Starting phenix.real_space_refine on Tue Jul 29 03:45:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xy9_33514/07_2025/7xy9_33514.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy9_33514/07_2025/7xy9_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_33514/07_2025/7xy9_33514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy9_33514/07_2025/7xy9_33514.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy9_33514/07_2025/7xy9_33514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy9_33514/07_2025/7xy9_33514.cif" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.79, per 1000 atoms: 0.71 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: 2.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.49 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: 3.55 Time building geometry restraints manager: 3.29 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: 0.02 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: 1.420 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.730 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.820 ------------------------------------------------------------------------------- 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 : 4.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (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 TRP 0.006 0.001 TRP C 90 HIS 0.004 0.001 HIS D 157 PHE 0.008 0.001 PHE C 124 TYR 0.008 0.001 TYR D 311 ARG 0.001 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.16132 ( 436) hydrogen bonds : angle 6.65038 ( 1203) metal coordination : bond 0.19504 ( 8) covalent geometry : bond 0.00226 (10608) covalent geometry : angle 0.54448 (14344) *********************** 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 : 1.307 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: 1.6443 time to fit residues: 245.3431 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 : 1.264 ------------------------------------------------------------------------------- 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 114 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105819 restraints weight = 8782.060| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.32 r_work: 0.3099 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.007 0.067 10616 Z= 0.294 Angle : 0.770 9.106 14344 Z= 0.418 Chirality : 0.056 0.197 1592 Planarity : 0.006 0.066 1856 Dihedral : 8.193 59.688 1488 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.62 % Allowed : 16.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1360 helix: 0.55 (0.23), residues: 452 sheet: 0.16 (0.27), residues: 332 loop : -0.78 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 110 HIS 0.006 0.002 HIS A 157 PHE 0.016 0.002 PHE D 124 TYR 0.014 0.003 TYR C 311 ARG 0.006 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.07349 ( 436) hydrogen bonds : angle 5.46892 ( 1203) metal coordination : bond 0.01519 ( 8) covalent geometry : bond 0.00674 (10608) covalent geometry : angle 0.77020 (14344) *********************** 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 175 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.274 Fit side-chains REVERT: A 92 THR cc_start: 0.8523 (m) cc_final: 0.8033 (p) REVERT: A 106 MET cc_start: 0.8187 (mmt) cc_final: 0.7918 (mmm) REVERT: A 335 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.5834 (mpm) REVERT: B 16 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7783 (tp30) REVERT: C 335 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.5820 (mpm) REVERT: D 16 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7578 (tp30) outliers start: 39 outliers final: 22 residues processed: 161 average time/residue: 1.5237 time to fit residues: 262.6168 Evaluate side-chains 157 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 9 ILE Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain C residue 9 ILE 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 16 GLU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN D 54 ASN ** D 96 GLN ** 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 = 0.3617 r_free = 0.3617 target = 0.136720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111435 restraints weight = 8956.373| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.34 r_work: 0.3182 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10616 Z= 0.108 Angle : 0.549 8.885 14344 Z= 0.293 Chirality : 0.047 0.228 1592 Planarity : 0.004 0.057 1856 Dihedral : 7.152 58.979 1478 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.14 % Allowed : 18.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1360 helix: 1.03 (0.24), residues: 452 sheet: 0.36 (0.28), residues: 328 loop : -0.77 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.006 0.001 HIS D 157 PHE 0.009 0.001 PHE B 124 TYR 0.010 0.001 TYR D 311 ARG 0.001 0.000 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 436) hydrogen bonds : angle 4.65277 ( 1203) metal coordination : bond 0.00272 ( 8) covalent geometry : bond 0.00226 (10608) covalent geometry : angle 0.54899 (14344) *********************** 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 152 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.339 Fit side-chains REVERT: A 92 THR cc_start: 0.8284 (m) cc_final: 0.7834 (p) REVERT: A 106 MET cc_start: 0.8158 (mmt) cc_final: 0.7878 (mmm) REVERT: B 106 MET cc_start: 0.8043 (mmt) cc_final: 0.7734 (mmm) REVERT: B 225 SER cc_start: 0.8713 (m) cc_final: 0.8441 (t) REVERT: B 335 MET cc_start: 0.7999 (mmp) cc_final: 0.7628 (mpm) REVERT: C 106 MET cc_start: 0.8054 (mmt) cc_final: 0.7739 (mmm) REVERT: D 106 MET cc_start: 0.8128 (mmt) cc_final: 0.7770 (mmm) REVERT: D 335 MET cc_start: 0.8009 (mmp) cc_final: 0.7764 (mpm) REVERT: D 339 ASP cc_start: 0.7676 (p0) cc_final: 0.7348 (m-30) outliers start: 23 outliers final: 12 residues processed: 145 average time/residue: 1.6921 time to fit residues: 263.0255 Evaluate side-chains 139 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LYS 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 254 LYS Chi-restraints excluded: chain C residue 295 CYS 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 294 LEU Chi-restraints excluded: chain D residue 295 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3576 r_free = 0.3576 target = 0.133292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107877 restraints weight = 8896.318| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.34 r_work: 0.3130 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10616 Z= 0.173 Angle : 0.624 9.169 14344 Z= 0.337 Chirality : 0.049 0.201 1592 Planarity : 0.005 0.061 1856 Dihedral : 6.854 58.561 1469 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.60 % Allowed : 17.38 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1360 helix: 0.85 (0.24), residues: 452 sheet: 0.09 (0.27), residues: 332 loop : -0.76 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS A 102 PHE 0.013 0.001 PHE D 124 TYR 0.012 0.002 TYR A 311 ARG 0.003 0.000 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.05743 ( 436) hydrogen bonds : angle 4.94603 ( 1203) metal coordination : bond 0.00797 ( 8) covalent geometry : bond 0.00385 (10608) covalent geometry : angle 0.62427 (14344) *********************** 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 159 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.119 Fit side-chains REVERT: A 92 THR cc_start: 0.8386 (m) cc_final: 0.7899 (p) REVERT: A 106 MET cc_start: 0.8146 (mmt) cc_final: 0.7869 (mmm) REVERT: B 106 MET cc_start: 0.8113 (mmt) cc_final: 0.7830 (mmm) REVERT: B 225 SER cc_start: 0.8692 (m) cc_final: 0.8393 (t) REVERT: D 106 MET cc_start: 0.8192 (mmt) cc_final: 0.7832 (mmm) REVERT: D 138 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7866 (ptpp) REVERT: D 339 ASP cc_start: 0.7650 (p0) cc_final: 0.7380 (m-30) outliers start: 28 outliers final: 15 residues processed: 147 average time/residue: 1.6450 time to fit residues: 257.8822 Evaluate side-chains 143 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 254 LYS Chi-restraints excluded: chain A residue 295 CYS 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 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 138 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 39 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.134024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108591 restraints weight = 8877.132| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.34 r_work: 0.3140 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10616 Z= 0.155 Angle : 0.604 9.264 14344 Z= 0.325 Chirality : 0.049 0.210 1592 Planarity : 0.005 0.061 1856 Dihedral : 6.712 59.205 1467 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.25 % Allowed : 17.01 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1360 helix: 0.87 (0.24), residues: 452 sheet: 0.07 (0.27), residues: 332 loop : -0.77 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.004 0.001 HIS A 102 PHE 0.012 0.001 PHE B 124 TYR 0.011 0.002 TYR D 311 ARG 0.003 0.000 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.05406 ( 436) hydrogen bonds : angle 4.85292 ( 1203) metal coordination : bond 0.00698 ( 8) covalent geometry : bond 0.00342 (10608) covalent geometry : angle 0.60418 (14344) *********************** 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 161 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.229 Fit side-chains REVERT: A 0 HIS cc_start: 0.5868 (OUTLIER) cc_final: 0.4829 (m-70) REVERT: A 92 THR cc_start: 0.8369 (m) cc_final: 0.7881 (p) REVERT: A 106 MET cc_start: 0.8114 (mmt) cc_final: 0.7842 (mmm) REVERT: A 335 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7728 (mpm) REVERT: B 106 MET cc_start: 0.8088 (mmt) cc_final: 0.7798 (mmm) REVERT: B 225 SER cc_start: 0.8691 (m) cc_final: 0.8393 (t) REVERT: B 335 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7663 (mpm) REVERT: C 106 MET cc_start: 0.8146 (mmt) cc_final: 0.7804 (mmm) REVERT: C 294 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7122 (mt) REVERT: C 335 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7649 (mpm) REVERT: D 106 MET cc_start: 0.8174 (mmt) cc_final: 0.7827 (mmm) REVERT: D 335 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7792 (mpm) outliers start: 35 outliers final: 18 residues processed: 147 average time/residue: 1.5919 time to fit residues: 249.9096 Evaluate side-chains 149 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 254 LYS Chi-restraints excluded: chain A residue 295 CYS 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 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 224 GLU Chi-restraints excluded: chain C residue 225 SER 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 294 LEU Chi-restraints excluded: chain D residue 295 CYS Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN D 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110801 restraints weight = 8970.324| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.35 r_work: 0.3172 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0915 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= 0.113 Angle : 0.548 9.514 14344 Z= 0.293 Chirality : 0.047 0.231 1592 Planarity : 0.004 0.058 1856 Dihedral : 6.394 59.914 1467 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.42 % Allowed : 18.22 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1360 helix: 1.09 (0.25), residues: 452 sheet: 0.33 (0.28), residues: 328 loop : -0.75 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS D 157 PHE 0.011 0.001 PHE A 124 TYR 0.010 0.001 TYR D 311 ARG 0.002 0.000 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 436) hydrogen bonds : angle 4.57964 ( 1203) metal coordination : bond 0.00448 ( 8) covalent geometry : bond 0.00243 (10608) covalent geometry : angle 0.54844 (14344) *********************** 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 154 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.245 Fit side-chains REVERT: A 92 THR cc_start: 0.8261 (m) cc_final: 0.7779 (p) REVERT: A 106 MET cc_start: 0.8085 (mmt) cc_final: 0.7778 (mmm) REVERT: A 335 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7682 (mpm) REVERT: B 106 MET cc_start: 0.8072 (mmt) cc_final: 0.7744 (mmm) REVERT: B 225 SER cc_start: 0.8722 (m) cc_final: 0.8430 (t) REVERT: B 335 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7674 (mpm) REVERT: C 106 MET cc_start: 0.8127 (mmt) cc_final: 0.7825 (mmm) REVERT: C 335 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7605 (mpm) REVERT: D 106 MET cc_start: 0.8155 (mmt) cc_final: 0.7845 (mmm) REVERT: D 335 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7773 (mpm) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 1.5702 time to fit residues: 239.6189 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 : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 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 225 SER 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 335 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 132 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3568 r_free = 0.3568 target = 0.132675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107138 restraints weight = 9044.291| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.35 r_work: 0.3119 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10616 Z= 0.208 Angle : 0.657 9.551 14344 Z= 0.356 Chirality : 0.051 0.188 1592 Planarity : 0.005 0.061 1856 Dihedral : 6.818 59.185 1467 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.51 % Allowed : 17.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1360 helix: 0.78 (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 TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS A 102 PHE 0.014 0.002 PHE C 124 TYR 0.013 0.002 TYR A 311 ARG 0.004 0.001 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.06119 ( 436) hydrogen bonds : angle 5.00186 ( 1203) metal coordination : bond 0.00931 ( 8) covalent geometry : bond 0.00470 (10608) covalent geometry : angle 0.65653 (14344) *********************** 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 154 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.203 Fit side-chains REVERT: A 0 HIS cc_start: 0.5868 (OUTLIER) cc_final: 0.4801 (m-70) REVERT: A 92 THR cc_start: 0.8390 (m) cc_final: 0.7889 (p) REVERT: A 106 MET cc_start: 0.8176 (mmt) cc_final: 0.7869 (mmm) REVERT: A 335 MET cc_start: 0.8159 (mmp) cc_final: 0.7747 (mpm) REVERT: B 106 MET cc_start: 0.8127 (mmt) cc_final: 0.7800 (mmm) REVERT: B 335 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7669 (mpm) REVERT: C 106 MET cc_start: 0.8180 (mmt) cc_final: 0.7856 (mmm) REVERT: C 335 MET cc_start: 0.8084 (mmp) cc_final: 0.7643 (mpm) REVERT: D 138 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7899 (ptpp) REVERT: D 335 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7767 (mpm) outliers start: 27 outliers final: 19 residues processed: 144 average time/residue: 1.5624 time to fit residues: 240.4661 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 : 1.152 ------------------------------------------------------------------------------- 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 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 224 GLU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 254 LYS 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 138 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 135 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.133622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108218 restraints weight = 8933.267| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.34 r_work: 0.3135 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10616 Z= 0.165 Angle : 0.618 9.874 14344 Z= 0.333 Chirality : 0.049 0.216 1592 Planarity : 0.005 0.061 1856 Dihedral : 6.729 59.759 1467 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.51 % Allowed : 17.66 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1360 helix: 0.80 (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 TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS B 102 PHE 0.013 0.001 PHE A 124 TYR 0.011 0.002 TYR C 311 ARG 0.003 0.000 ARG D 304 Details of bonding type rmsd hydrogen bonds : bond 0.05533 ( 436) hydrogen bonds : angle 4.87333 ( 1203) metal coordination : bond 0.00761 ( 8) covalent geometry : bond 0.00366 (10608) covalent geometry : angle 0.61751 (14344) *********************** 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 151 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.124 Fit side-chains REVERT: A 0 HIS cc_start: 0.5853 (OUTLIER) cc_final: 0.4793 (m-70) REVERT: A 92 THR cc_start: 0.8370 (m) cc_final: 0.7880 (p) REVERT: A 106 MET cc_start: 0.8120 (mmt) cc_final: 0.7801 (mmm) REVERT: A 335 MET cc_start: 0.8102 (mmp) cc_final: 0.7690 (mpm) REVERT: B 106 MET cc_start: 0.8096 (mmt) cc_final: 0.7766 (mmm) REVERT: B 335 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7667 (mpm) REVERT: C 106 MET cc_start: 0.8146 (mmt) cc_final: 0.7814 (mmm) REVERT: C 335 MET cc_start: 0.8017 (mmp) cc_final: 0.7574 (mpm) REVERT: D 106 MET cc_start: 0.8163 (mmt) cc_final: 0.7803 (mmm) REVERT: D 138 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7898 (ptpp) REVERT: D 335 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7748 (mpm) outliers start: 27 outliers final: 19 residues processed: 141 average time/residue: 1.5407 time to fit residues: 232.5534 Evaluate side-chains 146 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 224 GLU Chi-restraints excluded: chain C residue 225 SER 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 107 LEU Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 295 CYS 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 123 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 125 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109025 restraints weight = 8973.851| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.35 r_work: 0.3145 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 0.025 10616 Z= 0.146 Angle : 0.596 9.924 14344 Z= 0.320 Chirality : 0.048 0.219 1592 Planarity : 0.005 0.061 1856 Dihedral : 6.599 59.866 1467 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.32 % Allowed : 17.84 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1360 helix: 0.89 (0.24), residues: 452 sheet: 0.19 (0.28), residues: 304 loop : -0.86 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.004 0.001 HIS B 102 PHE 0.012 0.001 PHE A 124 TYR 0.011 0.002 TYR D 311 ARG 0.003 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 436) hydrogen bonds : angle 4.76976 ( 1203) metal coordination : bond 0.00644 ( 8) covalent geometry : bond 0.00321 (10608) covalent geometry : angle 0.59554 (14344) *********************** 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 148 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.219 Fit side-chains REVERT: A 0 HIS cc_start: 0.5863 (OUTLIER) cc_final: 0.4806 (m-70) REVERT: A 92 THR cc_start: 0.8328 (m) cc_final: 0.7843 (p) REVERT: A 106 MET cc_start: 0.8124 (mmt) cc_final: 0.7812 (mmm) REVERT: A 335 MET cc_start: 0.8094 (mmp) cc_final: 0.7713 (mpm) REVERT: B 106 MET cc_start: 0.8145 (mmt) cc_final: 0.7830 (mmm) REVERT: B 225 SER cc_start: 0.8715 (m) cc_final: 0.8421 (t) REVERT: B 335 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7701 (mpm) REVERT: C 106 MET cc_start: 0.8168 (mmt) cc_final: 0.7923 (mmm) REVERT: C 335 MET cc_start: 0.7999 (mmp) cc_final: 0.7588 (mpm) REVERT: D 106 MET cc_start: 0.8190 (mmt) cc_final: 0.7813 (mmm) REVERT: D 138 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7893 (ptpp) REVERT: D 335 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7756 (mpm) outliers start: 25 outliers final: 18 residues processed: 139 average time/residue: 1.4803 time to fit residues: 219.9693 Evaluate side-chains 144 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 224 GLU Chi-restraints excluded: chain C residue 225 SER 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 107 LEU Chi-restraints excluded: chain D residue 138 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 59 HIS C 54 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112640 restraints weight = 8942.158| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.35 r_work: 0.3200 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.331 10616 Z= 0.147 Angle : 0.538 10.470 14344 Z= 0.286 Chirality : 0.046 0.249 1592 Planarity : 0.004 0.060 1856 Dihedral : 6.169 59.478 1467 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.04 % Allowed : 17.84 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1360 helix: 1.18 (0.25), residues: 452 sheet: 0.36 (0.28), residues: 328 loop : -0.73 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS D 157 PHE 0.010 0.001 PHE A 124 TYR 0.009 0.001 TYR D 311 ARG 0.001 0.000 ARG C 304 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 436) hydrogen bonds : angle 4.40538 ( 1203) metal coordination : bond 0.11702 ( 8) covalent geometry : bond 0.00213 (10608) covalent geometry : angle 0.53806 (14344) ********************** 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 146 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.350 Fit side-chains REVERT: A 92 THR cc_start: 0.8207 (m) cc_final: 0.7734 (p) REVERT: A 106 MET cc_start: 0.8129 (mmt) cc_final: 0.7827 (mmm) REVERT: A 335 MET cc_start: 0.7989 (mmp) cc_final: 0.7648 (mpm) REVERT: B 106 MET cc_start: 0.8023 (mmt) cc_final: 0.7707 (mmm) REVERT: B 225 SER cc_start: 0.8695 (m) cc_final: 0.8427 (t) REVERT: B 335 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7566 (mpm) REVERT: C 106 MET cc_start: 0.8092 (mmt) cc_final: 0.7794 (mmm) REVERT: C 335 MET cc_start: 0.7956 (mmp) cc_final: 0.7573 (mpm) REVERT: D 106 MET cc_start: 0.8105 (mmt) cc_final: 0.7825 (mmm) REVERT: D 138 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7781 (ptpp) REVERT: D 335 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7722 (mpm) outliers start: 22 outliers final: 10 residues processed: 139 average time/residue: 1.4407 time to fit residues: 214.8057 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 : 1.224 ------------------------------------------------------------------------------- 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 295 CYS 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 225 SER Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 335 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 108 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 54 ASN ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113713 restraints weight = 9041.760| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.36 r_work: 0.3213 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0962 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= 0.098 Angle : 0.532 10.223 14344 Z= 0.281 Chirality : 0.046 0.243 1592 Planarity : 0.004 0.060 1856 Dihedral : 5.828 58.709 1463 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.49 % Allowed : 18.40 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.23), residues: 1360 helix: 1.30 (0.25), residues: 452 sheet: 0.50 (0.28), residues: 328 loop : -0.72 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 90 HIS 0.005 0.001 HIS D 157 PHE 0.010 0.001 PHE A 124 TYR 0.008 0.001 TYR D 311 ARG 0.001 0.000 ARG B 299 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 436) hydrogen bonds : angle 4.30310 ( 1203) metal coordination : bond 0.00474 ( 8) covalent geometry : bond 0.00209 (10608) covalent geometry : angle 0.53195 (14344) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8859.06 seconds wall clock time: 154 minutes 41.82 seconds (9281.82 seconds total)