Starting phenix.real_space_refine on Fri Mar 14 03:19:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gvk_51637/03_2025/9gvk_51637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gvk_51637/03_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_51637/03_2025/9gvk_51637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gvk_51637/03_2025/9gvk_51637.map" model { file = "/net/cci-nas-00/data/ceres_data/9gvk_51637/03_2025/9gvk_51637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gvk_51637/03_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-5624/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: 7.18, per 1000 atoms: 0.74 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: 2.67 Conformation dependent library (CDL) restraints added in 1.1 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: 1.11 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: 2.65 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2110 1.33 - 1.45: 1942 1.45 - 1.57: 5676 1.57 - 1.69: 10 1.69 - 1.81: 96 Bond restraints: 9834 Sorted by residual: bond pdb=" CA ALA D 82 " pdb=" CB ALA D 82 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.55e-02 4.16e+03 9.47e+00 bond pdb=" N ASP F 101 " pdb=" CA ASP F 101 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.33e-02 5.65e+03 7.13e+00 bond pdb=" N GLU C 138 " pdb=" CA GLU C 138 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.41e-02 5.03e+03 6.25e+00 bond pdb=" C LEU D 84 " pdb=" O LEU D 84 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.15e-02 7.56e+03 6.11e+00 bond pdb=" C ALA D 82 " pdb=" O ALA D 82 " ideal model delta sigma weight residual 1.236 1.209 0.028 1.15e-02 7.56e+03 5.74e+00 ... (remaining 9829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 13093 2.35 - 4.71: 191 4.71 - 7.06: 37 7.06 - 9.41: 6 9.41 - 11.77: 3 Bond angle restraints: 13330 Sorted by residual: angle pdb=" N LEU D 84 " pdb=" CA LEU D 84 " pdb=" C LEU D 84 " ideal model delta sigma weight residual 111.07 104.93 6.14 1.07e+00 8.73e-01 3.29e+01 angle pdb=" N LYS D 81 " pdb=" CA LYS D 81 " pdb=" C LYS D 81 " ideal model delta sigma weight residual 111.28 105.34 5.94 1.09e+00 8.42e-01 2.97e+01 angle pdb=" C LYS D 81 " pdb=" CA LYS D 81 " pdb=" CB LYS D 81 " ideal model delta sigma weight residual 110.79 104.18 6.61 1.66e+00 3.63e-01 1.58e+01 angle pdb=" CB MET E 205 " pdb=" CG MET E 205 " pdb=" SD MET E 205 " ideal model delta sigma weight residual 112.70 124.47 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA ASP F 220 " pdb=" C ASP F 220 " pdb=" O ASP F 220 " ideal model delta sigma weight residual 122.03 117.56 4.47 1.17e+00 7.31e-01 1.46e+01 ... (remaining 13325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4954 17.53 - 35.06: 737 35.06 - 52.58: 239 52.58 - 70.11: 43 70.11 - 87.64: 13 Dihedral angle restraints: 5986 sinusoidal: 2418 harmonic: 3568 Sorted by residual: dihedral pdb=" CA GLU C 361 " pdb=" C GLU C 361 " pdb=" N PRO C 362 " pdb=" CA PRO C 362 " ideal model delta harmonic sigma weight residual 180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C LYS D 81 " pdb=" N LYS D 81 " pdb=" CA LYS D 81 " pdb=" CB LYS D 81 " ideal model delta harmonic sigma weight residual -122.60 -112.58 -10.02 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" CA THR E 346 " pdb=" C THR E 346 " pdb=" N PRO E 347 " pdb=" CA PRO E 347 " ideal model delta harmonic sigma weight residual 180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1291 0.058 - 0.116: 224 0.116 - 0.174: 34 0.174 - 0.232: 1 0.232 - 0.291: 3 Chirality restraints: 1553 Sorted by residual: chirality pdb=" CB ILE D 40 " pdb=" CA ILE D 40 " pdb=" CG1 ILE D 40 " pdb=" CG2 ILE D 40 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA LEU D 84 " pdb=" N LEU D 84 " pdb=" C LEU D 84 " pdb=" CB LEU D 84 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LYS D 81 " pdb=" N LYS D 81 " pdb=" C LYS D 81 " pdb=" CB LYS D 81 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1550 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 190 " 0.019 2.00e-02 2.50e+03 2.12e-02 7.85e+00 pdb=" CG PHE C 190 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 190 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE C 190 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 190 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 190 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 190 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 80 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO C 81 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 76 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 77 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 77 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 77 " -0.032 5.00e-02 4.00e+02 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 70 2.60 - 3.18: 8085 3.18 - 3.75: 15343 3.75 - 4.33: 19872 4.33 - 4.90: 33256 Nonbonded interactions: 76626 Sorted by model distance: nonbonded pdb=" OE1 GLN F 94 " pdb="MG MG F 603 " model vdw 2.026 2.170 nonbonded pdb=" OE1 GLN D 94 " pdb="MG MG D 301 " model vdw 2.040 2.170 nonbonded pdb="MG MG D 301 " pdb=" O2B ATP F 601 " model vdw 2.043 2.170 nonbonded pdb=" OD1 ASP C 123 " pdb=" OG1 THR C 126 " model vdw 2.203 3.040 nonbonded pdb=" O PRO C 167 " pdb=" OG SER C 170 " model vdw 2.292 3.040 ... (remaining 76621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 3 and (name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or resid 4 through 228)) selection = (chain 'F' and resid 3 through 228) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.920 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 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 : 1.851 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: 0.2451 time to fit residues: 62.0462 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 : 1.410 ------------------------------------------------------------------------------- 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 = 0.149347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100227 restraints weight = 15646.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103598 restraints weight = 7780.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105686 restraints weight = 5190.995| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 68.080 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 : 1.828 Fit side-chains REVERT: C 175 MET cc_start: 0.4492 (pmm) cc_final: 0.4248 (tmm) REVERT: C 201 MET cc_start: 0.8168 (ppp) cc_final: 0.7633 (ppp) REVERT: C 293 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8389 (ptpp) REVERT: E 51 PHE cc_start: 0.8178 (t80) cc_final: 0.7969 (t80) REVERT: D 83 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7477 (tm-30) REVERT: D 190 GLU cc_start: 0.7507 (tp30) cc_final: 0.6666 (tp30) outliers start: 27 outliers final: 9 residues processed: 201 average time/residue: 0.2382 time to fit residues: 66.1521 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 : 1.138 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN D 10 ASN ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3836 r_free = 0.3836 target = 0.145423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.095559 restraints weight = 15885.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098786 restraints weight = 7878.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100921 restraints weight = 5298.160| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9834 Z= 0.338 Angle : 0.616 7.796 13330 Z= 0.321 Chirality : 0.045 0.191 1553 Planarity : 0.005 0.045 1703 Dihedral : 6.791 72.879 1412 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.65 % Allowed : 32.66 % Favored : 62.69 % 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: -0.41 (0.25), residues: 1246 helix: 1.33 (0.23), residues: 571 sheet: -0.60 (0.43), residues: 160 loop : -2.08 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 377 HIS 0.004 0.001 HIS D 96 PHE 0.025 0.002 PHE E 319 TYR 0.009 0.001 TYR E 322 ARG 0.004 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 210 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8416 (ppp) cc_final: 0.7839 (ppp) REVERT: C 381 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7925 (tt) REVERT: D 166 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9282 (tp) REVERT: D 190 GLU cc_start: 0.7685 (tp30) cc_final: 0.7301 (tp30) REVERT: D 193 ARG cc_start: 0.7601 (ttp-110) cc_final: 0.7370 (mtm110) outliers start: 48 outliers final: 33 residues processed: 203 average time/residue: 0.2327 time to fit residues: 65.2577 Evaluate side-chains 195 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3876 r_free = 0.3876 target = 0.149051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099707 restraints weight = 15570.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103076 restraints weight = 7653.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105296 restraints weight = 5093.513| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9834 Z= 0.154 Angle : 0.538 7.181 13330 Z= 0.279 Chirality : 0.042 0.165 1553 Planarity : 0.004 0.045 1703 Dihedral : 6.478 74.768 1412 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.29 % Allowed : 33.91 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.25), residues: 1246 helix: 1.78 (0.23), residues: 564 sheet: -0.91 (0.40), residues: 178 loop : -1.98 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 249 HIS 0.002 0.000 HIS D 137 PHE 0.026 0.001 PHE C 190 TYR 0.010 0.001 TYR E 214 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 213 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8389 (ppp) cc_final: 0.8006 (ppp) REVERT: C 293 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8474 (ptpp) REVERT: D 83 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7844 (tm-30) REVERT: D 190 GLU cc_start: 0.7634 (tp30) cc_final: 0.7138 (tp30) REVERT: D 193 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.7271 (ttp-110) outliers start: 34 outliers final: 17 residues processed: 208 average time/residue: 0.2175 time to fit residues: 62.6707 Evaluate side-chains 185 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 187 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 E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 410 VAL 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: 5.9990 chunk 62 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 33 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN 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 = 0.3851 r_free = 0.3851 target = 0.146728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097272 restraints weight = 15527.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100529 restraints weight = 7710.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102702 restraints weight = 5172.950| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9834 Z= 0.257 Angle : 0.573 8.355 13330 Z= 0.296 Chirality : 0.043 0.173 1553 Planarity : 0.004 0.046 1703 Dihedral : 6.507 76.329 1412 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.75 % Allowed : 33.04 % Favored : 62.21 % 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: -0.20 (0.25), residues: 1246 helix: 1.63 (0.23), residues: 566 sheet: -0.84 (0.42), residues: 166 loop : -1.98 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 249 HIS 0.003 0.001 HIS D 96 PHE 0.022 0.002 PHE E 319 TYR 0.008 0.001 TYR E 322 ARG 0.003 0.000 ARG D 142 *********************** 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 222 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8438 (ppp) cc_final: 0.8044 (ppp) REVERT: C 293 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8508 (ptpp) REVERT: C 381 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7831 (tt) REVERT: D 83 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7803 (tm-30) REVERT: D 166 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9262 (tp) REVERT: D 190 GLU cc_start: 0.7631 (tp30) cc_final: 0.7336 (tp30) outliers start: 49 outliers final: 33 residues processed: 213 average time/residue: 0.2050 time to fit residues: 61.8594 Evaluate side-chains 203 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 TYR Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain C residue 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 373 SER Chi-restraints excluded: chain E residue 382 TYR 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 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 96 HIS Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 224 THR 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: 8.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 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 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099908 restraints weight = 15654.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099794 restraints weight = 7670.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099641 restraints weight = 5737.614| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9834 Z= 0.315 Angle : 0.609 8.214 13330 Z= 0.314 Chirality : 0.044 0.184 1553 Planarity : 0.004 0.046 1703 Dihedral : 6.598 80.390 1412 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.43 % Allowed : 31.98 % Favored : 62.60 % 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: -0.37 (0.25), residues: 1246 helix: 1.40 (0.23), residues: 571 sheet: -0.73 (0.44), residues: 160 loop : -2.06 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 249 HIS 0.004 0.001 HIS D 96 PHE 0.023 0.002 PHE E 319 TYR 0.009 0.001 TYR E 322 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 227 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8442 (ppp) cc_final: 0.8092 (ppp) REVERT: C 293 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8543 (ptpp) REVERT: C 381 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7894 (tt) REVERT: E 392 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8466 (mp) REVERT: D 83 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7840 (tm-30) REVERT: D 166 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9295 (tp) REVERT: D 190 GLU cc_start: 0.7649 (tp30) cc_final: 0.7169 (tp30) REVERT: D 193 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.7178 (ttp-110) REVERT: F 195 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8005 (mt0) outliers start: 56 outliers final: 42 residues processed: 218 average time/residue: 0.2159 time to fit residues: 65.9466 Evaluate side-chains 204 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 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 385 VAL 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 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 96 HIS Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 195 GLN Chi-restraints excluded: chain F residue 208 LEU 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: 0.7980 chunk 100 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS D 10 ASN D 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.146780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102691 restraints weight = 15758.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101835 restraints weight = 7655.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101910 restraints weight = 6248.285| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9834 Z= 0.225 Angle : 0.576 8.240 13330 Z= 0.296 Chirality : 0.043 0.177 1553 Planarity : 0.004 0.047 1703 Dihedral : 6.490 81.828 1412 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.33 % Allowed : 31.98 % Favored : 62.69 % 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: -0.26 (0.25), residues: 1246 helix: 1.56 (0.23), residues: 571 sheet: -0.80 (0.44), residues: 157 loop : -2.04 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 78 HIS 0.002 0.001 HIS D 141 PHE 0.022 0.002 PHE C 190 TYR 0.009 0.001 TYR E 322 ARG 0.003 0.000 ARG D 219 *********************** 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 214 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8378 (ppp) cc_final: 0.7979 (ppp) REVERT: C 293 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8534 (ptpp) REVERT: C 381 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7943 (tt) REVERT: E 392 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8527 (mp) REVERT: D 219 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7722 (ttm-80) REVERT: F 195 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7983 (mt0) outliers start: 55 outliers final: 41 residues processed: 208 average time/residue: 0.2517 time to fit residues: 74.2817 Evaluate side-chains 207 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 373 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 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 197 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 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 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: 8.9990 chunk 8 optimal weight: 30.0000 chunk 59 optimal weight: 0.0000 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 overall best weight: 0.9124 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.148774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100032 restraints weight = 15796.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103328 restraints weight = 7736.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105549 restraints weight = 5121.045| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1616 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= 0.159 Angle : 0.567 9.884 13330 Z= 0.286 Chirality : 0.043 0.233 1553 Planarity : 0.004 0.048 1703 Dihedral : 6.308 81.587 1412 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.26 % Allowed : 32.95 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.25), residues: 1246 helix: 1.80 (0.23), residues: 571 sheet: -0.74 (0.43), residues: 160 loop : -2.04 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 78 HIS 0.003 0.001 HIS E 201 PHE 0.016 0.001 PHE E 319 TYR 0.007 0.001 TYR E 322 ARG 0.003 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 222 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8431 (ppp) cc_final: 0.7997 (ppp) REVERT: C 293 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8508 (ptpp) REVERT: E 392 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8450 (mp) REVERT: D 166 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9237 (tp) REVERT: D 190 GLU cc_start: 0.7511 (tp30) cc_final: 0.7026 (tp30) REVERT: F 195 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7913 (mt0) outliers start: 44 outliers final: 31 residues processed: 216 average time/residue: 0.2425 time to fit residues: 73.8334 Evaluate side-chains 195 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 350 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 195 GLN 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: 0.7980 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 123 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.148028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098650 restraints weight = 15579.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102057 restraints weight = 7635.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.104250 restraints weight = 5069.970| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9834 Z= 0.204 Angle : 0.587 10.022 13330 Z= 0.297 Chirality : 0.043 0.239 1553 Planarity : 0.004 0.049 1703 Dihedral : 6.316 80.364 1412 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.07 % Allowed : 32.85 % Favored : 63.08 % 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: -0.06 (0.25), residues: 1246 helix: 1.83 (0.23), residues: 565 sheet: -0.86 (0.42), residues: 165 loop : -1.97 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 78 HIS 0.002 0.001 HIS F 96 PHE 0.041 0.002 PHE C 190 TYR 0.009 0.001 TYR E 214 ARG 0.004 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: 42 poor density : 171 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: C 201 MET cc_start: 0.8416 (ppp) cc_final: 0.8144 (ppp) REVERT: C 293 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8520 (ptpp) REVERT: C 332 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8581 (mt) REVERT: C 381 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7916 (tt) REVERT: E 392 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8444 (mp) REVERT: D 166 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9246 (tp) REVERT: F 195 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.7946 (mt0) outliers start: 42 outliers final: 35 residues processed: 208 average time/residue: 0.2140 time to fit residues: 62.3588 Evaluate side-chains 203 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 342 ASN Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 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 385 VAL 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 54 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 84 LEU 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 195 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 60 optimal weight: 0.0370 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 43 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.150515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101584 restraints weight = 15708.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105072 restraints weight = 7626.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107370 restraints weight = 5012.210| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1657 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 : 0.582 12.033 13330 Z= 0.292 Chirality : 0.042 0.242 1553 Planarity : 0.004 0.050 1703 Dihedral : 6.166 77.549 1412 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.59 % Allowed : 33.62 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.05 (0.25), residues: 1246 helix: 2.01 (0.23), residues: 569 sheet: -0.90 (0.42), residues: 166 loop : -2.04 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 78 HIS 0.002 0.000 HIS D 137 PHE 0.035 0.001 PHE C 190 TYR 0.010 0.001 TYR E 214 ARG 0.005 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: 37 poor density : 177 time to evaluate : 1.133 Fit side-chains REVERT: C 175 MET cc_start: 0.4558 (pmm) cc_final: 0.4306 (tmm) REVERT: C 201 MET cc_start: 0.8292 (ppp) cc_final: 0.7989 (ppp) REVERT: C 272 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8629 (p) REVERT: C 293 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8446 (ptpp) REVERT: E 392 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8440 (mp) REVERT: F 195 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: F 205 ASP cc_start: 0.8196 (t0) cc_final: 0.7488 (t0) outliers start: 37 outliers final: 29 residues processed: 209 average time/residue: 0.2016 time to fit residues: 58.7080 Evaluate side-chains 202 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 350 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain E residue 65 HIS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 382 TYR Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain E residue 410 VAL 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 101 ASP Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 195 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 26 HIS 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 = 0.3902 r_free = 0.3902 target = 0.150832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.101804 restraints weight = 15462.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105341 restraints weight = 7546.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107589 restraints weight = 4957.386| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1699 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= 0.154 Angle : 0.595 12.448 13330 Z= 0.299 Chirality : 0.042 0.246 1553 Planarity : 0.004 0.048 1703 Dihedral : 6.145 76.542 1412 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.71 % Allowed : 35.08 % Favored : 62.21 % 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: 2.03 (0.23), residues: 570 sheet: -0.84 (0.42), residues: 166 loop : -2.00 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 78 HIS 0.001 0.000 HIS D 137 PHE 0.030 0.001 PHE C 190 TYR 0.010 0.001 TYR E 214 ARG 0.005 0.000 ARG E 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.24 seconds wall clock time: 73 minutes 1.51 seconds (4381.51 seconds total)