Starting phenix.real_space_refine on Wed Mar 4 04:48:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xy9_33514/03_2026/7xy9_33514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy9_33514/03_2026/7xy9_33514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xy9_33514/03_2026/7xy9_33514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy9_33514/03_2026/7xy9_33514.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy9_33514/03_2026/7xy9_33514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy9_33514/03_2026/7xy9_33514.cif" } resolution = 2.12 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= 0.001 sd= 0.110 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 Zn 4 6.06 5 Mg 8 5.21 5 S 72 5.16 5 C 6640 2.51 5 N 1808 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10962 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "D" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2594 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "C" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Classifications: {'water': 146} Link IDs: {None: 145} Chain: "D" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Classifications: {'water': 150} Link IDs: {None: 149} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 286 SG CYS A 37 70.821 60.293 24.390 1.00 40.90 S ATOM 2132 SG CYS A 295 64.935 51.850 36.905 1.00 39.55 S ATOM 4726 SG CYS B 295 43.904 51.877 46.832 1.00 35.49 S ATOM 2880 SG CYS B 37 38.029 60.293 59.329 1.00 38.05 S ATOM 7320 SG CYS C 295 65.020 30.263 46.889 1.00 36.74 S ATOM 5474 SG CYS C 37 70.759 21.742 59.360 1.00 40.13 S ATOM 9914 SG CYS D 295 43.871 30.247 36.849 1.00 37.58 S ATOM 8068 SG CYS D 37 38.064 21.769 24.366 1.00 40.89 S Time building chain proxies: 2.88, per 1000 atoms: 0.26 Number of scatterers: 10962 At special positions: 0 Unit cell: (109.699, 82.9026, 84.5774, 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) Zn 4 29.99 S 72 16.00 Mg 8 11.99 O 2430 8.00 N 1808 7.00 C 6640 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: 0.61 Conformation dependent library (CDL) restraints added in 371.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 59 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 37 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 59 " pdb="ZN ZN B 503 " - pdb=" SG CYS B 37 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 37 " pdb=" ZN D 503 " pdb="ZN ZN D 503 " - pdb=" NE2 HIS D 59 " pdb="ZN ZN D 503 " - pdb=" SG CYS D 37 " 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 14 sheets defined 35.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.601A pdb=" N ILE A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 47 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.708A pdb=" N GLY A 221 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.924A pdb=" N MET A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.925A pdb=" N LYS A 318 " --> pdb=" O ASP A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'B' and resid 37 through 47 removed outlier: 3.588A pdb=" N ILE B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.726A pdb=" N GLY B 221 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.584A pdb=" N MET B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.931A pdb=" N LYS B 318 " --> pdb=" O ASP B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'C' and resid 37 through 47 removed outlier: 3.629A pdb=" N ILE C 41 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 217 through 221 removed outlier: 3.702A pdb=" N GLY C 221 " --> pdb=" O TYR C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 245 through 255 removed outlier: 3.912A pdb=" N MET C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 315 through 318 removed outlier: 3.942A pdb=" N LYS C 318 " --> pdb=" O ASP C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 318' Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.592A pdb=" N ILE D 41 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 150 through 162 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 200 through 211 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.921A pdb=" N MET D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 315 through 318 removed outlier: 3.960A pdb=" N LYS D 318 " --> pdb=" O ASP D 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 315 through 318' Processing helix chain 'D' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 6.544A pdb=" N LYS A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.598A pdb=" N ILE A 28 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL A 62 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 61 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 83 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 126 removed outlier: 4.355A pdb=" N VAL A 320 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 348 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS A 322 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 350 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE A 324 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 214 through 216 removed outlier: 8.908A pdb=" N ASP A 237 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 261 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ASP B 237 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 261 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 17 Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 126 removed outlier: 6.596A pdb=" N ILE B 28 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 62 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA B 61 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 83 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126 removed outlier: 4.344A pdb=" N VAL B 320 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL B 348 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS B 322 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 350 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE B 324 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 17 removed outlier: 6.574A pdb=" N LYS C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 126 removed outlier: 6.596A pdb=" N ILE C 28 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 62 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA C 61 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 124 through 126 removed outlier: 4.378A pdb=" N VAL C 320 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL C 348 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS C 322 " --> pdb=" O VAL C 348 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 350 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE C 324 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 214 through 216 removed outlier: 8.902A pdb=" N ASP C 237 " --> pdb=" O GLY C 259 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 261 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N ASP D 237 " --> pdb=" O GLY D 259 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D 261 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 17 removed outlier: 6.566A pdb=" N LYS D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 124 through 126 removed outlier: 6.520A pdb=" N ILE D 28 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 62 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA D 61 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 124 through 126 removed outlier: 4.336A pdb=" N VAL D 320 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 348 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N HIS D 322 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE D 350 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE D 324 " --> pdb=" O ILE D 350 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1203 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: 1.81 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3426 1.34 - 1.46: 2195 1.46 - 1.58: 4859 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 10608 Sorted by residual: bond pdb=" C CYS D 295 " pdb=" N PRO D 296 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.01e-02 9.80e+03 1.32e+00 bond pdb=" C CYS C 295 " pdb=" N PRO C 296 " ideal model delta sigma weight residual 1.333 1.345 -0.011 1.01e-02 9.80e+03 1.19e+00 bond pdb=" N CYS D 295 " pdb=" CA CYS D 295 " ideal model delta sigma weight residual 1.463 1.457 0.007 6.90e-03 2.10e+04 9.23e-01 bond pdb=" C LEU D 294 " pdb=" N CYS D 295 " ideal model delta sigma weight residual 1.341 1.327 0.013 1.65e-02 3.67e+03 6.53e-01 bond pdb=" CA TYR D 218 " pdb=" CB TYR D 218 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 ... (remaining 10603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 14157 2.00 - 4.00: 156 4.00 - 6.00: 26 6.00 - 8.00: 4 8.00 - 10.00: 1 Bond angle restraints: 14344 Sorted by residual: angle pdb=" CG1 ILE A 175 " pdb=" CB ILE A 175 " pdb=" CG2 ILE A 175 " ideal model delta sigma weight residual 110.70 100.70 10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N LEU B 294 " pdb=" CA LEU B 294 " pdb=" C LEU B 294 " ideal model delta sigma weight residual 110.65 106.59 4.06 1.26e+00 6.30e-01 1.04e+01 angle pdb=" C MET B 147 " pdb=" N ILE B 148 " pdb=" CA ILE B 148 " ideal model delta sigma weight residual 120.33 122.90 -2.57 8.00e-01 1.56e+00 1.03e+01 angle pdb=" N LEU A 294 " pdb=" CA LEU A 294 " pdb=" C LEU A 294 " ideal model delta sigma weight residual 110.65 106.62 4.03 1.26e+00 6.30e-01 1.03e+01 angle pdb=" N PRO C 296 " pdb=" CA PRO C 296 " pdb=" C PRO C 296 " ideal model delta sigma weight residual 110.50 115.01 -4.51 1.57e+00 4.06e-01 8.25e+00 ... (remaining 14339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 5471 17.42 - 34.84: 580 34.84 - 52.26: 168 52.26 - 69.68: 65 69.68 - 87.10: 24 Dihedral angle restraints: 6308 sinusoidal: 2492 harmonic: 3816 Sorted by residual: dihedral pdb=" CA CYS A 295 " pdb=" C CYS A 295 " pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA CYS B 295 " pdb=" C CYS B 295 " pdb=" N PRO B 296 " pdb=" CA PRO B 296 " ideal model delta harmonic sigma weight residual -180.00 -152.14 -27.86 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA CYS D 295 " pdb=" C CYS D 295 " pdb=" N PRO D 296 " pdb=" CA PRO D 296 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1231 0.049 - 0.097: 258 0.097 - 0.146: 102 0.146 - 0.194: 0 0.194 - 0.243: 1 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CB ILE A 175 " pdb=" CA ILE A 175 " pdb=" CG1 ILE A 175 " pdb=" CG2 ILE A 175 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA VAL B 62 " pdb=" N VAL B 62 " pdb=" C VAL B 62 " pdb=" CB VAL B 62 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA VAL A 62 " pdb=" N VAL A 62 " pdb=" C VAL A 62 " pdb=" CB VAL A 62 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1589 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 200 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.01e+00 pdb=" N PRO A 201 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 200 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 201 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 200 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 201 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 201 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 201 " 0.029 5.00e-02 4.00e+02 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 145 2.57 - 3.15: 8664 3.15 - 3.74: 18347 3.74 - 4.32: 27448 4.32 - 4.90: 42748 Nonbonded interactions: 97352 Sorted by model distance: nonbonded pdb=" OD2 ASP C 150 " pdb="ZN ZN C 503 " model vdw 1.988 2.230 nonbonded pdb=" OD2 ASP D 150 " pdb="ZN ZN D 503 " model vdw 1.996 2.230 nonbonded pdb=" NE2 HIS A 157 " pdb="MG MG A 403 " model vdw 2.038 2.250 nonbonded pdb=" NE2 HIS B 157 " pdb="MG MG B 502 " model vdw 2.039 2.250 nonbonded pdb=" NE2 HIS C 157 " pdb="MG MG C 502 " model vdw 2.040 2.250 ... (remaining 97347 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 0 through 351 or resid 402)) selection = (chain 'B' and (resid 0 through 351 or resid 502)) selection = (chain 'C' and (resid 0 through 351 or resid 502)) selection = (chain 'D' and (resid 0 through 351 or resid 502)) } 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: 2.470 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.840 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 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 : 0.006 0.252 10616 Z= 0.210 Angle : 0.544 10.000 14344 Z= 0.292 Chirality : 0.046 0.243 1592 Planarity : 0.004 0.056 1856 Dihedral : 17.431 87.100 3884 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.67 % Allowed : 19.80 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.23), residues: 1360 helix: 1.10 (0.25), residues: 452 sheet: 0.81 (0.31), residues: 304 loop : -0.56 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 304 TYR 0.008 0.001 TYR D 311 PHE 0.008 0.001 PHE C 124 TRP 0.006 0.001 TRP C 90 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00226 (10608) covalent geometry : angle 0.54448 (14344) hydrogen bonds : bond 0.16132 ( 436) hydrogen bonds : angle 6.65038 ( 1203) metal coordination : bond 0.19504 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.346 Fit side-chains REVERT: A 92 THR cc_start: 0.8827 (m) cc_final: 0.8521 (p) REVERT: C 340 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7879 (ptmt) outliers start: 18 outliers final: 16 residues processed: 140 average time/residue: 0.7039 time to fit residues: 104.6418 Evaluate side-chains 141 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110787 restraints weight = 8882.119| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.34 r_work: 0.3169 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.307 10616 Z= 0.188 Angle : 0.576 8.846 14344 Z= 0.307 Chirality : 0.047 0.214 1592 Planarity : 0.004 0.057 1856 Dihedral : 7.454 58.686 1488 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.97 % Allowed : 17.84 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.23), residues: 1360 helix: 1.12 (0.25), residues: 452 sheet: 0.77 (0.30), residues: 304 loop : -0.76 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 304 TYR 0.011 0.001 TYR D 311 PHE 0.012 0.001 PHE D 124 TRP 0.006 0.001 TRP D 90 HIS 0.004 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00277 (10608) covalent geometry : angle 0.57568 (14344) hydrogen bonds : bond 0.05118 ( 436) hydrogen bonds : angle 4.95018 ( 1203) metal coordination : bond 0.14943 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.336 Fit side-chains REVERT: A 92 THR cc_start: 0.8399 (m) cc_final: 0.7946 (p) REVERT: A 106 MET cc_start: 0.8094 (mmt) cc_final: 0.7862 (mmm) REVERT: A 335 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.5649 (mpm) REVERT: B 225 SER cc_start: 0.8691 (m) cc_final: 0.8460 (t) outliers start: 32 outliers final: 16 residues processed: 153 average time/residue: 0.6816 time to fit residues: 111.2538 Evaluate side-chains 141 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109106 restraints weight = 9120.987| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.36 r_work: 0.3146 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10616 Z= 0.146 Angle : 0.588 9.031 14344 Z= 0.317 Chirality : 0.048 0.214 1592 Planarity : 0.005 0.058 1856 Dihedral : 7.079 59.787 1472 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.16 % Allowed : 17.29 % Favored : 79.55 % 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 (0.22), residues: 1360 helix: 1.04 (0.24), residues: 452 sheet: 0.41 (0.28), residues: 328 loop : -0.75 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.011 0.002 TYR D 311 PHE 0.013 0.001 PHE B 124 TRP 0.006 0.001 TRP D 90 HIS 0.004 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00319 (10608) covalent geometry : angle 0.58850 (14344) hydrogen bonds : bond 0.05379 ( 436) hydrogen bonds : angle 4.88943 ( 1203) metal coordination : bond 0.00570 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.318 Fit side-chains REVERT: A 92 THR cc_start: 0.8356 (m) cc_final: 0.7878 (p) REVERT: A 106 MET cc_start: 0.8224 (mmt) cc_final: 0.7999 (mmm) REVERT: A 335 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.5698 (mpm) REVERT: A 340 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7804 (ptmt) REVERT: B 225 SER cc_start: 0.8716 (m) cc_final: 0.8432 (t) REVERT: B 335 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7643 (mpm) REVERT: C 335 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7652 (mpm) REVERT: D 335 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7736 (mpm) outliers start: 34 outliers final: 17 residues processed: 150 average time/residue: 0.6546 time to fit residues: 104.7389 Evaluate side-chains 150 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110178 restraints weight = 9121.007| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.36 r_work: 0.3161 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10616 Z= 0.127 Angle : 0.563 9.207 14344 Z= 0.302 Chirality : 0.047 0.222 1592 Planarity : 0.004 0.056 1856 Dihedral : 6.732 58.566 1471 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.97 % Allowed : 17.57 % Favored : 79.46 % 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 (0.22), residues: 1360 helix: 1.06 (0.24), residues: 452 sheet: 0.40 (0.28), residues: 328 loop : -0.76 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 304 TYR 0.010 0.001 TYR D 311 PHE 0.012 0.001 PHE A 124 TRP 0.006 0.001 TRP D 90 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00274 (10608) covalent geometry : angle 0.56343 (14344) hydrogen bonds : bond 0.04850 ( 436) hydrogen bonds : angle 4.70038 ( 1203) metal coordination : bond 0.00448 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.329 Fit side-chains REVERT: A 92 THR cc_start: 0.8289 (m) cc_final: 0.7809 (p) REVERT: A 106 MET cc_start: 0.8115 (mmt) cc_final: 0.7882 (mmm) REVERT: A 335 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.5719 (mpm) REVERT: B 225 SER cc_start: 0.8718 (m) cc_final: 0.8443 (t) REVERT: B 335 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7668 (mpm) REVERT: C 106 MET cc_start: 0.8117 (mmt) cc_final: 0.7893 (mmm) REVERT: C 335 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7588 (mpm) REVERT: D 106 MET cc_start: 0.8149 (mmt) cc_final: 0.7800 (mmm) REVERT: D 325 ARG cc_start: 0.8301 (tpt170) cc_final: 0.7865 (mpt90) REVERT: D 335 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7753 (mpm) outliers start: 32 outliers final: 14 residues processed: 144 average time/residue: 0.6903 time to fit residues: 106.0720 Evaluate side-chains 141 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106840 restraints weight = 9090.175| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.35 r_work: 0.3114 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10616 Z= 0.217 Angle : 0.669 9.450 14344 Z= 0.363 Chirality : 0.051 0.190 1592 Planarity : 0.005 0.061 1856 Dihedral : 6.959 58.720 1468 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.60 % Allowed : 17.75 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.19 (0.22), residues: 1360 helix: 0.71 (0.24), residues: 452 sheet: 0.02 (0.27), residues: 332 loop : -0.79 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 304 TYR 0.013 0.002 TYR B 311 PHE 0.015 0.002 PHE C 124 TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00491 (10608) covalent geometry : angle 0.66924 (14344) hydrogen bonds : bond 0.06331 ( 436) hydrogen bonds : angle 5.09010 ( 1203) metal coordination : bond 0.00889 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.292 Fit side-chains REVERT: A 92 THR cc_start: 0.8422 (m) cc_final: 0.7914 (p) REVERT: A 106 MET cc_start: 0.8144 (mmt) cc_final: 0.7860 (mmm) REVERT: A 335 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.5847 (mpm) REVERT: A 340 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7888 (ptmt) REVERT: B 106 MET cc_start: 0.8123 (mmt) cc_final: 0.7828 (mmm) REVERT: C 294 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7239 (mt) outliers start: 28 outliers final: 20 residues processed: 150 average time/residue: 0.6872 time to fit residues: 109.8297 Evaluate side-chains 149 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 342 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107209 restraints weight = 9150.197| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.36 r_work: 0.3119 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10616 Z= 0.197 Angle : 0.652 9.800 14344 Z= 0.352 Chirality : 0.050 0.207 1592 Planarity : 0.005 0.063 1856 Dihedral : 6.944 59.137 1468 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.97 % Allowed : 17.38 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -0.25 (0.22), residues: 1360 helix: 0.67 (0.24), residues: 452 sheet: -0.04 (0.27), residues: 332 loop : -0.82 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 304 TYR 0.012 0.002 TYR A 311 PHE 0.014 0.002 PHE B 124 TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00443 (10608) covalent geometry : angle 0.65200 (14344) hydrogen bonds : bond 0.06032 ( 436) hydrogen bonds : angle 5.02060 ( 1203) metal coordination : bond 0.00831 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.428 Fit side-chains REVERT: A 0 HIS cc_start: 0.5906 (OUTLIER) cc_final: 0.4863 (m-70) REVERT: A 92 THR cc_start: 0.8396 (m) cc_final: 0.7894 (p) REVERT: A 106 MET cc_start: 0.8134 (mmt) cc_final: 0.7833 (mmm) REVERT: A 335 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.5810 (mpm) REVERT: A 340 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7877 (ptmt) REVERT: B 106 MET cc_start: 0.8116 (mmt) cc_final: 0.7875 (mmm) REVERT: B 225 SER cc_start: 0.8690 (m) cc_final: 0.8378 (t) REVERT: B 335 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7711 (mpm) REVERT: C 138 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7925 (ptpp) REVERT: C 294 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7163 (mt) REVERT: C 335 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7650 (mpm) REVERT: D 335 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7684 (mpm) outliers start: 32 outliers final: 18 residues processed: 147 average time/residue: 0.7379 time to fit residues: 115.4660 Evaluate side-chains 153 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109291 restraints weight = 9094.567| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.36 r_work: 0.3149 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10616 Z= 0.134 Angle : 0.581 9.637 14344 Z= 0.311 Chirality : 0.048 0.222 1592 Planarity : 0.004 0.061 1856 Dihedral : 6.635 59.636 1468 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.51 % Allowed : 17.75 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % 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: -0.02 (0.22), residues: 1360 helix: 0.93 (0.24), residues: 452 sheet: 0.18 (0.27), residues: 328 loop : -0.82 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 304 TYR 0.010 0.001 TYR D 311 PHE 0.012 0.001 PHE A 124 TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00291 (10608) covalent geometry : angle 0.58060 (14344) hydrogen bonds : bond 0.05023 ( 436) hydrogen bonds : angle 4.71494 ( 1203) metal coordination : bond 0.00510 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.455 Fit side-chains REVERT: A 92 THR cc_start: 0.8324 (m) cc_final: 0.7832 (p) REVERT: A 106 MET cc_start: 0.8093 (mmt) cc_final: 0.7816 (mmm) REVERT: A 335 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.5767 (mpm) REVERT: A 340 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7847 (ptmt) REVERT: B 106 MET cc_start: 0.8048 (mmt) cc_final: 0.7748 (mmm) REVERT: B 225 SER cc_start: 0.8710 (m) cc_final: 0.8419 (t) REVERT: B 335 MET cc_start: 0.8048 (mmp) cc_final: 0.7665 (mpm) REVERT: C 106 MET cc_start: 0.8121 (mmt) cc_final: 0.7859 (mmm) REVERT: C 335 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7641 (mpm) REVERT: D 106 MET cc_start: 0.8213 (mmt) cc_final: 0.7844 (mmm) REVERT: D 335 MET cc_start: 0.8081 (mmp) cc_final: 0.7698 (mpm) outliers start: 27 outliers final: 17 residues processed: 139 average time/residue: 0.7234 time to fit residues: 106.9933 Evaluate side-chains 143 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 132 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN C 54 ASN D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113396 restraints weight = 9133.975| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.36 r_work: 0.3209 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10616 Z= 0.097 Angle : 0.525 9.997 14344 Z= 0.278 Chirality : 0.046 0.242 1592 Planarity : 0.004 0.057 1856 Dihedral : 6.113 59.572 1467 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.58 % Allowed : 18.49 % Favored : 79.93 % 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: 0.27 (0.23), residues: 1360 helix: 1.22 (0.25), residues: 452 sheet: 0.44 (0.28), residues: 328 loop : -0.76 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 299 TYR 0.009 0.001 TYR D 311 PHE 0.010 0.001 PHE B 124 TRP 0.006 0.001 TRP D 90 HIS 0.006 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00208 (10608) covalent geometry : angle 0.52508 (14344) hydrogen bonds : bond 0.03886 ( 436) hydrogen bonds : angle 4.31458 ( 1203) metal coordination : bond 0.00239 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.428 Fit side-chains REVERT: A 92 THR cc_start: 0.8192 (m) cc_final: 0.7709 (p) REVERT: A 106 MET cc_start: 0.8116 (mmt) cc_final: 0.7814 (mmm) REVERT: A 335 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.5769 (mpm) REVERT: B 106 MET cc_start: 0.7992 (mmt) cc_final: 0.7642 (mmm) REVERT: B 225 SER cc_start: 0.8696 (m) cc_final: 0.8428 (t) REVERT: B 248 ILE cc_start: 0.7914 (tp) cc_final: 0.7698 (tp) REVERT: B 335 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7599 (mpm) REVERT: C 106 MET cc_start: 0.8081 (mmt) cc_final: 0.7793 (mmm) REVERT: C 335 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7604 (mpm) REVERT: D 106 MET cc_start: 0.8096 (mmt) cc_final: 0.7807 (mmm) REVERT: D 230 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8436 (mp) REVERT: D 335 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7574 (mpm) outliers start: 17 outliers final: 8 residues processed: 137 average time/residue: 0.6975 time to fit residues: 101.6906 Evaluate side-chains 133 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 24 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 93 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 96 GLN C 54 ASN D 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107401 restraints weight = 9113.065| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.36 r_work: 0.3123 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10616 Z= 0.200 Angle : 0.655 9.471 14344 Z= 0.353 Chirality : 0.050 0.186 1592 Planarity : 0.005 0.059 1856 Dihedral : 6.697 58.194 1467 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.67 % Allowed : 18.49 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: -0.14 (0.22), residues: 1360 helix: 0.82 (0.24), residues: 452 sheet: 0.12 (0.28), residues: 308 loop : -0.85 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 304 TYR 0.012 0.002 TYR B 311 PHE 0.014 0.002 PHE A 124 TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00453 (10608) covalent geometry : angle 0.65461 (14344) hydrogen bonds : bond 0.05987 ( 436) hydrogen bonds : angle 4.93122 ( 1203) metal coordination : bond 0.00817 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.367 Fit side-chains REVERT: A 92 THR cc_start: 0.8383 (m) cc_final: 0.7873 (p) REVERT: A 106 MET cc_start: 0.8181 (mmt) cc_final: 0.7876 (mmm) REVERT: A 335 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.5782 (mpm) REVERT: A 340 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7848 (ptmt) REVERT: B 106 MET cc_start: 0.8156 (mmt) cc_final: 0.7890 (mmm) REVERT: B 335 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7691 (mpm) REVERT: C 106 MET cc_start: 0.8180 (mmt) cc_final: 0.7844 (mmm) REVERT: C 138 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7847 (ptpp) REVERT: C 335 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7637 (mpm) REVERT: D 335 MET cc_start: 0.8070 (mmp) cc_final: 0.7666 (mpm) outliers start: 18 outliers final: 13 residues processed: 133 average time/residue: 0.7112 time to fit residues: 100.8652 Evaluate side-chains 139 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106378 restraints weight = 9091.412| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.36 r_work: 0.3110 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10616 Z= 0.236 Angle : 0.700 9.621 14344 Z= 0.380 Chirality : 0.052 0.172 1592 Planarity : 0.005 0.059 1856 Dihedral : 6.949 58.952 1467 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.95 % Allowed : 18.31 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.35 (0.22), residues: 1360 helix: 0.55 (0.23), residues: 452 sheet: -0.11 (0.26), residues: 332 loop : -0.84 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 304 TYR 0.013 0.003 TYR C 311 PHE 0.015 0.002 PHE B 124 TRP 0.006 0.002 TRP D 90 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00537 (10608) covalent geometry : angle 0.70037 (14344) hydrogen bonds : bond 0.06560 ( 436) hydrogen bonds : angle 5.13590 ( 1203) metal coordination : bond 0.01052 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.491 Fit side-chains REVERT: A 92 THR cc_start: 0.8418 (m) cc_final: 0.7910 (p) REVERT: A 106 MET cc_start: 0.8187 (mmt) cc_final: 0.7853 (mmm) REVERT: A 335 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.5858 (mpm) REVERT: A 340 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7916 (ptmt) REVERT: B 335 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7708 (mpm) REVERT: D 335 MET cc_start: 0.8099 (mmp) cc_final: 0.7696 (mpm) outliers start: 21 outliers final: 15 residues processed: 144 average time/residue: 0.6895 time to fit residues: 106.0098 Evaluate side-chains 146 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 54 ASN D 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110058 restraints weight = 9119.781| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.36 r_work: 0.3160 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10616 Z= 0.123 Angle : 0.575 10.147 14344 Z= 0.306 Chirality : 0.047 0.235 1592 Planarity : 0.004 0.059 1856 Dihedral : 6.502 58.747 1467 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.30 % Allowed : 18.68 % Favored : 80.02 % 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: -0.04 (0.22), residues: 1360 helix: 0.97 (0.24), residues: 452 sheet: 0.22 (0.28), residues: 304 loop : -0.89 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 304 TYR 0.010 0.001 TYR D 311 PHE 0.011 0.001 PHE D 124 TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00265 (10608) covalent geometry : angle 0.57535 (14344) hydrogen bonds : bond 0.04718 ( 436) hydrogen bonds : angle 4.62393 ( 1203) metal coordination : bond 0.00372 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4092.91 seconds wall clock time: 70 minutes 16.46 seconds (4216.46 seconds total)