Starting phenix.real_space_refine on Thu Jul 2 11:06:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g3d_50994/07_2026/9g3d_50994.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g3d_50994/07_2026/9g3d_50994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g3d_50994/07_2026/9g3d_50994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g3d_50994/07_2026/9g3d_50994.map" model { file = "/net/cci-nas-00/data/ceres_data/9g3d_50994/07_2026/9g3d_50994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g3d_50994/07_2026/9g3d_50994.cif" } resolution = 3.24 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= 0.011 sd= 0.124 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 28 5.16 5 C 5448 2.51 5 N 1322 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8210 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3155 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain: "B" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3200 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 887 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 878 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 2.07, per 1000 atoms: 0.25 Number of scatterers: 8210 At special positions: 0 Unit cell: (69.496, 88.914, 119.574, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 2 15.00 O 1410 8.00 N 1322 7.00 C 5448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 102 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 414.3 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 68.8% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.812A pdb=" N LEU A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.728A pdb=" N ASP A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.558A pdb=" N ARG A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 79 removed outlier: 4.085A pdb=" N PHE A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 88 through 125 removed outlier: 4.169A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.885A pdb=" N SER A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 175 removed outlier: 3.735A pdb=" N GLU A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 226 removed outlier: 4.443A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.575A pdb=" N VAL A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 263 through 288 removed outlier: 4.456A pdb=" N GLY A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 345 removed outlier: 3.678A pdb=" N LEU A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Proline residue: A 340 - end of helix Processing helix chain 'A' and resid 348 through 392 removed outlier: 4.368A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 370 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 377 " --> pdb=" O TRP A 373 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.847A pdb=" N LEU B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 50 through 53 removed outlier: 3.781A pdb=" N TRP B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 54 through 79 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.636A pdb=" N ILE B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 125 removed outlier: 4.150A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.883A pdb=" N SER B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 175 removed outlier: 3.740A pdb=" N GLU B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.535A pdb=" N VAL B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 227 removed outlier: 4.306A pdb=" N MET B 196 " --> pdb=" O GLN B 192 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 262 Processing helix chain 'B' and resid 263 through 290 removed outlier: 4.375A pdb=" N GLY B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 330 removed outlier: 3.725A pdb=" N LEU B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.598A pdb=" N LEU B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Proline residue: B 340 - end of helix Processing helix chain 'B' and resid 348 through 392 removed outlier: 3.723A pdb=" N THR B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B 377 " --> pdb=" O TRP B 373 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLU B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 11 Processing sheet with id=AA2, first strand: chain 'C' and resid 18 through 19 removed outlier: 7.335A pdb=" N VAL C 18 " --> pdb=" O SER C 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 27 Processing sheet with id=AA4, first strand: chain 'C' and resid 64 through 66 removed outlier: 6.605A pdb=" N TRP C 42 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA C 56 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET C 40 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 64 through 66 removed outlier: 6.605A pdb=" N TRP C 42 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA C 56 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET C 40 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.558A pdb=" N GLY D 16 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 118 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 120 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET D 40 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA D 56 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP D 42 " --> pdb=" O VAL D 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.558A pdb=" N GLY D 16 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 118 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 120 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 23 through 27 570 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1331 1.33 - 1.45: 2533 1.45 - 1.57: 4536 1.57 - 1.69: 4 1.69 - 1.82: 50 Bond restraints: 8454 Sorted by residual: bond pdb=" CA PHE A 52 " pdb=" C PHE A 52 " ideal model delta sigma weight residual 1.523 1.502 0.022 1.80e-02 3.09e+03 1.43e+00 bond pdb=" CB MET B 205 " pdb=" CG MET B 205 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.16e+00 bond pdb=" CB THR A 195 " pdb=" CG2 THR A 195 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 bond pdb=" SD MET B 205 " pdb=" CE MET B 205 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 7.40e-01 bond pdb=" CG MET B 205 " pdb=" SD MET B 205 " ideal model delta sigma weight residual 1.803 1.783 0.020 2.50e-02 1.60e+03 6.66e-01 ... (remaining 8449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 11367 1.74 - 3.48: 115 3.48 - 5.21: 15 5.21 - 6.95: 7 6.95 - 8.69: 2 Bond angle restraints: 11506 Sorted by residual: angle pdb=" CA PHE A 52 " pdb=" C PHE A 52 " pdb=" N TRP A 53 " ideal model delta sigma weight residual 118.27 113.86 4.41 1.59e+00 3.96e-01 7.70e+00 angle pdb=" CB MET A 196 " pdb=" CG MET A 196 " pdb=" SD MET A 196 " ideal model delta sigma weight residual 112.70 121.01 -8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" CA LEU B 181 " pdb=" CB LEU B 181 " pdb=" CG LEU B 181 " ideal model delta sigma weight residual 116.30 124.99 -8.69 3.50e+00 8.16e-02 6.16e+00 angle pdb=" N GLN A 273 " pdb=" CA GLN A 273 " pdb=" CB GLN A 273 " ideal model delta sigma weight residual 110.12 113.42 -3.30 1.47e+00 4.63e-01 5.02e+00 angle pdb=" CA ARG A 167 " pdb=" CB ARG A 167 " pdb=" CG ARG A 167 " ideal model delta sigma weight residual 114.10 110.22 3.88 2.00e+00 2.50e-01 3.77e+00 ... (remaining 11501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4273 17.42 - 34.85: 411 34.85 - 52.27: 93 52.27 - 69.70: 12 69.70 - 87.12: 5 Dihedral angle restraints: 4794 sinusoidal: 1854 harmonic: 2940 Sorted by residual: dihedral pdb=" CA SER A 54 " pdb=" C SER A 54 " pdb=" N LEU A 55 " pdb=" CA LEU A 55 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LYS B 8 " pdb=" C LYS B 8 " pdb=" N PRO B 9 " pdb=" CA PRO B 9 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PHE B 6 " pdb=" C PHE B 6 " pdb=" N PRO B 7 " pdb=" CA PRO B 7 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 4791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 782 0.028 - 0.056: 301 0.056 - 0.084: 119 0.084 - 0.113: 47 0.113 - 0.141: 11 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA VAL C 106 " pdb=" N VAL C 106 " pdb=" C VAL C 106 " pdb=" CB VAL C 106 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA PRO A 234 " pdb=" N PRO A 234 " pdb=" C PRO A 234 " pdb=" CB PRO A 234 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CB VAL B 261 " pdb=" CA VAL B 261 " pdb=" CG1 VAL B 261 " pdb=" CG2 VAL B 261 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 1257 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 295 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 296 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 294 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 295 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 162 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C TYR A 162 " 0.025 2.00e-02 2.50e+03 pdb=" O TYR A 162 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 163 " -0.008 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2041 2.80 - 3.32: 7812 3.32 - 3.85: 13619 3.85 - 4.37: 15318 4.37 - 4.90: 27689 Nonbonded interactions: 66479 Sorted by model distance: nonbonded pdb=" O ILE D 36 " pdb=" OG SER D 59 " model vdw 2.269 3.040 nonbonded pdb=" O TRP A 83 " pdb=" OG SER A 87 " model vdw 2.283 3.040 nonbonded pdb=" O VAL C 35 " pdb=" NH2 ARG C 78 " model vdw 2.292 3.120 nonbonded pdb=" O ILE C 36 " pdb=" OG SER C 59 " model vdw 2.293 3.040 nonbonded pdb=" O TRP B 83 " pdb=" OG SER B 87 " model vdw 2.296 3.040 ... (remaining 66474 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' selection = (chain 'B' and (resid 6 through 393 or resid 501)) } ncs_group { reference = (chain 'C' and resid 8 through 121) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8456 Z= 0.135 Angle : 0.491 8.690 11510 Z= 0.260 Chirality : 0.038 0.141 1260 Planarity : 0.004 0.060 1416 Dihedral : 14.249 87.123 2916 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: 0.87 (0.27), residues: 1002 helix: 1.50 (0.20), residues: 653 sheet: -0.43 (0.52), residues: 98 loop : -1.40 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.016 0.001 TYR B 368 PHE 0.015 0.001 PHE A 389 TRP 0.008 0.001 TRP A 53 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8454) covalent geometry : angle 0.49060 / 0.26 (11506) SS BOND : bond 0.00285 / 0.14 ( 2) SS BOND : angle 1.13718 / 0.68 ( 4) hydrogen bonds : bond 0.12118 / 8.45 ( 554) hydrogen bonds : angle 6.11768 / 4.65 ( 1671) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.347 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0921 time to fit residues: 11.0595 Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN C 38 ASN ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.166809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127143 restraints weight = 9449.305| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.07 r_work: 0.3288 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8456 Z= 0.122 Angle : 0.482 8.290 11510 Z= 0.255 Chirality : 0.039 0.142 1260 Planarity : 0.004 0.056 1416 Dihedral : 5.273 50.497 1170 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.48 % Allowed : 4.88 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.27), residues: 1002 helix: 2.05 (0.20), residues: 654 sheet: -0.13 (0.55), residues: 94 loop : -1.48 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 78 TYR 0.012 0.001 TYR B 368 PHE 0.035 0.001 PHE A 389 TRP 0.008 0.001 TRP A 53 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8454) covalent geometry : angle 0.48202 / 0.25 (11506) SS BOND : bond 0.00234 / 0.12 ( 2) SS BOND : angle 1.07718 / 0.67 ( 4) hydrogen bonds : bond 0.04682 / 3.13 ( 554) hydrogen bonds : angle 4.16113 / 3.10 ( 1671) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.290 Fit side-chains REVERT: A 273 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7587 (mp10) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.0906 time to fit residues: 9.2137 Evaluate side-chains 71 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 307 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 0.0770 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128507 restraints weight = 9315.063| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.96 r_work: 0.3297 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8456 Z= 0.114 Angle : 0.454 7.272 11510 Z= 0.240 Chirality : 0.038 0.139 1260 Planarity : 0.004 0.055 1416 Dihedral : 5.173 50.439 1170 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.71 % Allowed : 6.31 % Favored : 92.98 % 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: 1.66 (0.27), residues: 1002 helix: 2.19 (0.20), residues: 655 sheet: 0.12 (0.56), residues: 93 loop : -1.48 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 51 TYR 0.013 0.001 TYR B 162 PHE 0.026 0.001 PHE A 389 TRP 0.009 0.001 TRP A 53 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 8454) covalent geometry : angle 0.45400 / 0.24 (11506) SS BOND : bond 0.00182 / 0.09 ( 2) SS BOND : angle 0.99360 / 0.62 ( 4) hydrogen bonds : bond 0.04355 / 2.91 ( 554) hydrogen bonds : angle 3.90634 / 2.89 ( 1671) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.296 Fit side-chains REVERT: A 273 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7607 (mp10) REVERT: B 196 MET cc_start: 0.7978 (tpp) cc_final: 0.7574 (tpp) outliers start: 6 outliers final: 3 residues processed: 75 average time/residue: 0.0926 time to fit residues: 9.8420 Evaluate side-chains 73 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 86 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.168786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.128428 restraints weight = 9592.361| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.13 r_work: 0.3292 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8456 Z= 0.112 Angle : 0.450 6.592 11510 Z= 0.238 Chirality : 0.038 0.140 1260 Planarity : 0.003 0.053 1416 Dihedral : 5.134 50.480 1170 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.95 % Allowed : 7.14 % Favored : 91.90 % 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: 1.75 (0.27), residues: 1002 helix: 2.25 (0.20), residues: 655 sheet: 0.24 (0.54), residues: 100 loop : -1.51 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 51 TYR 0.013 0.001 TYR C 101 PHE 0.021 0.001 PHE A 389 TRP 0.008 0.001 TRP A 53 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8454) covalent geometry : angle 0.44988 / 0.24 (11506) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 0.95867 / 0.59 ( 4) hydrogen bonds : bond 0.04233 / 2.82 ( 554) hydrogen bonds : angle 3.80656 / 2.81 ( 1671) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.289 Fit side-chains REVERT: A 273 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7603 (mp10) REVERT: B 196 MET cc_start: 0.7864 (tpp) cc_final: 0.7558 (tpp) outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 0.0930 time to fit residues: 9.8536 Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 307 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.168128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128044 restraints weight = 9500.516| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.24 r_work: 0.3284 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8456 Z= 0.121 Angle : 0.453 6.396 11510 Z= 0.239 Chirality : 0.038 0.138 1260 Planarity : 0.003 0.052 1416 Dihedral : 5.125 50.814 1170 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.95 % Allowed : 8.45 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.27), residues: 1002 helix: 2.24 (0.20), residues: 655 sheet: 0.31 (0.54), residues: 100 loop : -1.52 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 51 TYR 0.014 0.001 TYR B 162 PHE 0.019 0.001 PHE A 389 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8454) covalent geometry : angle 0.45231 / 0.24 (11506) SS BOND : bond 0.00222 / 0.11 ( 2) SS BOND : angle 1.01621 / 0.62 ( 4) hydrogen bonds : bond 0.04335 / 2.88 ( 554) hydrogen bonds : angle 3.79717 / 2.80 ( 1671) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.408 Fit side-chains REVERT: A 193 GLU cc_start: 0.7954 (tp30) cc_final: 0.7402 (mm-30) REVERT: A 273 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: A 317 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8529 (ttp) REVERT: B 196 MET cc_start: 0.7753 (tpp) cc_final: 0.7502 (tpp) REVERT: B 214 MET cc_start: 0.8621 (mtt) cc_final: 0.8268 (mtt) REVERT: D 89 MET cc_start: 0.8180 (ptm) cc_final: 0.7898 (ptm) outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.0833 time to fit residues: 9.1452 Evaluate side-chains 75 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126008 restraints weight = 9320.968| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.72 r_work: 0.3279 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8456 Z= 0.155 Angle : 0.485 6.449 11510 Z= 0.258 Chirality : 0.039 0.140 1260 Planarity : 0.004 0.052 1416 Dihedral : 5.233 51.152 1170 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.07 % Allowed : 9.40 % Favored : 89.52 % 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: 1.63 (0.27), residues: 1002 helix: 2.12 (0.20), residues: 655 sheet: 0.23 (0.53), residues: 101 loop : -1.48 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 51 TYR 0.016 0.001 TYR B 162 PHE 0.019 0.001 PHE A 389 TRP 0.005 0.001 TRP A 53 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 8454) covalent geometry : angle 0.48468 / 0.26 (11506) SS BOND : bond 0.00297 / 0.15 ( 2) SS BOND : angle 1.25365 / 0.75 ( 4) hydrogen bonds : bond 0.04744 / 3.15 ( 554) hydrogen bonds : angle 3.90954 / 2.88 ( 1671) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.291 Fit side-chains REVERT: A 193 GLU cc_start: 0.8165 (tp30) cc_final: 0.7651 (mm-30) REVERT: A 273 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: A 317 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8646 (ttp) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.0930 time to fit residues: 10.8213 Evaluate side-chains 80 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.167349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126207 restraints weight = 9537.929| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.31 r_work: 0.3255 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8456 Z= 0.133 Angle : 0.471 6.564 11510 Z= 0.248 Chirality : 0.039 0.137 1260 Planarity : 0.004 0.052 1416 Dihedral : 5.223 50.794 1170 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.07 % Allowed : 10.00 % Favored : 88.93 % 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: 1.69 (0.27), residues: 1002 helix: 2.17 (0.20), residues: 655 sheet: 0.30 (0.54), residues: 99 loop : -1.47 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 51 TYR 0.014 0.001 TYR B 162 PHE 0.017 0.001 PHE A 389 TRP 0.005 0.001 TRP A 53 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8454) covalent geometry : angle 0.47017 / 0.25 (11506) SS BOND : bond 0.00233 / 0.12 ( 2) SS BOND : angle 1.10176 / 0.67 ( 4) hydrogen bonds : bond 0.04532 / 3.01 ( 554) hydrogen bonds : angle 3.85324 / 2.84 ( 1671) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.290 Fit side-chains REVERT: A 193 GLU cc_start: 0.7959 (tp30) cc_final: 0.7400 (mm-30) REVERT: A 273 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: B 196 MET cc_start: 0.8193 (tpp) cc_final: 0.7696 (tpp) REVERT: D 89 MET cc_start: 0.8173 (ptm) cc_final: 0.7941 (ptm) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.0897 time to fit residues: 10.2989 Evaluate side-chains 79 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 67 optimal weight: 0.0980 chunk 90 optimal weight: 0.8980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128651 restraints weight = 9248.824| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.99 r_work: 0.3359 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8456 Z= 0.096 Angle : 0.433 6.180 11510 Z= 0.227 Chirality : 0.037 0.136 1260 Planarity : 0.003 0.052 1416 Dihedral : 5.058 48.805 1170 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.71 % Allowed : 10.48 % Favored : 88.81 % 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: 1.94 (0.27), residues: 1002 helix: 2.40 (0.20), residues: 655 sheet: 0.10 (0.52), residues: 107 loop : -1.42 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 167 TYR 0.009 0.001 TYR A 162 PHE 0.015 0.001 PHE A 389 TRP 0.012 0.001 TRP A 53 HIS 0.002 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.10 ( 8454) covalent geometry : angle 0.43245 / 0.23 (11506) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 0.76441 / 0.49 ( 4) hydrogen bonds : bond 0.03779 / 2.52 ( 554) hydrogen bonds : angle 3.61245 / 2.66 ( 1671) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7667 (mp10) REVERT: B 82 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8024 (tmt170) REVERT: B 196 MET cc_start: 0.8196 (tpp) cc_final: 0.7672 (tpp) REVERT: D 38 ASN cc_start: 0.7721 (m-40) cc_final: 0.7365 (m-40) REVERT: D 89 MET cc_start: 0.8178 (ptm) cc_final: 0.7789 (ptm) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.1013 time to fit residues: 10.7783 Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.169519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128130 restraints weight = 9503.713| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.25 r_work: 0.3280 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8456 Z= 0.128 Angle : 0.480 8.360 11510 Z= 0.250 Chirality : 0.038 0.137 1260 Planarity : 0.004 0.052 1416 Dihedral : 5.058 50.197 1170 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.83 % Allowed : 10.83 % Favored : 88.33 % 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: 1.85 (0.27), residues: 1002 helix: 2.29 (0.20), residues: 655 sheet: 0.40 (0.54), residues: 99 loop : -1.44 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 51 TYR 0.015 0.001 TYR B 162 PHE 0.017 0.001 PHE A 389 TRP 0.006 0.001 TRP A 53 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8454) covalent geometry : angle 0.47946 / 0.25 (11506) SS BOND : bond 0.00217 / 0.11 ( 2) SS BOND : angle 1.04174 / 0.63 ( 4) hydrogen bonds : bond 0.04269 / 2.84 ( 554) hydrogen bonds : angle 3.74770 / 2.76 ( 1671) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: B 82 ARG cc_start: 0.8295 (ttm170) cc_final: 0.7989 (tmt170) REVERT: B 196 MET cc_start: 0.8168 (tpp) cc_final: 0.7668 (tpp) REVERT: D 89 MET cc_start: 0.8180 (ptm) cc_final: 0.7855 (ptm) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.0994 time to fit residues: 10.0535 Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 3 optimal weight: 0.0000 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.168609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131550 restraints weight = 9249.361| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.69 r_work: 0.3360 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8456 Z= 0.105 Angle : 0.456 7.591 11510 Z= 0.238 Chirality : 0.037 0.137 1260 Planarity : 0.003 0.052 1416 Dihedral : 5.044 49.547 1170 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.71 % Allowed : 11.31 % Favored : 87.98 % 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: 1.92 (0.27), residues: 1002 helix: 2.40 (0.20), residues: 653 sheet: 0.11 (0.53), residues: 106 loop : -1.41 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 167 TYR 0.012 0.001 TYR B 162 PHE 0.016 0.001 PHE A 389 TRP 0.010 0.001 TRP A 53 HIS 0.002 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 8454) covalent geometry : angle 0.45532 / 0.24 (11506) SS BOND : bond 0.00129 / 0.07 ( 2) SS BOND : angle 0.86883 / 0.54 ( 4) hydrogen bonds : bond 0.03952 / 2.63 ( 554) hydrogen bonds : angle 3.65403 / 2.70 ( 1671) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 273 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7717 (mp10) REVERT: B 82 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8074 (tmt170) REVERT: B 196 MET cc_start: 0.8230 (tpp) cc_final: 0.7792 (tpp) REVERT: D 89 MET cc_start: 0.8228 (ptm) cc_final: 0.7831 (ptm) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.0952 time to fit residues: 9.6775 Evaluate side-chains 72 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 273 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 370 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126964 restraints weight = 9257.916| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.73 r_work: 0.3323 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8456 Z= 0.120 Angle : 0.468 7.625 11510 Z= 0.245 Chirality : 0.038 0.147 1260 Planarity : 0.003 0.052 1416 Dihedral : 5.055 50.196 1170 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.83 % Allowed : 11.55 % Favored : 87.62 % 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: 1.88 (0.27), residues: 1002 helix: 2.33 (0.20), residues: 653 sheet: 0.39 (0.54), residues: 99 loop : -1.42 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 51 TYR 0.015 0.001 TYR B 173 PHE 0.016 0.001 PHE A 389 TRP 0.006 0.001 TRP A 53 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8454) covalent geometry : angle 0.46814 / 0.24 (11506) SS BOND : bond 0.00193 / 0.10 ( 2) SS BOND : angle 0.99466 / 0.60 ( 4) hydrogen bonds : bond 0.04187 / 2.79 ( 554) hydrogen bonds : angle 3.72488 / 2.75 ( 1671) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.56 seconds wall clock time: 32 minutes 0.36 seconds (1920.36 seconds total)