Starting phenix.real_space_refine on Wed Mar 4 18:34:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7snh_25226/03_2026/7snh_25226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7snh_25226/03_2026/7snh_25226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7snh_25226/03_2026/7snh_25226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7snh_25226/03_2026/7snh_25226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7snh_25226/03_2026/7snh_25226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7snh_25226/03_2026/7snh_25226.map" } resolution = 2.2 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= 0.009 sd= 0.234 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 80 5.16 5 C 10028 2.51 5 N 2724 2.21 5 O 2972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 15828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "B" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "C" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "D" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.06, per 1000 atoms: 0.19 Number of scatterers: 15828 At special positions: 0 Unit cell: (90.47, 115.37, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 24 15.00 O 2972 8.00 N 2724 7.00 C 10028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 596.3 milliseconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 6 sheets defined 43.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 5.022A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 76 through 89 Proline residue: A 86 - end of helix removed outlier: 3.635A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 217 removed outlier: 4.551A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 3.646A pdb=" N PHE A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 4.373A pdb=" N ARG A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.600A pdb=" N CYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.125A pdb=" N ALA A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 476 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.045A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.023A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 76 through 89 Proline residue: B 86 - end of helix removed outlier: 3.675A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 176 through 189 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 205 through 217 removed outlier: 4.551A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 3.647A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.375A pdb=" N ARG B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.599A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.139A pdb=" N ALA B 318 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.043A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 5.025A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 76 through 89 Proline residue: C 86 - end of helix removed outlier: 3.674A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 205 through 217 removed outlier: 4.536A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.648A pdb=" N PHE C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 removed outlier: 4.375A pdb=" N ARG C 257 " --> pdb=" O PHE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 273 Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.600A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 315 through 320 removed outlier: 4.141A pdb=" N ALA C 318 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 447 Processing helix chain 'C' and resid 454 through 476 Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 489 through 500 removed outlier: 4.042A pdb=" N ASP C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 removed outlier: 5.019A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 76 through 89 Proline residue: D 86 - end of helix removed outlier: 3.678A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 205 through 217 removed outlier: 4.541A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 removed outlier: 3.645A pdb=" N PHE D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 259 removed outlier: 4.375A pdb=" N ARG D 257 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.602A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 315 through 320 removed outlier: 4.134A pdb=" N ALA D 318 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 447 Processing helix chain 'D' and resid 454 through 476 Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.044A pdb=" N ASP D 493 " --> pdb=" O PRO D 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.517A pdb=" N ARG A 136 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE A 168 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 138 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 483 removed outlier: 6.461A pdb=" N ALA A 367 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL A 400 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL B 400 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 367 " --> pdb=" O VAL B 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.536A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE B 199 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 169 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 198 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.536A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 480 through 483 removed outlier: 6.459A pdb=" N ALA C 367 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL C 400 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL D 400 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA D 367 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.529A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 199 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 169 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG D 198 " --> pdb=" O VAL D 453 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 3622 1.45 - 1.57: 8868 1.57 - 1.69: 40 1.69 - 1.81: 132 Bond restraints: 16228 Sorted by residual: bond pdb=" O2B NAP B 602 " pdb=" P2B NAP B 602 " ideal model delta sigma weight residual 1.736 1.597 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" O2B NAP A 602 " pdb=" P2B NAP A 602 " ideal model delta sigma weight residual 1.736 1.597 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O2B NAP D 602 " pdb=" P2B NAP D 602 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O2B NAP C 602 " pdb=" P2B NAP C 602 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.603 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 16223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 21317 1.84 - 3.69: 548 3.69 - 5.53: 119 5.53 - 7.38: 28 7.38 - 9.22: 16 Bond angle restraints: 22028 Sorted by residual: angle pdb=" N PHE C 138 " pdb=" CA PHE C 138 " pdb=" C PHE C 138 " ideal model delta sigma weight residual 108.20 113.47 -5.27 1.71e+00 3.42e-01 9.51e+00 angle pdb=" C2A NAP B 601 " pdb=" N3A NAP B 601 " pdb=" C4A NAP B 601 " ideal model delta sigma weight residual 111.82 121.04 -9.22 3.00e+00 1.11e-01 9.44e+00 angle pdb=" N PHE D 138 " pdb=" CA PHE D 138 " pdb=" C PHE D 138 " ideal model delta sigma weight residual 108.20 113.43 -5.23 1.71e+00 3.42e-01 9.35e+00 angle pdb=" C2A NAP D 601 " pdb=" N3A NAP D 601 " pdb=" C4A NAP D 601 " ideal model delta sigma weight residual 111.82 120.99 -9.17 3.00e+00 1.11e-01 9.35e+00 angle pdb=" C2A NAP A 601 " pdb=" N3A NAP A 601 " pdb=" C4A NAP A 601 " ideal model delta sigma weight residual 111.82 120.99 -9.17 3.00e+00 1.11e-01 9.33e+00 ... (remaining 22023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8315 17.92 - 35.84: 1111 35.84 - 53.76: 423 53.76 - 71.69: 121 71.69 - 89.61: 58 Dihedral angle restraints: 10028 sinusoidal: 4484 harmonic: 5544 Sorted by residual: dihedral pdb=" CA ARG A 348 " pdb=" C ARG A 348 " pdb=" N TRP A 349 " pdb=" CA TRP A 349 " ideal model delta harmonic sigma weight residual -180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG D 348 " pdb=" C ARG D 348 " pdb=" N TRP D 349 " pdb=" CA TRP D 349 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG C 348 " pdb=" C ARG C 348 " pdb=" N TRP C 349 " pdb=" CA TRP C 349 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 10025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1686 0.044 - 0.088: 466 0.088 - 0.133: 168 0.133 - 0.177: 16 0.177 - 0.221: 8 Chirality restraints: 2344 Sorted by residual: chirality pdb=" C1B NAP D 601 " pdb=" C2B NAP D 601 " pdb=" N9A NAP D 601 " pdb=" O4B NAP D 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1B NAP B 601 " pdb=" C2B NAP B 601 " pdb=" N9A NAP B 601 " pdb=" O4B NAP B 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " pdb=" N9A NAP C 601 " pdb=" O4B NAP C 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2341 not shown) Planarity restraints: 2816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 143 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO D 144 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 143 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A 144 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 143 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO B 144 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 144 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 144 " -0.040 5.00e-02 4.00e+02 ... (remaining 2813 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1669 2.75 - 3.29: 15381 3.29 - 3.83: 28851 3.83 - 4.36: 35352 4.36 - 4.90: 57211 Nonbonded interactions: 138464 Sorted by model distance: nonbonded pdb=" OH TYR B 139 " pdb=" OE2 GLU B 170 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 202 " pdb=" NE2 GLN B 395 " model vdw 2.231 3.120 nonbonded pdb=" OH TYR D 202 " pdb=" NE2 GLN D 395 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR C 202 " pdb=" NE2 GLN C 395 " model vdw 2.232 3.120 nonbonded pdb=" OH TYR A 202 " pdb=" NE2 GLN A 395 " model vdw 2.233 3.120 ... (remaining 138459 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 0.139 16228 Z= 0.313 Angle : 0.747 9.219 22028 Z= 0.347 Chirality : 0.047 0.221 2344 Planarity : 0.006 0.073 2816 Dihedral : 20.228 89.608 6460 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.32 % Allowed : 21.22 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.45 (0.19), residues: 1888 helix: 0.81 (0.20), residues: 696 sheet: -0.37 (0.23), residues: 444 loop : 0.49 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 246 TYR 0.020 0.002 TYR D 202 PHE 0.022 0.001 PHE C 88 TRP 0.016 0.001 TRP D 164 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00626 (16228) covalent geometry : angle 0.74663 (22028) hydrogen bonds : bond 0.16560 ( 703) hydrogen bonds : angle 7.13787 ( 2007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.564 Fit side-chains REVERT: B 66 PHE cc_start: 0.7894 (m-80) cc_final: 0.7677 (m-80) outliers start: 22 outliers final: 16 residues processed: 221 average time/residue: 0.6684 time to fit residues: 161.7242 Evaluate side-chains 216 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 202 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 340 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0050 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 4.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 185 ASN A 186 HIS B 185 ASN B 186 HIS C 186 HIS D 185 ASN D 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133551 restraints weight = 13216.734| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.92 r_work: 0.3149 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16228 Z= 0.180 Angle : 0.597 5.794 22028 Z= 0.319 Chirality : 0.046 0.149 2344 Planarity : 0.006 0.077 2816 Dihedral : 14.824 82.844 2656 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.04 % Allowed : 20.14 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.39 (0.19), residues: 1888 helix: 0.70 (0.19), residues: 708 sheet: -0.54 (0.26), residues: 392 loop : 0.53 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 487 TYR 0.018 0.002 TYR D 118 PHE 0.013 0.002 PHE A 88 TRP 0.014 0.001 TRP B 164 HIS 0.004 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00393 (16228) covalent geometry : angle 0.59716 (22028) hydrogen bonds : bond 0.05408 ( 703) hydrogen bonds : angle 5.91785 ( 2007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.562 Fit side-chains REVERT: A 58 ASP cc_start: 0.7761 (m-30) cc_final: 0.7425 (m-30) REVERT: A 102 PHE cc_start: 0.7336 (m-80) cc_final: 0.6818 (m-80) REVERT: A 404 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8934 (ppp) REVERT: A 476 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8276 (mmtm) REVERT: B 58 ASP cc_start: 0.7762 (m-30) cc_final: 0.7534 (m-30) REVERT: B 102 PHE cc_start: 0.7281 (m-80) cc_final: 0.6864 (m-80) REVERT: B 132 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7862 (t) REVERT: B 404 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8925 (ppp) REVERT: C 102 PHE cc_start: 0.7243 (m-80) cc_final: 0.6831 (m-80) REVERT: C 404 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8929 (ppp) REVERT: C 411 MET cc_start: 0.5480 (OUTLIER) cc_final: 0.4423 (tmt) REVERT: D 58 ASP cc_start: 0.7790 (m-30) cc_final: 0.7457 (m-30) REVERT: D 102 PHE cc_start: 0.7334 (m-80) cc_final: 0.6814 (m-80) REVERT: D 132 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7857 (t) REVERT: D 404 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8930 (ppp) outliers start: 34 outliers final: 13 residues processed: 232 average time/residue: 0.6682 time to fit residues: 169.3791 Evaluate side-chains 219 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 74 optimal weight: 0.3980 chunk 113 optimal weight: 9.9990 chunk 147 optimal weight: 0.0270 chunk 4 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 overall best weight: 2.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN C 185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135498 restraints weight = 13473.794| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.79 r_work: 0.3182 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16228 Z= 0.127 Angle : 0.523 5.280 22028 Z= 0.279 Chirality : 0.043 0.143 2344 Planarity : 0.005 0.045 2816 Dihedral : 14.070 80.621 2644 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.18 % Allowed : 19.42 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.53 (0.19), residues: 1888 helix: 0.98 (0.20), residues: 700 sheet: -0.59 (0.26), residues: 392 loop : 0.52 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.016 0.001 TYR A 118 PHE 0.014 0.001 PHE A 88 TRP 0.014 0.001 TRP A 164 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00268 (16228) covalent geometry : angle 0.52252 (22028) hydrogen bonds : bond 0.04502 ( 703) hydrogen bonds : angle 5.57119 ( 2007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 0.450 Fit side-chains REVERT: A 64 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.6950 (m-40) REVERT: A 182 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.7261 (ttm-80) REVERT: A 201 HIS cc_start: 0.7210 (p90) cc_final: 0.7002 (p90) REVERT: A 404 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8798 (ppp) REVERT: A 411 MET cc_start: 0.5387 (OUTLIER) cc_final: 0.4413 (tmt) REVERT: B 132 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7829 (t) REVERT: B 192 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8327 (mtm-85) REVERT: B 404 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8798 (ppp) REVERT: B 411 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.4449 (tmt) REVERT: C 64 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.6952 (m-40) REVERT: C 102 PHE cc_start: 0.7278 (m-80) cc_final: 0.6917 (m-80) REVERT: C 201 HIS cc_start: 0.7205 (p90) cc_final: 0.6995 (p90) REVERT: C 404 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8810 (ppp) REVERT: C 411 MET cc_start: 0.5488 (OUTLIER) cc_final: 0.4406 (tmt) REVERT: D 99 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: D 102 PHE cc_start: 0.7352 (m-80) cc_final: 0.6831 (m-80) REVERT: D 132 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7859 (t) REVERT: D 404 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8810 (ppp) REVERT: D 411 MET cc_start: 0.5391 (OUTLIER) cc_final: 0.4408 (tmt) outliers start: 53 outliers final: 11 residues processed: 249 average time/residue: 0.6806 time to fit residues: 185.2319 Evaluate side-chains 226 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 28 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.176629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134693 restraints weight = 13371.307| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.91 r_work: 0.3180 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16228 Z= 0.128 Angle : 0.522 5.257 22028 Z= 0.278 Chirality : 0.043 0.140 2344 Planarity : 0.005 0.046 2816 Dihedral : 13.634 77.686 2640 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.00 % Allowed : 19.42 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.56 (0.19), residues: 1888 helix: 1.04 (0.20), residues: 700 sheet: -0.58 (0.26), residues: 396 loop : 0.50 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 487 TYR 0.023 0.002 TYR B 147 PHE 0.016 0.001 PHE A 88 TRP 0.013 0.001 TRP D 164 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00274 (16228) covalent geometry : angle 0.52213 (22028) hydrogen bonds : bond 0.04356 ( 703) hydrogen bonds : angle 5.46563 ( 2007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.626 Fit side-chains REVERT: A 64 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.6942 (m-40) REVERT: A 411 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.4427 (tmt) REVERT: A 476 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8298 (mmtm) REVERT: B 99 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: B 132 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7828 (t) REVERT: B 411 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.4470 (tmt) REVERT: C 64 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.6929 (m-40) REVERT: C 411 MET cc_start: 0.5526 (OUTLIER) cc_final: 0.4401 (tmt) REVERT: D 64 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.6940 (m-40) REVERT: D 99 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: D 102 PHE cc_start: 0.7338 (m-80) cc_final: 0.6843 (m-80) REVERT: D 132 SER cc_start: 0.8014 (OUTLIER) cc_final: 0.7786 (t) REVERT: D 411 MET cc_start: 0.5445 (OUTLIER) cc_final: 0.4401 (tmt) outliers start: 50 outliers final: 9 residues processed: 244 average time/residue: 0.6850 time to fit residues: 182.7091 Evaluate side-chains 216 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 147 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 411 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 103 optimal weight: 30.0000 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137901 restraints weight = 13484.512| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.84 r_work: 0.3242 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16228 Z= 0.101 Angle : 0.496 5.183 22028 Z= 0.263 Chirality : 0.042 0.139 2344 Planarity : 0.004 0.042 2816 Dihedral : 12.473 71.335 2640 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.46 % Allowed : 19.30 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.61 (0.19), residues: 1888 helix: 1.14 (0.20), residues: 704 sheet: -0.66 (0.26), residues: 396 loop : 0.52 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 439 TYR 0.017 0.001 TYR C 118 PHE 0.015 0.001 PHE A 88 TRP 0.013 0.001 TRP D 164 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00212 (16228) covalent geometry : angle 0.49561 (22028) hydrogen bonds : bond 0.03703 ( 703) hydrogen bonds : angle 5.27135 ( 2007) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.520 Fit side-chains REVERT: A 411 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.4887 (mpp) REVERT: B 99 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: B 132 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7813 (t) REVERT: B 411 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.4464 (tmt) REVERT: C 99 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6237 (mp0) REVERT: C 411 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.4404 (tmt) REVERT: D 132 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7818 (t) REVERT: D 411 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4860 (mpp) outliers start: 41 outliers final: 14 residues processed: 231 average time/residue: 0.6979 time to fit residues: 175.8745 Evaluate side-chains 220 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 74 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 92 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN C 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.135150 restraints weight = 13231.407| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.58 r_work: 0.3155 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16228 Z= 0.173 Angle : 0.568 5.408 22028 Z= 0.302 Chirality : 0.045 0.136 2344 Planarity : 0.006 0.082 2816 Dihedral : 12.517 64.640 2640 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.34 % Allowed : 19.00 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.61 (0.19), residues: 1888 helix: 1.08 (0.20), residues: 704 sheet: -0.52 (0.27), residues: 388 loop : 0.51 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 487 TYR 0.022 0.002 TYR D 118 PHE 0.017 0.002 PHE A 88 TRP 0.011 0.002 TRP A 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00384 (16228) covalent geometry : angle 0.56768 (22028) hydrogen bonds : bond 0.04825 ( 703) hydrogen bonds : angle 5.53852 ( 2007) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.669 Fit side-chains REVERT: A 411 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.4442 (tmt) REVERT: A 476 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8313 (mmtm) REVERT: B 99 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: B 411 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.4507 (tmt) REVERT: C 411 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.4581 (tmt) REVERT: D 411 MET cc_start: 0.5537 (OUTLIER) cc_final: 0.4440 (tmt) outliers start: 39 outliers final: 15 residues processed: 235 average time/residue: 0.6939 time to fit residues: 177.8668 Evaluate side-chains 216 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 145 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134331 restraints weight = 13244.536| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.81 r_work: 0.3157 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16228 Z= 0.167 Angle : 0.565 5.385 22028 Z= 0.301 Chirality : 0.044 0.136 2344 Planarity : 0.005 0.072 2816 Dihedral : 12.193 59.238 2640 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.10 % Allowed : 19.30 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.60 (0.19), residues: 1888 helix: 1.06 (0.20), residues: 704 sheet: -0.53 (0.27), residues: 388 loop : 0.51 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 487 TYR 0.019 0.002 TYR A 118 PHE 0.018 0.002 PHE A 88 TRP 0.013 0.001 TRP C 164 HIS 0.004 0.001 HIS C 155 Details of bonding type rmsd covalent geometry : bond 0.00368 (16228) covalent geometry : angle 0.56458 (22028) hydrogen bonds : bond 0.04771 ( 703) hydrogen bonds : angle 5.55803 ( 2007) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.596 Fit side-chains REVERT: A 411 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.4533 (tmt) REVERT: A 476 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8304 (mmtm) REVERT: B 99 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: B 411 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.4558 (tmt) REVERT: C 99 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6375 (mp0) REVERT: C 411 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.4630 (tmt) REVERT: D 102 PHE cc_start: 0.7307 (m-80) cc_final: 0.6723 (m-80) REVERT: D 411 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.4516 (tmt) outliers start: 35 outliers final: 18 residues processed: 227 average time/residue: 0.6961 time to fit residues: 172.3477 Evaluate side-chains 223 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 187 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 104 optimal weight: 30.0000 chunk 4 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.136313 restraints weight = 13299.639| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.66 r_work: 0.3166 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.140 Angle : 0.541 5.253 22028 Z= 0.288 Chirality : 0.044 0.139 2344 Planarity : 0.005 0.052 2816 Dihedral : 11.721 59.216 2640 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.04 % Allowed : 19.24 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.64 (0.19), residues: 1888 helix: 1.10 (0.20), residues: 704 sheet: -0.52 (0.27), residues: 388 loop : 0.52 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 439 TYR 0.016 0.002 TYR C 118 PHE 0.017 0.001 PHE A 88 TRP 0.013 0.001 TRP A 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00304 (16228) covalent geometry : angle 0.54098 (22028) hydrogen bonds : bond 0.04451 ( 703) hydrogen bonds : angle 5.48042 ( 2007) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.528 Fit side-chains REVERT: A 411 MET cc_start: 0.5582 (OUTLIER) cc_final: 0.4512 (tmt) REVERT: A 476 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8294 (mmtm) REVERT: B 99 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: B 411 MET cc_start: 0.5649 (OUTLIER) cc_final: 0.4594 (tmt) REVERT: C 64 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7100 (m110) REVERT: C 99 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: C 411 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.4550 (tmt) REVERT: D 99 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: D 102 PHE cc_start: 0.7279 (m-80) cc_final: 0.6716 (m-80) REVERT: D 411 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.4933 (mpp) outliers start: 34 outliers final: 13 residues processed: 228 average time/residue: 0.6647 time to fit residues: 165.1923 Evaluate side-chains 219 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 170 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN C 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.174648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133332 restraints weight = 13193.244| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.76 r_work: 0.3151 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16228 Z= 0.186 Angle : 0.592 5.472 22028 Z= 0.315 Chirality : 0.045 0.139 2344 Planarity : 0.006 0.093 2816 Dihedral : 11.976 59.558 2640 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.86 % Allowed : 19.42 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.53 (0.19), residues: 1888 helix: 0.92 (0.20), residues: 708 sheet: -0.49 (0.27), residues: 388 loop : 0.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 487 TYR 0.019 0.002 TYR A 118 PHE 0.020 0.002 PHE A 88 TRP 0.013 0.002 TRP A 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00414 (16228) covalent geometry : angle 0.59230 (22028) hydrogen bonds : bond 0.05051 ( 703) hydrogen bonds : angle 5.61719 ( 2007) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.491 Fit side-chains REVERT: A 411 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.4553 (tmt) REVERT: A 476 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8306 (mmtm) REVERT: B 182 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7254 (ttm-80) REVERT: B 411 MET cc_start: 0.5686 (OUTLIER) cc_final: 0.4628 (tmt) REVERT: C 99 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: C 404 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8797 (ppp) REVERT: C 411 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.4629 (tmt) REVERT: D 102 PHE cc_start: 0.7283 (m-80) cc_final: 0.6697 (m-80) REVERT: D 404 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8794 (ppp) REVERT: D 411 MET cc_start: 0.5619 (OUTLIER) cc_final: 0.4520 (tmt) outliers start: 31 outliers final: 16 residues processed: 218 average time/residue: 0.7212 time to fit residues: 171.2048 Evaluate side-chains 220 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 148 optimal weight: 6.9990 chunk 94 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134720 restraints weight = 13239.208| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.64 r_work: 0.3139 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16228 Z= 0.186 Angle : 0.595 5.507 22028 Z= 0.317 Chirality : 0.045 0.139 2344 Planarity : 0.006 0.085 2816 Dihedral : 11.968 59.710 2640 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.56 % Allowed : 19.90 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1888 helix: 0.84 (0.20), residues: 712 sheet: -0.48 (0.27), residues: 388 loop : 0.52 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 136 TYR 0.018 0.002 TYR A 118 PHE 0.021 0.002 PHE A 88 TRP 0.014 0.002 TRP B 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00414 (16228) covalent geometry : angle 0.59538 (22028) hydrogen bonds : bond 0.05026 ( 703) hydrogen bonds : angle 5.64792 ( 2007) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.659 Fit side-chains REVERT: A 411 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.4622 (tmt) REVERT: A 476 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8315 (mmtm) REVERT: B 102 PHE cc_start: 0.7242 (m-80) cc_final: 0.6658 (m-80) REVERT: B 182 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7297 (ttm-80) REVERT: B 411 MET cc_start: 0.5759 (OUTLIER) cc_final: 0.4676 (tmt) REVERT: C 99 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: C 102 PHE cc_start: 0.7251 (m-80) cc_final: 0.6693 (m-80) REVERT: C 404 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8830 (ppp) REVERT: C 411 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.4614 (tmt) REVERT: D 102 PHE cc_start: 0.7218 (m-80) cc_final: 0.6611 (m-80) REVERT: D 404 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8831 (ppp) REVERT: D 411 MET cc_start: 0.5726 (OUTLIER) cc_final: 0.4613 (tmt) outliers start: 26 outliers final: 16 residues processed: 215 average time/residue: 0.7004 time to fit residues: 164.2410 Evaluate side-chains 222 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 104 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS B 155 HIS C 133 GLN C 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135834 restraints weight = 13224.166| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.81 r_work: 0.3160 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16228 Z= 0.141 Angle : 0.553 5.295 22028 Z= 0.294 Chirality : 0.044 0.144 2344 Planarity : 0.005 0.049 2816 Dihedral : 11.535 58.965 2640 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.74 % Allowed : 19.60 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.60 (0.19), residues: 1888 helix: 1.03 (0.20), residues: 704 sheet: -0.49 (0.27), residues: 388 loop : 0.52 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 175 TYR 0.013 0.002 TYR B 118 PHE 0.019 0.001 PHE A 88 TRP 0.015 0.001 TRP A 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00308 (16228) covalent geometry : angle 0.55327 (22028) hydrogen bonds : bond 0.04479 ( 703) hydrogen bonds : angle 5.52685 ( 2007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7354.59 seconds wall clock time: 125 minutes 29.20 seconds (7529.20 seconds total)