planarity : 0.004 0.045 1703 Dihedral : 6.572 76.388 1412 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.94 % Allowed : 32.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1246 helix: 1.52 (0.23), residues: 572 sheet: -0.82 (0.43), residues: 160 loop : -2.08 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 78 HIS 0.005 0.001 HIS C 72 PHE 0.022 0.002 PHE E 319 TYR 0.012 0.001 TYR E 262 ARG 0.004 0.000 ARG F 214 *********************** 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 224 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8439 (ppp) cc_final: 0.8051 (ppp) REVERT: C 293 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8539 (ptpp) REVERT: C 381 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7880 (tt) REVERT: D 83 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7781 (tm-30) REVERT: D 166 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9259 (tp) REVERT: F 17 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6254 (pt0) REVERT: F 195 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7937 (mt0) outliers start: 51 outliers final: 35 residues processed: 217 average time/residue: 0.2229 time to fit residues: 67.2112 Evaluate side-chains 202 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain C residue 100 ASP 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 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 292 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 8 CYS 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 17 GLU 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 Chi-restraints excluded: chain F residue 222 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 102 optimal weight: 0.0770 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN D 10 ASN D 26 HIS D 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.143180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098137 restraints weight = 15686.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097873 restraints weight = 7877.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097796 restraints weight = 5852.260| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9834 Z= 0.388 Angle : 0.661 7.343 13330 Z= 0.343 Chirality : 0.046 0.197 1553 Planarity : 0.005 0.047 1703 Dihedral : 6.845 84.261 1412 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.88 % Allowed : 31.40 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1246 helix: 1.17 (0.22), residues: 571 sheet: -0.92 (0.42), residues: 168 loop : -2.11 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 78 HIS 0.005 0.001 HIS D 96 PHE 0.026 0.002 PHE E 319 TYR 0.012 0.002 TYR E 262 ARG 0.003 0.000 ARG F 219 *********************** 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 239 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: C 28 TRP cc_start: 0.6667 (m100) cc_final: 0.6244 (m-10) REVERT: C 65 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: C 201 MET cc_start: 0.8393 (ppp) cc_final: 0.8087 (ppp) REVERT: C 293 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8544 (ptpp) REVERT: C 381 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7992 (tt) REVERT: E 392 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8456 (mp) REVERT: D 83 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7875 (tm-30) REVERT: D 166 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9315 (tp) REVERT: D 190 GLU cc_start: 0.7673 (tp30) cc_final: 0.7345 (tp30) REVERT: F 195 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8056 (mt0) outliers start: 71 outliers final: 47 residues processed: 228 average time/residue: 0.2352 time to fit residues: 75.4114 Evaluate side-chains 207 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 47 VAL 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 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 323 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 292 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain E residue 371 LEU 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 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 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 84 LEU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 224 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 ASN D 26 HIS D 192 ASN D 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095199 restraints weight = 15865.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098467 restraints weight = 7941.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100594 restraints weight = 5315.496| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9834 Z= 0.320 Angle : 0.626 8.132 13330 Z= 0.322 Chirality : 0.045 0.186 1553 Planarity : 0.004 0.048 1703 Dihedral : 6.755 86.371 1412 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 6.01 % Allowed : 32.46 % Favored : 61.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1246 helix: 1.24 (0.22), residues: 571 sheet: -0.87 (0.44), residues: 160 loop : -2.17 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 78 HIS 0.004 0.001 HIS D 96 PHE 0.023 0.002 PHE C 190 TYR 0.010 0.001 TYR E 262 ARG 0.003 0.000 ARG D 193 *********************** 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 218 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 156 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8474 (ppp) cc_final: 0.7976 (ppp) REVERT: C 293 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8544 (ptpp) REVERT: C 381 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7981 (tt) REVERT: E 392 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8483 (mp) REVERT: D 166 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9303 (tp) REVERT: F 195 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8009 (mt0) outliers start: 62 outliers final: 47 residues processed: 209 average time/residue: 0.2211 time to fit residues: 64.3005 Evaluate side-chains 209 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 157 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 47 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 75 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 219 ILE Chi-restraints excluded: chain C residue 260 VAL 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 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 292 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 373 SER 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 24 VAL Chi-restraints excluded: chain D residue 54 LEU 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 135 LEU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 222 ARG 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 40 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 chunk 46 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 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 = 0.3865 r_free = 0.3865 target = 0.147896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098802 restraints weight = 15807.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102168 restraints weight = 7693.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104377 restraints weight = 5094.729| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9834 Z= 0.168 Angle : 0.579 9.792 13330 Z= 0.295 Chirality : 0.043 0.239 1553 Planarity : 0.004 0.048 1703 Dihedral : 6.455 84.678 1412 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 4.65 % Allowed : 33.91 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.25), residues: 1246 helix: 1.77 (0.23), residues: 564 sheet: -0.86 (0.42), residues: 169 loop : -2.09 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 78 HIS 0.002 0.001 HIS D 141 PHE 0.015 0.001 PHE E 319 TYR 0.010 0.001 TYR E 262 ARG 0.004 0.000 ARG D 142 *********************** 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 223 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8481 (ppp) cc_final: 0.8103 (ppp) REVERT: C 293 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8516 (ptpp) REVERT: E 392 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 190 GLU cc_start: 0.7565 (tp30) cc_final: 0.6838 (tp30) REVERT: F 129 MET cc_start: 0.8904 (tpp) cc_final: 0.8585 (mmt) REVERT: F 195 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7959 (mt0) outliers start: 48 outliers final: 35 residues processed: 214 average time/residue: 0.2226 time to fit residues: 66.1603 Evaluate side-chains 199 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 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 230 LEU Chi-restraints excluded: chain C residue 246 TRP Chi-restraints excluded: chain C residue 272 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 55 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 206 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 331 SER 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 197 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 224 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 123 optimal weight: 0.0670 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.145547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095757 restraints weight = 15665.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099074 restraints weight = 7793.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101114 restraints weight = 5225.074| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9834 Z= 0.302 Angle : 0.632 10.520 13330 Z= 0.323 Chirality : 0.045 0.239 1553 Planarity : 0.005 0.050 1703 Dihedral : 6.572 87.122 1412 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.55 % Allowed : 34.01 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1246 helix: 1.45 (0.23), residues: 570 sheet: -0.78 (0.44), residues: 163 loop : -2.14 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 78 HIS 0.004 0.001 HIS D 96 PHE 0.046 0.002 PHE C 190 TYR 0.010 0.001 TYR E 322 ARG 0.005 0.000 ARG F 193 *********************** 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 213 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8461 (ppp) cc_final: 0.8199 (ppp) REVERT: C 293 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8540 (ptpp) REVERT: C 381 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7924 (tt) REVERT: E 12 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8303 (mmt-90) REVERT: E 392 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8488 (mp) REVERT: D 83 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 219 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7778 (ttm-80) REVERT: F 38 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8171 (ttm) REVERT: F 195 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8021 (mt0) outliers start: 47 outliers final: 38 residues processed: 206 average time/residue: 0.2548 time to fit residues: 73.5859 Evaluate side-chains 211 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 75 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 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 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 12 ARG Chi-restraints excluded: chain E residue 55 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 292 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 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 38 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.148236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098851 restraints weight = 15749.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102279 restraints weight = 7704.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104350 restraints weight = 5115.270| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9834 Z= 0.179 Angle : 0.597 10.183 13330 Z= 0.303 Chirality : 0.043 0.247 1553 Planarity : 0.004 0.051 1703 Dihedral : 6.367 85.789 1412 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.68 % Allowed : 34.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1246 helix: 1.82 (0.23), residues: 564 sheet: -0.86 (0.42), residues: 169 loop : -2.05 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 78 HIS 0.002 0.000 HIS D 137 PHE 0.040 0.002 PHE C 190 TYR 0.010 0.001 TYR E 262 ARG 0.004 0.000 ARG D 193 ********************** 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 214 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.056 Fit side-chains REVERT: C 201 MET cc_start: 0.8454 (ppp) cc_final: 0.8038 (ppp) REVERT: C 293 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8504 (ptpp) REVERT: E 392 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8452 (mp) REVERT: D 83 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7690 (tm-30) REVERT: D 219 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7760 (ttm-80) REVERT: F 195 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7975 (mt0) outliers start: 38 outliers final: 31 residues processed: 210 average time/residue: 0.2412 time to fit residues: 69.6926 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 : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 75 LEU 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 272 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 55 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 331 SER 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 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 195 GLN Chi-restraints excluded: chain F residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 0.0470 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 0.0000 chunk 102 optimal weight: 5.9990 chunk 86 optimal weight: 0.0060 chunk 67 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101824 restraints weight = 15498.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105330 restraints weight = 7554.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107596 restraints weight = 4933.635| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9834 Z= 0.148 Angle : 0.589 9.815 13330 Z= 0.295 Chirality : 0.043 0.244 1553 Planarity : 0.004 0.049 1703 Dihedral : 6.165 81.300 1412 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.71 % Allowed : 35.85 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1246 helix: 1.99 (0.23), residues: 568 sheet: -0.86 (0.42), residues: 169 loop : -2.09 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 78 HIS 0.002 0.000 HIS D 137 PHE 0.034 0.001 PHE C 190 TYR 0.010 0.001 TYR E 262 ARG 0.005 0.000 ARG D 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3275.38 seconds wall clock time: 59 minutes 29.82 seconds (3569.82 seconds total)