Starting phenix.real_space_refine on Tue Nov 18 15:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ood_3837/11_2025/5ood_3837.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ood_3837/11_2025/5ood_3837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ood_3837/11_2025/5ood_3837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ood_3837/11_2025/5ood_3837.map" model { file = "/net/cci-nas-00/data/ceres_data/5ood_3837/11_2025/5ood_3837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ood_3837/11_2025/5ood_3837.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {' MG': 1, '9ZK': 2, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' MG': 1, '9ZK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' MG': 1, '9ZK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' MG': 1, '9ZK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14910 At special positions: 0 Unit cell: (91.56, 94.83, 190.75, 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 105 16.00 P 15 15.00 Mg 5 11.99 O 2865 8.00 N 2495 7.00 C 9425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 719.2 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 52.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.689A pdb=" N PHE A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.391A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.689A pdb=" N PHE B 90 " --> pdb=" O TRP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.390A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.688A pdb=" N PHE C 90 " --> pdb=" O TRP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.390A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 358 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.690A pdb=" N PHE D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.015A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.391A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 91 removed outlier: 3.689A pdb=" N PHE E 90 " --> pdb=" O TRP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.390A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 356 Processing helix chain 'E' and resid 358 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.785A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.216A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.217A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 5.784A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 750 hydrogen bonds defined for protein. 1845 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: 2.84 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2460 1.28 - 1.41: 3850 1.41 - 1.54: 8730 1.54 - 1.68: 15 1.68 - 1.81: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.13e+01 bond pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sigma weight residual 1.610 1.482 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sigma weight residual 1.610 1.482 0.128 2.00e-02 2.50e+03 4.12e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 18959 2.74 - 5.49: 1420 5.49 - 8.23: 226 8.23 - 10.97: 65 10.97 - 13.71: 20 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta sigma weight residual 120.03 128.55 -8.52 9.90e-01 1.02e+00 7.40e+01 angle pdb=" C HIS B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta sigma weight residual 120.03 128.54 -8.51 9.90e-01 1.02e+00 7.39e+01 angle pdb=" C HIS A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 120.03 128.50 -8.47 9.90e-01 1.02e+00 7.31e+01 angle pdb=" C HIS D 101 " pdb=" N PRO D 102 " pdb=" CA PRO D 102 " ideal model delta sigma weight residual 120.03 128.49 -8.46 9.90e-01 1.02e+00 7.31e+01 angle pdb=" C HIS E 101 " pdb=" N PRO E 102 " pdb=" CA PRO E 102 " ideal model delta sigma weight residual 120.03 128.48 -8.45 9.90e-01 1.02e+00 7.29e+01 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 8895 33.06 - 66.11: 160 66.11 - 99.17: 95 99.17 - 132.23: 35 132.23 - 165.28: 55 Dihedral angle restraints: 9240 sinusoidal: 3880 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.40 133.60 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.43 133.57 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 166.44 133.56 1 2.00e+01 2.50e-03 4.05e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1524 0.071 - 0.142: 650 0.142 - 0.213: 96 0.213 - 0.284: 5 0.284 - 0.355: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C25 9ZK D 404 " pdb=" C26 9ZK D 404 " pdb=" C36 9ZK D 404 " pdb=" N23 9ZK D 404 " both_signs ideal model delta sigma weight residual False 2.15 2.50 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C25 9ZK A 403 " pdb=" C26 9ZK A 403 " pdb=" C36 9ZK A 403 " pdb=" N23 9ZK A 403 " both_signs ideal model delta sigma weight residual False 2.15 2.50 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C25 9ZK A 405 " pdb=" C26 9ZK A 405 " pdb=" C36 9ZK A 405 " pdb=" N23 9ZK A 405 " both_signs ideal model delta sigma weight residual False 2.15 2.50 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.095 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO C 164 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.095 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO B 164 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " 0.095 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO E 164 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.073 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 123 2.58 - 3.16: 14112 3.16 - 3.74: 22926 3.74 - 4.32: 35604 4.32 - 4.90: 54919 Nonbonded interactions: 127684 Sorted by model distance: nonbonded pdb=" O3 PO4 A 402 " pdb="MG MG A 404 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 B 402 " pdb="MG MG B 403 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 C 402 " pdb="MG MG C 403 " model vdw 1.995 2.170 nonbonded pdb=" O3 PO4 E 402 " pdb="MG MG E 403 " model vdw 1.996 2.170 nonbonded pdb=" O3 PO4 D 402 " pdb="MG MG D 403 " model vdw 1.997 2.170 ... (remaining 127679 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 'A' and resid 5 through 402) selection = (chain 'B' and resid 5 through 402) selection = (chain 'C' and resid 5 through 402) selection = (chain 'D' and resid 5 through 402) selection = (chain 'E' and resid 5 through 402) } 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.220 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.017 0.129 15240 Z= 1.020 Angle : 1.689 13.713 20690 Z= 1.041 Chirality : 0.074 0.355 2280 Planarity : 0.017 0.145 2630 Dihedral : 23.090 165.281 5810 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 2.46 % Allowed : 5.52 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.19), residues: 1830 helix: -1.54 (0.16), residues: 725 sheet: -0.78 (0.31), residues: 225 loop : -0.69 (0.23), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 256 TYR 0.029 0.006 TYR A 294 PHE 0.011 0.003 PHE B 90 TRP 0.027 0.006 TRP D 340 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.01705 (15240) covalent geometry : angle 1.68928 (20690) hydrogen bonds : bond 0.17104 ( 740) hydrogen bonds : angle 7.88416 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 THR cc_start: 0.8897 (m) cc_final: 0.8642 (p) REVERT: A 291 LYS cc_start: 0.8911 (tttt) cc_final: 0.7833 (mptt) REVERT: A 349 LEU cc_start: 0.8276 (tp) cc_final: 0.7952 (mt) REVERT: B 66 THR cc_start: 0.9254 (m) cc_final: 0.8938 (p) REVERT: B 191 LYS cc_start: 0.8858 (tttt) cc_final: 0.8312 (ttpt) REVERT: B 215 LYS cc_start: 0.8369 (mttt) cc_final: 0.7914 (mtpt) REVERT: B 222 ASP cc_start: 0.7998 (t0) cc_final: 0.7724 (m-30) REVERT: B 239 SER cc_start: 0.8846 (t) cc_final: 0.8463 (p) REVERT: B 290 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8436 (mtt180) REVERT: B 291 LYS cc_start: 0.8685 (tttt) cc_final: 0.7909 (mttp) REVERT: B 314 GLN cc_start: 0.7470 (tp40) cc_final: 0.7167 (tp40) REVERT: B 340 TRP cc_start: 0.8261 (t60) cc_final: 0.7673 (t60) REVERT: C 78 ASN cc_start: 0.8432 (t0) cc_final: 0.8173 (t0) REVERT: C 87 HIS cc_start: 0.7909 (t70) cc_final: 0.7527 (t-170) REVERT: D 56 ASP cc_start: 0.7754 (m-30) cc_final: 0.7127 (t0) REVERT: D 78 ASN cc_start: 0.8371 (t0) cc_final: 0.7698 (t0) REVERT: D 214 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 244 ASP cc_start: 0.7594 (p0) cc_final: 0.7377 (p0) REVERT: D 260 THR cc_start: 0.9256 (p) cc_final: 0.8194 (m) REVERT: D 283 MET cc_start: 0.8381 (mmp) cc_final: 0.7759 (ttm) REVERT: D 355 MET cc_start: 0.7844 (mmm) cc_final: 0.7406 (mmt) REVERT: D 358 THR cc_start: 0.8741 (m) cc_final: 0.8467 (p) REVERT: E 41 GLN cc_start: 0.7990 (mt0) cc_final: 0.7597 (mm-40) REVERT: E 43 VAL cc_start: 0.6549 (t) cc_final: 0.6225 (t) REVERT: E 61 LYS cc_start: 0.8423 (mmtt) cc_final: 0.8143 (mmpt) REVERT: E 78 ASN cc_start: 0.8054 (t0) cc_final: 0.6943 (t0) REVERT: E 81 ASP cc_start: 0.8203 (m-30) cc_final: 0.7715 (m-30) REVERT: E 82 MET cc_start: 0.7750 (tpt) cc_final: 0.7421 (tpt) REVERT: E 84 LYS cc_start: 0.8400 (tptt) cc_final: 0.8165 (tttt) REVERT: E 115 ASN cc_start: 0.8737 (t0) cc_final: 0.8523 (t0) REVERT: E 276 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8675 (mt-10) REVERT: E 284 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7527 (tmtt) REVERT: E 304 THR cc_start: 0.8582 (p) cc_final: 0.8268 (m) REVERT: E 336 LYS cc_start: 0.8173 (ptmt) cc_final: 0.7708 (ttpt) outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 0.1412 time to fit residues: 126.6578 Evaluate side-chains 313 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN C 115 ASN C 246 GLN D 87 HIS D 115 ASN ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 354 GLN E 88 HIS E 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110375 restraints weight = 26732.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113446 restraints weight = 13157.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115475 restraints weight = 7888.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116804 restraints weight = 5423.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117763 restraints weight = 4136.444| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15240 Z= 0.152 Angle : 0.769 9.281 20690 Z= 0.384 Chirality : 0.047 0.223 2280 Planarity : 0.008 0.065 2630 Dihedral : 29.450 171.505 2330 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.54 % Favored : 95.14 % Rotamer: Outliers : 1.92 % Allowed : 10.93 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.20), residues: 1830 helix: -0.05 (0.18), residues: 800 sheet: -0.45 (0.27), residues: 295 loop : -0.36 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 290 TYR 0.019 0.001 TYR E 306 PHE 0.031 0.002 PHE C 352 TRP 0.027 0.002 TRP A 340 HIS 0.010 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00333 (15240) covalent geometry : angle 0.76872 (20690) hydrogen bonds : bond 0.03815 ( 740) hydrogen bonds : angle 5.58509 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 406 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8934 (t0) cc_final: 0.8576 (t0) REVERT: A 206 ARG cc_start: 0.8377 (ttp80) cc_final: 0.8105 (ttm170) REVERT: A 249 THR cc_start: 0.8905 (m) cc_final: 0.8350 (p) REVERT: A 259 GLU cc_start: 0.8018 (tp30) cc_final: 0.7698 (tp30) REVERT: A 291 LYS cc_start: 0.8779 (tttt) cc_final: 0.7944 (mptt) REVERT: A 314 GLN cc_start: 0.7936 (tt0) cc_final: 0.7596 (mt0) REVERT: A 340 TRP cc_start: 0.8727 (t60) cc_final: 0.7696 (t60) REVERT: A 344 SER cc_start: 0.8776 (m) cc_final: 0.8176 (p) REVERT: B 66 THR cc_start: 0.8998 (m) cc_final: 0.8695 (t) REVERT: B 191 LYS cc_start: 0.8851 (tttt) cc_final: 0.8303 (ttmt) REVERT: B 291 LYS cc_start: 0.8360 (tttt) cc_final: 0.7576 (mttt) REVERT: B 305 MET cc_start: 0.7740 (mtp) cc_final: 0.7406 (mtp) REVERT: B 314 GLN cc_start: 0.7385 (tp40) cc_final: 0.7055 (tp40) REVERT: B 325 MET cc_start: 0.5520 (mmt) cc_final: 0.5310 (mmt) REVERT: C 68 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8612 (mmmm) REVERT: C 87 HIS cc_start: 0.7594 (t70) cc_final: 0.7021 (t-90) REVERT: C 241 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 283 MET cc_start: 0.8868 (mmm) cc_final: 0.8657 (mmm) REVERT: D 56 ASP cc_start: 0.7523 (m-30) cc_final: 0.7165 (t0) REVERT: D 59 GLN cc_start: 0.8874 (mm110) cc_final: 0.8673 (mm110) REVERT: D 78 ASN cc_start: 0.7573 (t0) cc_final: 0.7364 (t0) REVERT: D 191 LYS cc_start: 0.8897 (tttt) cc_final: 0.8447 (mtpp) REVERT: D 201 VAL cc_start: 0.8732 (m) cc_final: 0.8523 (p) REVERT: D 283 MET cc_start: 0.7938 (mmp) cc_final: 0.7392 (ttm) REVERT: D 360 GLN cc_start: 0.8186 (pp30) cc_final: 0.6968 (pp30) REVERT: E 84 LYS cc_start: 0.8230 (tptt) cc_final: 0.7748 (tptt) REVERT: E 292 ASP cc_start: 0.8158 (t70) cc_final: 0.7594 (t70) outliers start: 30 outliers final: 19 residues processed: 428 average time/residue: 0.1197 time to fit residues: 77.0835 Evaluate side-chains 318 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 299 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS B 92 ASN B 225 ASN C 41 GLN C 115 ASN C 128 ASN C 225 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS E 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097927 restraints weight = 27974.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100782 restraints weight = 14017.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102668 restraints weight = 8465.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103913 restraints weight = 5860.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104718 restraints weight = 4499.671| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 15240 Z= 0.311 Angle : 0.848 8.405 20690 Z= 0.423 Chirality : 0.052 0.258 2280 Planarity : 0.007 0.065 2630 Dihedral : 28.772 179.270 2330 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.25 % Favored : 94.48 % Rotamer: Outliers : 3.96 % Allowed : 12.27 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1830 helix: -0.04 (0.18), residues: 810 sheet: -0.69 (0.28), residues: 305 loop : 0.08 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 335 TYR 0.023 0.002 TYR A 133 PHE 0.024 0.003 PHE B 90 TRP 0.025 0.003 TRP B 79 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00737 (15240) covalent geometry : angle 0.84837 (20690) hydrogen bonds : bond 0.04507 ( 740) hydrogen bonds : angle 5.57006 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 302 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8852 (t0) cc_final: 0.8483 (t0) REVERT: A 117 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 120 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9149 (p) REVERT: A 226 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 249 THR cc_start: 0.8977 (m) cc_final: 0.8542 (p) REVERT: A 291 LYS cc_start: 0.9013 (tttt) cc_final: 0.7876 (mptt) REVERT: A 314 GLN cc_start: 0.8098 (tt0) cc_final: 0.7629 (mt0) REVERT: B 140 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8989 (mm) REVERT: B 291 LYS cc_start: 0.8584 (tttt) cc_final: 0.7622 (mttt) REVERT: B 314 GLN cc_start: 0.7750 (tp40) cc_final: 0.7492 (tp40) REVERT: C 68 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8707 (mmmm) REVERT: C 87 HIS cc_start: 0.7611 (t70) cc_final: 0.7102 (t-90) REVERT: C 191 LYS cc_start: 0.8956 (tttt) cc_final: 0.8728 (tttp) REVERT: C 221 LEU cc_start: 0.8775 (tp) cc_final: 0.8494 (tt) REVERT: C 238 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8546 (mmmm) REVERT: C 283 MET cc_start: 0.8982 (mmm) cc_final: 0.8391 (mmt) REVERT: C 325 MET cc_start: 0.8825 (mmm) cc_final: 0.8619 (mmm) REVERT: D 56 ASP cc_start: 0.7589 (m-30) cc_final: 0.7043 (t0) REVERT: D 61 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8586 (mmmt) REVERT: D 191 LYS cc_start: 0.8814 (tttt) cc_final: 0.8581 (ttpp) REVERT: D 283 MET cc_start: 0.8196 (mmp) cc_final: 0.7395 (ttm) REVERT: D 297 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8366 (m110) REVERT: D 346 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8791 (tp) REVERT: E 84 LYS cc_start: 0.8099 (tptt) cc_final: 0.7630 (tptt) REVERT: E 124 PHE cc_start: 0.8093 (m-10) cc_final: 0.7544 (m-10) REVERT: E 292 ASP cc_start: 0.8320 (t70) cc_final: 0.7991 (t70) REVERT: E 355 MET cc_start: 0.7070 (mtt) cc_final: 0.6852 (mmm) outliers start: 62 outliers final: 40 residues processed: 346 average time/residue: 0.1115 time to fit residues: 59.6976 Evaluate side-chains 303 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 357 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 354 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 88 HIS E 101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102012 restraints weight = 27103.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104984 restraints weight = 13497.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106951 restraints weight = 8114.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108179 restraints weight = 5573.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109079 restraints weight = 4288.979| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15240 Z= 0.146 Angle : 0.693 7.380 20690 Z= 0.337 Chirality : 0.046 0.230 2280 Planarity : 0.005 0.056 2630 Dihedral : 27.709 179.556 2330 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.64 % Favored : 95.19 % Rotamer: Outliers : 3.32 % Allowed : 14.25 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1830 helix: 0.32 (0.18), residues: 800 sheet: -0.65 (0.27), residues: 305 loop : 0.31 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 335 TYR 0.015 0.001 TYR A 133 PHE 0.029 0.002 PHE C 352 TRP 0.018 0.002 TRP A 340 HIS 0.013 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00341 (15240) covalent geometry : angle 0.69308 (20690) hydrogen bonds : bond 0.03365 ( 740) hydrogen bonds : angle 5.10264 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8745 (t0) cc_final: 0.7764 (t0) REVERT: A 81 ASP cc_start: 0.8188 (m-30) cc_final: 0.7544 (m-30) REVERT: A 117 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 184 ASP cc_start: 0.7863 (m-30) cc_final: 0.7578 (m-30) REVERT: A 226 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 249 THR cc_start: 0.8922 (m) cc_final: 0.8581 (p) REVERT: A 291 LYS cc_start: 0.8910 (tttt) cc_final: 0.7565 (mmtt) REVERT: A 314 GLN cc_start: 0.8019 (tt0) cc_final: 0.7620 (mt0) REVERT: B 154 ASP cc_start: 0.8054 (t0) cc_final: 0.7797 (m-30) REVERT: B 191 LYS cc_start: 0.8822 (tttt) cc_final: 0.8156 (ttmt) REVERT: B 257 CYS cc_start: 0.8539 (t) cc_final: 0.7779 (p) REVERT: B 259 GLU cc_start: 0.7913 (tp30) cc_final: 0.7690 (tp30) REVERT: B 290 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8136 (mtt180) REVERT: B 291 LYS cc_start: 0.8434 (tttt) cc_final: 0.7582 (mttp) REVERT: B 314 GLN cc_start: 0.7657 (tp40) cc_final: 0.7288 (tp40) REVERT: C 132 MET cc_start: 0.8404 (ppp) cc_final: 0.8098 (ppp) REVERT: C 191 LYS cc_start: 0.8939 (tttt) cc_final: 0.8691 (tttp) REVERT: D 56 ASP cc_start: 0.7252 (m-30) cc_final: 0.6836 (t0) REVERT: D 61 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8439 (mmmt) REVERT: D 191 LYS cc_start: 0.8772 (tttt) cc_final: 0.8483 (mtpp) REVERT: D 283 MET cc_start: 0.8211 (mmp) cc_final: 0.7330 (ttm) REVERT: D 325 MET cc_start: 0.8275 (mmm) cc_final: 0.7833 (mmp) REVERT: E 21 PHE cc_start: 0.7593 (m-80) cc_final: 0.7370 (m-80) REVERT: E 84 LYS cc_start: 0.8104 (tptt) cc_final: 0.7578 (tptt) REVERT: E 124 PHE cc_start: 0.7928 (m-10) cc_final: 0.7598 (m-10) REVERT: E 211 ASP cc_start: 0.8530 (t70) cc_final: 0.8275 (t70) REVERT: E 292 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7841 (t70) REVERT: E 355 MET cc_start: 0.6827 (mtt) cc_final: 0.6610 (mmm) outliers start: 52 outliers final: 32 residues processed: 336 average time/residue: 0.1168 time to fit residues: 59.9188 Evaluate side-chains 307 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 354 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 12 ASN ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097056 restraints weight = 27828.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099843 restraints weight = 13927.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.101687 restraints weight = 8456.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102829 restraints weight = 5873.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103679 restraints weight = 4563.150| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15240 Z= 0.263 Angle : 0.774 8.250 20690 Z= 0.378 Chirality : 0.050 0.258 2280 Planarity : 0.006 0.055 2630 Dihedral : 27.723 178.901 2330 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 3.96 % Allowed : 14.70 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1830 helix: 0.46 (0.19), residues: 755 sheet: -0.74 (0.28), residues: 305 loop : 0.29 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 335 TYR 0.013 0.002 TYR A 133 PHE 0.023 0.002 PHE B 90 TRP 0.017 0.002 TRP A 340 HIS 0.016 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00623 (15240) covalent geometry : angle 0.77379 (20690) hydrogen bonds : bond 0.03967 ( 740) hydrogen bonds : angle 5.33587 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8710 (t0) cc_final: 0.8364 (t0) REVERT: A 91 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.7006 (t80) REVERT: A 117 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7529 (mt-10) REVERT: A 120 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9115 (p) REVERT: A 226 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7993 (mm-30) REVERT: A 249 THR cc_start: 0.8966 (m) cc_final: 0.8593 (p) REVERT: A 291 LYS cc_start: 0.8969 (tttt) cc_final: 0.7823 (mptt) REVERT: A 314 GLN cc_start: 0.8118 (tt0) cc_final: 0.7707 (mt0) REVERT: B 154 ASP cc_start: 0.8165 (t0) cc_final: 0.7776 (m-30) REVERT: B 257 CYS cc_start: 0.8605 (t) cc_final: 0.7857 (p) REVERT: B 259 GLU cc_start: 0.7935 (tp30) cc_final: 0.7653 (tp30) REVERT: B 290 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8342 (mtt180) REVERT: B 291 LYS cc_start: 0.8540 (tttt) cc_final: 0.7521 (mttt) REVERT: B 314 GLN cc_start: 0.7758 (tp40) cc_final: 0.7479 (tp40) REVERT: C 44 MET cc_start: 0.6676 (mmm) cc_final: 0.6173 (mmm) REVERT: C 68 LYS cc_start: 0.8555 (mmmm) cc_final: 0.8269 (mttt) REVERT: C 191 LYS cc_start: 0.9032 (tttt) cc_final: 0.8822 (tttp) REVERT: C 284 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7459 (mmtp) REVERT: C 334 GLU cc_start: 0.8383 (mp0) cc_final: 0.8179 (mp0) REVERT: D 56 ASP cc_start: 0.7276 (m-30) cc_final: 0.6854 (t0) REVERT: D 191 LYS cc_start: 0.8806 (tttt) cc_final: 0.8484 (mtpp) REVERT: D 270 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6881 (tm-30) REVERT: D 283 MET cc_start: 0.8261 (mmp) cc_final: 0.7352 (ttm) REVERT: E 84 LYS cc_start: 0.8210 (tptt) cc_final: 0.7615 (tptt) REVERT: E 211 ASP cc_start: 0.8533 (t70) cc_final: 0.8277 (t70) REVERT: E 225 ASN cc_start: 0.8076 (m-40) cc_final: 0.7856 (t0) REVERT: E 292 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7853 (t0) outliers start: 62 outliers final: 45 residues processed: 302 average time/residue: 0.1147 time to fit residues: 53.2444 Evaluate side-chains 301 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102801 restraints weight = 27118.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105705 restraints weight = 13478.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107613 restraints weight = 8127.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108902 restraints weight = 5616.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109640 restraints weight = 4286.614| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15240 Z= 0.122 Angle : 0.655 7.467 20690 Z= 0.315 Chirality : 0.045 0.190 2280 Planarity : 0.005 0.050 2630 Dihedral : 26.974 175.392 2330 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 3.39 % Allowed : 15.27 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1830 helix: 0.41 (0.18), residues: 800 sheet: -0.79 (0.27), residues: 305 loop : 0.47 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 116 TYR 0.013 0.001 TYR C 306 PHE 0.030 0.001 PHE C 352 TRP 0.021 0.002 TRP E 79 HIS 0.007 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00281 (15240) covalent geometry : angle 0.65544 (20690) hydrogen bonds : bond 0.03072 ( 740) hydrogen bonds : angle 5.05049 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.627 Fit side-chains REVERT: A 78 ASN cc_start: 0.8610 (t0) cc_final: 0.7802 (t0) REVERT: A 81 ASP cc_start: 0.8220 (m-30) cc_final: 0.7686 (m-30) REVERT: A 91 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6815 (t80) REVERT: A 214 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 226 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 249 THR cc_start: 0.8906 (m) cc_final: 0.8626 (p) REVERT: A 291 LYS cc_start: 0.8910 (tttt) cc_final: 0.7776 (mptt) REVERT: A 314 GLN cc_start: 0.8110 (tt0) cc_final: 0.7697 (mt0) REVERT: A 336 LYS cc_start: 0.8213 (ptmt) cc_final: 0.7729 (pttp) REVERT: B 154 ASP cc_start: 0.7990 (t0) cc_final: 0.7610 (m-30) REVERT: B 191 LYS cc_start: 0.8811 (tttt) cc_final: 0.8146 (ttmt) REVERT: B 257 CYS cc_start: 0.8595 (t) cc_final: 0.7826 (p) REVERT: B 259 GLU cc_start: 0.7973 (tp30) cc_final: 0.7768 (tp30) REVERT: B 291 LYS cc_start: 0.8463 (tttt) cc_final: 0.7527 (mttm) REVERT: B 314 GLN cc_start: 0.7621 (tp40) cc_final: 0.7256 (tp40) REVERT: C 44 MET cc_start: 0.6537 (mmm) cc_final: 0.6158 (mmm) REVERT: C 68 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8241 (mttt) REVERT: C 191 LYS cc_start: 0.9031 (tttt) cc_final: 0.8813 (tttp) REVERT: C 270 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6104 (tm-30) REVERT: D 56 ASP cc_start: 0.7088 (m-30) cc_final: 0.6748 (t0) REVERT: D 191 LYS cc_start: 0.8730 (tttt) cc_final: 0.8471 (mtpp) REVERT: D 270 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 283 MET cc_start: 0.8239 (mmp) cc_final: 0.7431 (ttm) REVERT: D 354 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 21 PHE cc_start: 0.7829 (m-80) cc_final: 0.6947 (m-80) REVERT: E 41 GLN cc_start: 0.7657 (mp10) cc_final: 0.7364 (tt0) REVERT: E 84 LYS cc_start: 0.8190 (tptt) cc_final: 0.7579 (tptt) REVERT: E 225 ASN cc_start: 0.8010 (m-40) cc_final: 0.7790 (t0) REVERT: E 292 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7930 (t70) outliers start: 53 outliers final: 37 residues processed: 329 average time/residue: 0.1173 time to fit residues: 58.9589 Evaluate side-chains 310 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN E 12 ASN E 88 HIS E 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.099223 restraints weight = 27345.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102021 restraints weight = 13727.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103818 restraints weight = 8351.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105073 restraints weight = 5856.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105848 restraints weight = 4484.068| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15240 Z= 0.200 Angle : 0.710 8.615 20690 Z= 0.343 Chirality : 0.048 0.273 2280 Planarity : 0.005 0.049 2630 Dihedral : 26.925 172.447 2330 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.25 % Favored : 94.64 % Rotamer: Outliers : 4.22 % Allowed : 15.97 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1830 helix: 0.43 (0.19), residues: 780 sheet: -0.65 (0.28), residues: 295 loop : 0.45 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 290 TYR 0.012 0.001 TYR A 133 PHE 0.022 0.002 PHE C 352 TRP 0.017 0.002 TRP E 79 HIS 0.014 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00474 (15240) covalent geometry : angle 0.71034 (20690) hydrogen bonds : bond 0.03560 ( 740) hydrogen bonds : angle 5.14306 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 0.675 Fit side-chains REVERT: A 78 ASN cc_start: 0.8628 (t0) cc_final: 0.7827 (t0) REVERT: A 81 ASP cc_start: 0.8216 (m-30) cc_final: 0.7716 (m-30) REVERT: A 91 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6823 (t80) REVERT: A 249 THR cc_start: 0.8911 (m) cc_final: 0.8600 (p) REVERT: A 291 LYS cc_start: 0.8904 (tttt) cc_final: 0.7896 (mptt) REVERT: A 336 LYS cc_start: 0.8380 (ptmt) cc_final: 0.7786 (pttp) REVERT: B 154 ASP cc_start: 0.8120 (t0) cc_final: 0.7709 (m-30) REVERT: B 191 LYS cc_start: 0.8859 (tttt) cc_final: 0.8189 (ttmt) REVERT: B 257 CYS cc_start: 0.8557 (t) cc_final: 0.7824 (p) REVERT: B 259 GLU cc_start: 0.7976 (tp30) cc_final: 0.7732 (tp30) REVERT: B 290 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.7854 (mtt-85) REVERT: B 291 LYS cc_start: 0.8468 (tttt) cc_final: 0.7475 (mttt) REVERT: B 314 GLN cc_start: 0.7717 (tp40) cc_final: 0.7410 (tp40) REVERT: C 44 MET cc_start: 0.6645 (mmm) cc_final: 0.6346 (mmm) REVERT: C 68 LYS cc_start: 0.8561 (mmmm) cc_final: 0.8283 (mttt) REVERT: C 191 LYS cc_start: 0.9065 (tttt) cc_final: 0.8803 (tttp) REVERT: D 56 ASP cc_start: 0.7127 (m-30) cc_final: 0.6786 (t0) REVERT: D 191 LYS cc_start: 0.8742 (tttt) cc_final: 0.8483 (mtpp) REVERT: D 270 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7086 (tm-30) REVERT: D 283 MET cc_start: 0.8180 (mmp) cc_final: 0.7373 (ttm) REVERT: D 346 LEU cc_start: 0.9027 (tp) cc_final: 0.8808 (tp) REVERT: E 21 PHE cc_start: 0.7731 (m-80) cc_final: 0.7301 (m-80) REVERT: E 84 LYS cc_start: 0.8192 (tptt) cc_final: 0.7597 (tptt) REVERT: E 225 ASN cc_start: 0.8058 (m-40) cc_final: 0.7834 (t0) REVERT: E 292 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7939 (t70) outliers start: 66 outliers final: 52 residues processed: 312 average time/residue: 0.1197 time to fit residues: 57.1521 Evaluate side-chains 310 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 12 ASN E 88 HIS E 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103094 restraints weight = 27220.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106007 restraints weight = 13596.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107904 restraints weight = 8195.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109075 restraints weight = 5657.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109957 restraints weight = 4380.512| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15240 Z= 0.127 Angle : 0.662 8.190 20690 Z= 0.318 Chirality : 0.045 0.232 2280 Planarity : 0.005 0.049 2630 Dihedral : 26.552 170.376 2330 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.08 % Favored : 94.70 % Rotamer: Outliers : 3.51 % Allowed : 17.12 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1830 helix: 0.39 (0.19), residues: 795 sheet: -0.73 (0.28), residues: 300 loop : 0.51 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.013 0.001 TYR D 306 PHE 0.019 0.001 PHE C 352 TRP 0.018 0.002 TRP E 79 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00295 (15240) covalent geometry : angle 0.66225 (20690) hydrogen bonds : bond 0.03084 ( 740) hydrogen bonds : angle 5.01353 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8589 (t0) cc_final: 0.7701 (t0) REVERT: A 81 ASP cc_start: 0.8251 (m-30) cc_final: 0.7692 (m-30) REVERT: A 91 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6847 (t80) REVERT: A 206 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8053 (ttm170) REVERT: A 249 THR cc_start: 0.8925 (m) cc_final: 0.8642 (p) REVERT: A 336 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7786 (pttp) REVERT: B 191 LYS cc_start: 0.8799 (tttt) cc_final: 0.8126 (ttmt) REVERT: B 257 CYS cc_start: 0.8573 (t) cc_final: 0.7815 (p) REVERT: B 291 LYS cc_start: 0.8509 (tttt) cc_final: 0.7553 (mttt) REVERT: B 314 GLN cc_start: 0.7619 (tp40) cc_final: 0.7190 (tp40) REVERT: B 349 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7822 (mp) REVERT: C 44 MET cc_start: 0.6729 (mmm) cc_final: 0.6460 (mmm) REVERT: C 128 ASN cc_start: 0.7105 (t0) cc_final: 0.6686 (t0) REVERT: C 191 LYS cc_start: 0.9006 (tttt) cc_final: 0.8773 (tttp) REVERT: C 270 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6065 (tm-30) REVERT: D 56 ASP cc_start: 0.7101 (m-30) cc_final: 0.6767 (t0) REVERT: D 61 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8574 (mmtp) REVERT: D 191 LYS cc_start: 0.8685 (tttt) cc_final: 0.8472 (mtpp) REVERT: D 270 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7331 (tm-30) REVERT: D 283 MET cc_start: 0.8214 (mmp) cc_final: 0.7363 (ttm) REVERT: E 84 LYS cc_start: 0.8191 (tptt) cc_final: 0.7564 (tptt) REVERT: E 292 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7554 (t70) outliers start: 55 outliers final: 43 residues processed: 324 average time/residue: 0.1175 time to fit residues: 58.2837 Evaluate side-chains 313 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 88 HIS E 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.097515 restraints weight = 28048.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100273 restraints weight = 14120.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.102101 restraints weight = 8612.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103330 restraints weight = 6021.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104072 restraints weight = 4634.183| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15240 Z= 0.272 Angle : 0.783 8.584 20690 Z= 0.382 Chirality : 0.050 0.262 2280 Planarity : 0.006 0.051 2630 Dihedral : 27.013 173.850 2330 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.46 % Favored : 94.37 % Rotamer: Outliers : 4.03 % Allowed : 17.89 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1830 helix: 0.40 (0.19), residues: 780 sheet: -1.09 (0.29), residues: 270 loop : 0.12 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.014 0.002 TYR B 198 PHE 0.028 0.002 PHE C 352 TRP 0.019 0.002 TRP E 79 HIS 0.007 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00646 (15240) covalent geometry : angle 0.78297 (20690) hydrogen bonds : bond 0.03981 ( 740) hydrogen bonds : angle 5.30981 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 0.624 Fit side-chains REVERT: A 78 ASN cc_start: 0.8688 (t0) cc_final: 0.8386 (t0) REVERT: A 91 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6927 (t80) REVERT: A 249 THR cc_start: 0.8926 (m) cc_final: 0.8563 (p) REVERT: A 291 LYS cc_start: 0.8532 (tttt) cc_final: 0.7674 (mptt) REVERT: A 336 LYS cc_start: 0.8401 (ptmt) cc_final: 0.7771 (pttp) REVERT: B 191 LYS cc_start: 0.8865 (tttt) cc_final: 0.8217 (ttmt) REVERT: B 257 CYS cc_start: 0.8600 (t) cc_final: 0.7806 (p) REVERT: B 291 LYS cc_start: 0.8660 (tttt) cc_final: 0.7692 (mptt) REVERT: B 314 GLN cc_start: 0.7743 (tp40) cc_final: 0.7522 (tp40) REVERT: B 349 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7955 (mp) REVERT: C 44 MET cc_start: 0.6617 (mmm) cc_final: 0.6304 (mmm) REVERT: C 284 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7420 (mmtp) REVERT: D 56 ASP cc_start: 0.7136 (m-30) cc_final: 0.6772 (t0) REVERT: D 191 LYS cc_start: 0.8761 (tttt) cc_final: 0.8509 (mtpp) REVERT: D 270 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7246 (tm-30) REVERT: D 283 MET cc_start: 0.8215 (mmp) cc_final: 0.7397 (ttm) REVERT: D 299 MET cc_start: 0.8252 (mtm) cc_final: 0.7992 (mtm) REVERT: E 84 LYS cc_start: 0.8204 (tptt) cc_final: 0.7600 (tptt) REVERT: E 225 ASN cc_start: 0.8167 (m-40) cc_final: 0.7921 (t0) REVERT: E 292 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7916 (t70) outliers start: 63 outliers final: 53 residues processed: 310 average time/residue: 0.1127 time to fit residues: 54.2297 Evaluate side-chains 306 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 250 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 101 HIS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain E residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 0.3980 chunk 150 optimal weight: 0.0270 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 0.0570 chunk 96 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS B 92 ASN C 115 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106023 restraints weight = 27245.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108946 restraints weight = 13562.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110832 restraints weight = 8198.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112148 restraints weight = 5710.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112961 restraints weight = 4363.064| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15240 Z= 0.116 Angle : 0.680 11.514 20690 Z= 0.329 Chirality : 0.045 0.202 2280 Planarity : 0.005 0.051 2630 Dihedral : 26.508 172.006 2330 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.32 % Favored : 95.46 % Rotamer: Outliers : 2.17 % Allowed : 20.26 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1830 helix: 0.62 (0.19), residues: 755 sheet: -0.81 (0.28), residues: 290 loop : 0.46 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 290 TYR 0.040 0.001 TYR E 166 PHE 0.022 0.001 PHE C 352 TRP 0.018 0.002 TRP C 340 HIS 0.016 0.001 HIS E 101 Details of bonding type rmsd covalent geometry : bond 0.00254 (15240) covalent geometry : angle 0.67954 (20690) hydrogen bonds : bond 0.03003 ( 740) hydrogen bonds : angle 5.05545 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.8506 (t0) cc_final: 0.7767 (t0) REVERT: A 81 ASP cc_start: 0.8041 (m-30) cc_final: 0.7750 (m-30) REVERT: A 115 ASN cc_start: 0.8671 (t0) cc_final: 0.8360 (t0) REVERT: A 119 MET cc_start: 0.8992 (ttp) cc_final: 0.8708 (ttt) REVERT: A 336 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7736 (pttp) REVERT: B 65 LEU cc_start: 0.8158 (mt) cc_final: 0.7944 (mt) REVERT: B 191 LYS cc_start: 0.8814 (tttt) cc_final: 0.8159 (ttmt) REVERT: B 257 CYS cc_start: 0.8417 (t) cc_final: 0.7801 (p) REVERT: B 291 LYS cc_start: 0.8507 (tttt) cc_final: 0.7619 (mttt) REVERT: B 314 GLN cc_start: 0.7600 (tp40) cc_final: 0.7248 (tp40) REVERT: B 349 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7923 (mp) REVERT: C 44 MET cc_start: 0.6661 (mmm) cc_final: 0.6313 (mmm) REVERT: C 128 ASN cc_start: 0.7013 (t0) cc_final: 0.6602 (t0) REVERT: C 132 MET cc_start: 0.8428 (ppp) cc_final: 0.8035 (ppp) REVERT: C 270 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6116 (tm-30) REVERT: D 283 MET cc_start: 0.8140 (mmp) cc_final: 0.7356 (ttm) REVERT: D 355 MET cc_start: 0.6582 (mtm) cc_final: 0.5758 (mmm) REVERT: E 84 LYS cc_start: 0.8161 (tptt) cc_final: 0.7529 (tptt) REVERT: E 280 ASN cc_start: 0.8771 (m110) cc_final: 0.8396 (m-40) REVERT: E 292 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7271 (t70) outliers start: 34 outliers final: 24 residues processed: 324 average time/residue: 0.1100 time to fit residues: 55.5006 Evaluate side-chains 310 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 87 HIS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 252 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 88 HIS C 115 ASN C 354 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 41 GLN E 88 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103567 restraints weight = 27337.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106448 restraints weight = 13693.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108323 restraints weight = 8308.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109603 restraints weight = 5775.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110378 restraints weight = 4424.137| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15240 Z= 0.135 Angle : 0.697 10.489 20690 Z= 0.336 Chirality : 0.045 0.212 2280 Planarity : 0.005 0.048 2630 Dihedral : 26.118 167.939 2330 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 2.24 % Allowed : 20.26 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1830 helix: 0.66 (0.19), residues: 755 sheet: -0.72 (0.28), residues: 310 loop : 0.47 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 116 TYR 0.039 0.001 TYR E 166 PHE 0.021 0.002 PHE C 352 TRP 0.018 0.002 TRP E 79 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00316 (15240) covalent geometry : angle 0.69719 (20690) hydrogen bonds : bond 0.03217 ( 740) hydrogen bonds : angle 4.93355 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2414.05 seconds wall clock time: 42 minutes 45.54 seconds (2565.54 seconds total)