Starting phenix.real_space_refine on Fri Jul 3 18:29:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7snh_25226/07_2026/7snh_25226.cif Found real_map, /net/cci-nas-00/data/ceres_data/7snh_25226/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7snh_25226/07_2026/7snh_25226.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7snh_25226/07_2026/7snh_25226.cif" model { file = "/net/cci-nas-00/data/ceres_data/7snh_25226/07_2026/7snh_25226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7snh_25226/07_2026/7snh_25226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7snh_25226/07_2026/7snh_25226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7snh_25226/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.25, per 1000 atoms: 0.21 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: 1.27 Conformation dependent library (CDL) restraints added in 556.2 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: 0.35 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: 2.71 Time building geometry restraints manager: 1.68 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: 8171 17.92 - 35.84: 967 35.84 - 53.76: 367 53.76 - 71.69: 97 71.69 - 89.61: 58 Dihedral angle restraints: 9660 sinusoidal: 4116 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 9657 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: 0.06 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: 0.460 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: 0.050 Process input model: 14.530 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 : 19.524 89.608 6092 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/Z covalent geometry : bond 0.00626 / 0.31 (16228) covalent geometry : angle 0.74663 / 0.35 (22028) hydrogen bonds : bond 0.16560 / 10.83 ( 703) hydrogen bonds : angle 7.13787 / 5.17 ( 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 : 0.639 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: 0.6436 time to fit residues: 156.3836 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 : 0.577 ------------------------------------------------------------------------------- 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... A 133 GLN A 185 ASN A 186 HIS B 185 ASN B 186 HIS C 185 ASN C 186 HIS D 185 ASN D 186 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137377 restraints weight = 13202.193| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.59 r_work: 0.3114 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0722 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= 0.181 Angle : 0.599 5.722 22028 Z= 0.320 Chirality : 0.045 0.147 2344 Planarity : 0.006 0.077 2816 Dihedral : 12.118 81.461 2288 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.84 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: 0.40 (0.19), residues: 1888 helix: 0.72 (0.19), residues: 708 sheet: -0.53 (0.26), residues: 392 loop : 0.53 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 487 TYR 0.018 0.002 TYR D 118 PHE 0.013 0.002 PHE A 88 TRP 0.014 0.001 TRP A 164 HIS 0.003 0.001 HIS D 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (16228) covalent geometry : angle 0.59909 / 0.32 (22028) hydrogen bonds : bond 0.05421 / 3.50 ( 703) hydrogen bonds : angle 5.95716 / 4.36 ( 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 252 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.614 Fit side-chains REVERT: A 58 ASP cc_start: 0.7812 (m-30) cc_final: 0.7490 (m-30) REVERT: A 102 PHE cc_start: 0.7343 (m-80) cc_final: 0.6854 (m-80) REVERT: A 476 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8292 (mmtm) REVERT: B 66 PHE cc_start: 0.8110 (m-80) cc_final: 0.7898 (m-80) REVERT: B 102 PHE cc_start: 0.7303 (m-80) cc_final: 0.6878 (m-80) REVERT: B 132 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7854 (t) REVERT: C 102 PHE cc_start: 0.7258 (m-80) cc_final: 0.6826 (m-80) REVERT: C 411 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.4503 (tmt) REVERT: D 102 PHE cc_start: 0.7353 (m-80) cc_final: 0.6857 (m-80) REVERT: D 132 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7847 (t) outliers start: 34 outliers final: 13 residues processed: 234 average time/residue: 0.6285 time to fit residues: 161.2222 Evaluate side-chains 218 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 423 THR 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 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 423 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 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: 9.9990 chunk 113 optimal weight: 7.9990 chunk 147 optimal weight: 0.0050 chunk 4 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 overall best weight: 3.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN C 133 GLN C 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.174781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133824 restraints weight = 13457.671| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.73 r_work: 0.3159 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16228 Z= 0.164 Angle : 0.567 5.579 22028 Z= 0.303 Chirality : 0.044 0.144 2344 Planarity : 0.006 0.068 2816 Dihedral : 11.548 77.854 2276 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.12 % Allowed : 19.18 % Favored : 77.70 % 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: 0.46 (0.19), residues: 1888 helix: 0.88 (0.20), residues: 700 sheet: -0.61 (0.26), residues: 392 loop : 0.51 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 487 TYR 0.018 0.002 TYR A 118 PHE 0.016 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/Z covalent geometry : bond 0.00358 / 0.16 (16228) covalent geometry : angle 0.56715 / 0.30 (22028) hydrogen bonds : bond 0.05024 / 3.23 ( 703) hydrogen bonds : angle 5.72270 / 4.19 ( 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 258 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.608 Fit side-chains REVERT: A 64 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.6961 (m-40) REVERT: A 182 ARG cc_start: 0.7575 (ttp-110) cc_final: 0.7273 (ttm-80) REVERT: A 411 MET cc_start: 0.5474 (OUTLIER) cc_final: 0.4465 (tmt) REVERT: A 476 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8271 (mmtm) REVERT: B 64 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7001 (m-40) REVERT: B 132 SER cc_start: 0.8051 (OUTLIER) cc_final: 0.7832 (t) REVERT: B 178 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7522 (mp-120) REVERT: B 202 TYR cc_start: 0.7862 (t80) cc_final: 0.7660 (t80) REVERT: B 411 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.4484 (tmt) REVERT: C 64 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.6986 (m-40) REVERT: C 102 PHE cc_start: 0.7321 (m-80) cc_final: 0.6941 (m-80) REVERT: C 178 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7471 (mp-120) REVERT: C 411 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.4463 (tmt) REVERT: D 64 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.6960 (m-40) REVERT: D 99 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: D 102 PHE cc_start: 0.7316 (m-80) cc_final: 0.6832 (m-80) outliers start: 52 outliers final: 15 residues processed: 246 average time/residue: 0.6223 time to fit residues: 167.9040 Evaluate side-chains 224 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 298 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 B residue 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL 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 178 GLN 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 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 291 VAL Chi-restraints excluded: chain D residue 298 VAL 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: 7.9990 chunk 180 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 185 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN C 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.178460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138026 restraints weight = 13475.927| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.74 r_work: 0.3219 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16228 Z= 0.098 Angle : 0.491 5.102 22028 Z= 0.261 Chirality : 0.042 0.142 2344 Planarity : 0.004 0.044 2816 Dihedral : 10.829 70.094 2276 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.82 % Allowed : 18.65 % 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: 0.55 (0.19), residues: 1888 helix: 1.08 (0.20), residues: 700 sheet: -0.64 (0.26), residues: 396 loop : 0.49 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 439 TYR 0.014 0.001 TYR A 118 PHE 0.014 0.001 PHE A 88 TRP 0.014 0.001 TRP C 164 HIS 0.004 0.001 HIS C 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (16228) covalent geometry : angle 0.49075 / 0.26 (22028) hydrogen bonds : bond 0.03748 / 2.39 ( 703) hydrogen bonds : angle 5.33640 / 3.90 ( 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 262 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.547 Fit side-chains REVERT: A 64 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.6928 (m-40) REVERT: A 411 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.4424 (tmt) REVERT: A 413 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7321 (t80) REVERT: B 64 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.6873 (m-40) REVERT: B 99 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: B 132 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7829 (t) REVERT: B 411 MET cc_start: 0.5527 (OUTLIER) cc_final: 0.4481 (tmt) REVERT: C 64 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.6861 (m-40) REVERT: C 411 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.4401 (tmt) REVERT: D 64 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.6929 (m-40) REVERT: D 99 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: D 102 PHE cc_start: 0.7353 (m-80) cc_final: 0.6839 (m-80) REVERT: D 132 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7821 (t) REVERT: D 411 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.4474 (tmt) REVERT: D 413 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7297 (t80) outliers start: 47 outliers final: 7 residues processed: 246 average time/residue: 0.5996 time to fit residues: 161.9730 Evaluate side-chains 218 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 413 PHE Chi-restraints excluded: chain B residue 64 ASN 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 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 291 VAL Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 413 PHE 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: 20.0000 chunk 96 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 91 optimal weight: 0.0050 overall best weight: 3.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3991 r_free = 0.3991 target = 0.175410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133904 restraints weight = 13336.672| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.79 r_work: 0.3179 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16228 Z= 0.157 Angle : 0.554 5.246 22028 Z= 0.295 Chirality : 0.044 0.138 2344 Planarity : 0.005 0.042 2816 Dihedral : 10.759 64.940 2272 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.46 % Allowed : 18.23 % Favored : 79.32 % 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: 0.59 (0.19), residues: 1888 helix: 1.07 (0.20), residues: 704 sheet: -0.57 (0.26), residues: 388 loop : 0.50 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 463 TYR 0.020 0.002 TYR B 118 PHE 0.017 0.002 PHE A 88 TRP 0.012 0.001 TRP B 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (16228) covalent geometry : angle 0.55409 / 0.30 (22028) hydrogen bonds : bond 0.04658 / 2.98 ( 703) hydrogen bonds : angle 5.50875 / 4.03 ( 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 : 0.519 Fit side-chains REVERT: A 411 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.4460 (tmt) REVERT: B 64 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.6878 (m-40) REVERT: B 99 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: B 132 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7828 (t) REVERT: B 411 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.4446 (tmt) REVERT: C 64 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.6864 (m-40) REVERT: C 99 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: C 205 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7610 (mttm) REVERT: C 411 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.4464 (tmt) REVERT: D 99 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: D 411 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.4541 (tmt) outliers start: 41 outliers final: 10 residues processed: 232 average time/residue: 0.6246 time to fit residues: 158.5631 Evaluate side-chains 220 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 510 VAL Chi-restraints excluded: chain B residue 64 ASN 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 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 205 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 74 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3982 r_free = 0.3982 target = 0.174675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.132142 restraints weight = 13206.488| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.87 r_work: 0.3142 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16228 Z= 0.172 Angle : 0.574 5.375 22028 Z= 0.306 Chirality : 0.044 0.137 2344 Planarity : 0.005 0.040 2816 Dihedral : 10.610 58.954 2272 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.70 % Allowed : 18.59 % 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: 0.59 (0.19), residues: 1888 helix: 1.04 (0.20), residues: 708 sheet: -0.55 (0.26), residues: 388 loop : 0.52 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 487 TYR 0.020 0.002 TYR A 118 PHE 0.020 0.002 PHE A 88 TRP 0.013 0.001 TRP C 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16228) covalent geometry : angle 0.57433 / 0.31 (22028) hydrogen bonds : bond 0.04881 / 3.12 ( 703) hydrogen bonds : angle 5.61471 / 4.11 ( 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 250 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 0.591 Fit side-chains REVERT: A 99 GLU cc_start: 0.6509 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: A 411 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4615 (tmt) REVERT: A 476 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8330 (mmtm) REVERT: B 64 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.6911 (m-40) REVERT: B 99 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: B 411 MET cc_start: 0.5674 (OUTLIER) cc_final: 0.4587 (tmt) REVERT: C 64 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.6900 (m-40) REVERT: C 99 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: C 205 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7769 (tppt) REVERT: C 411 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.4624 (tmt) REVERT: D 99 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: D 102 PHE cc_start: 0.7294 (m-80) cc_final: 0.6689 (m-80) REVERT: D 411 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.4567 (tmt) outliers start: 45 outliers final: 12 residues processed: 236 average time/residue: 0.6315 time to fit residues: 163.0267 Evaluate side-chains 224 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU 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 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 64 ASN 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 205 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 8.9990 chunk 94 optimal weight: 30.0000 chunk 87 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3966 r_free = 0.3966 target = 0.173232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.130046 restraints weight = 13229.790| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.91 r_work: 0.3077 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16228 Z= 0.223 Angle : 0.627 5.733 22028 Z= 0.334 Chirality : 0.046 0.135 2344 Planarity : 0.005 0.039 2816 Dihedral : 10.536 59.927 2272 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.34 % Allowed : 18.47 % Favored : 79.20 % 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: 0.48 (0.19), residues: 1888 helix: 0.88 (0.20), residues: 712 sheet: -0.49 (0.27), residues: 388 loop : 0.45 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 463 TYR 0.023 0.002 TYR A 118 PHE 0.021 0.002 PHE A 88 TRP 0.014 0.002 TRP A 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (16228) covalent geometry : angle 0.62684 / 0.33 (22028) hydrogen bonds : bond 0.05431 / 3.47 ( 703) hydrogen bonds : angle 5.75425 / 4.20 ( 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 239 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.616 Fit side-chains REVERT: A 411 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.4704 (tmt) REVERT: A 476 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8348 (mmtm) REVERT: B 64 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.6980 (m-40) REVERT: B 99 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6205 (mp0) REVERT: B 102 PHE cc_start: 0.7256 (m-80) cc_final: 0.6681 (m-80) REVERT: B 182 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7345 (ttm-80) REVERT: B 411 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.4734 (tmt) REVERT: C 64 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.6989 (m-40) REVERT: C 99 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: C 102 PHE cc_start: 0.7284 (m-80) cc_final: 0.6722 (m-80) REVERT: C 205 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7628 (mttm) REVERT: C 411 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.4711 (tmt) REVERT: D 99 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: D 102 PHE cc_start: 0.7201 (m-80) cc_final: 0.6601 (m-80) REVERT: D 411 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.4685 (tmt) outliers start: 39 outliers final: 20 residues processed: 229 average time/residue: 0.6508 time to fit residues: 162.9757 Evaluate side-chains 224 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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 64 ASN 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 298 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 64 ASN Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 205 LYS 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 99 GLU 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: 0.8980 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 104 optimal weight: 30.0000 chunk 4 optimal weight: 0.0770 chunk 95 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 186 HIS C 133 GLN C 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131978 restraints weight = 13275.540| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.90 r_work: 0.3119 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1494 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= 0.145 Angle : 0.554 5.497 22028 Z= 0.296 Chirality : 0.043 0.139 2344 Planarity : 0.004 0.038 2816 Dihedral : 9.948 59.070 2272 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.64 % Allowed : 17.99 % Favored : 79.38 % 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: 1.07 (0.20), residues: 708 sheet: -0.54 (0.27), residues: 388 loop : 0.49 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.017 0.002 TYR A 118 PHE 0.019 0.001 PHE A 88 TRP 0.015 0.001 TRP A 164 HIS 0.003 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16228) covalent geometry : angle 0.55447 / 0.30 (22028) hydrogen bonds : bond 0.04577 / 2.92 ( 703) hydrogen bonds : angle 5.55298 / 4.06 ( 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 252 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.557 Fit side-chains REVERT: A 136 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7328 (mpp80) REVERT: A 411 MET cc_start: 0.5765 (OUTLIER) cc_final: 0.4628 (tmt) REVERT: A 476 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8351 (mmtm) REVERT: B 64 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.6932 (m-40) REVERT: B 99 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: B 102 PHE cc_start: 0.7234 (m-80) cc_final: 0.6685 (m-80) REVERT: B 136 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7281 (mpp80) REVERT: B 182 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.7302 (ttm-80) REVERT: B 411 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.4653 (tmt) REVERT: C 64 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.6929 (m-40) REVERT: C 99 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: C 102 PHE cc_start: 0.7231 (m-80) cc_final: 0.6705 (m-80) REVERT: C 182 ARG cc_start: 0.7669 (ttp-110) cc_final: 0.7281 (ttm-80) REVERT: C 205 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7665 (mttm) REVERT: C 411 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.4593 (tmt) REVERT: D 102 PHE cc_start: 0.7186 (m-80) cc_final: 0.6570 (m-80) REVERT: D 411 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.4623 (tmt) outliers start: 44 outliers final: 14 residues processed: 239 average time/residue: 0.6483 time to fit residues: 169.8161 Evaluate side-chains 223 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 ARG 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 A residue 510 VAL Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 ARG 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 64 ASN Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 205 LYS 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 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 170 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 186 HIS C 133 GLN C 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132817 restraints weight = 13194.798| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.87 r_work: 0.3163 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16228 Z= 0.171 Angle : 0.581 5.321 22028 Z= 0.309 Chirality : 0.044 0.139 2344 Planarity : 0.005 0.037 2816 Dihedral : 9.857 58.805 2272 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.28 % Allowed : 18.59 % Favored : 79.14 % 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: 0.51 (0.19), residues: 1888 helix: 0.93 (0.20), residues: 708 sheet: -0.51 (0.27), residues: 388 loop : 0.47 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 136 TYR 0.018 0.002 TYR A 118 PHE 0.021 0.002 PHE A 88 TRP 0.014 0.002 TRP A 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (16228) covalent geometry : angle 0.58064 / 0.31 (22028) hydrogen bonds : bond 0.04901 / 3.13 ( 703) hydrogen bonds : angle 5.61456 / 4.10 ( 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 238 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.512 Fit side-chains REVERT: A 136 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7266 (mpp80) REVERT: A 411 MET cc_start: 0.5735 (OUTLIER) cc_final: 0.4639 (tmt) REVERT: A 476 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8342 (mmtm) REVERT: B 64 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.6953 (m-40) REVERT: B 99 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6315 (mp0) REVERT: B 102 PHE cc_start: 0.7230 (m-80) cc_final: 0.6650 (m-80) REVERT: B 136 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7194 (mpp80) REVERT: B 182 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.7281 (ttm-80) REVERT: B 411 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.4654 (tmt) REVERT: C 64 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.6955 (m-40) REVERT: C 99 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: C 102 PHE cc_start: 0.7232 (m-80) cc_final: 0.6661 (m-80) REVERT: C 182 ARG cc_start: 0.7578 (ttp-110) cc_final: 0.7275 (ttm-80) REVERT: C 205 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7735 (tppt) REVERT: C 411 MET cc_start: 0.5710 (OUTLIER) cc_final: 0.4601 (tmt) REVERT: D 102 PHE cc_start: 0.7166 (m-80) cc_final: 0.6555 (m-80) REVERT: D 411 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.4641 (tmt) outliers start: 38 outliers final: 18 residues processed: 224 average time/residue: 0.6424 time to fit residues: 157.3669 Evaluate side-chains 225 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 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 64 ASN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 ARG 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 64 ASN Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 205 LYS 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 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=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: 9.9990 chunk 90 optimal weight: 3.9990 chunk 151 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 186 HIS C 133 GLN C 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132200 restraints weight = 13210.891| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.74 r_work: 0.3139 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16228 Z= 0.230 Angle : 0.643 5.710 22028 Z= 0.341 Chirality : 0.047 0.138 2344 Planarity : 0.005 0.039 2816 Dihedral : 10.100 59.894 2272 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.04 % Allowed : 18.88 % Favored : 79.08 % 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: 0.80 (0.20), residues: 712 sheet: -0.43 (0.27), residues: 388 loop : 0.45 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 136 TYR 0.022 0.002 TYR A 118 PHE 0.024 0.002 PHE A 88 TRP 0.014 0.002 TRP A 164 HIS 0.005 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (16228) covalent geometry : angle 0.64289 / 0.34 (22028) hydrogen bonds : bond 0.05488 / 3.51 ( 703) hydrogen bonds : angle 5.78575 / 4.22 ( 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 228 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.585 Fit side-chains REVERT: A 102 PHE cc_start: 0.7175 (m-80) cc_final: 0.6573 (m-80) REVERT: A 136 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7222 (mpp80) REVERT: A 411 MET cc_start: 0.5800 (OUTLIER) cc_final: 0.4617 (tmt) REVERT: A 476 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8325 (mmtm) REVERT: B 64 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7050 (m-40) REVERT: B 102 PHE cc_start: 0.7195 (m-80) cc_final: 0.6595 (m-80) REVERT: B 136 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7183 (mpp80) REVERT: B 182 ARG cc_start: 0.7628 (ttp-110) cc_final: 0.7279 (ttm-80) REVERT: B 411 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.4617 (tmt) REVERT: C 64 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7045 (m-40) REVERT: C 102 PHE cc_start: 0.7201 (m-80) cc_final: 0.6609 (m-80) REVERT: C 182 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7266 (ttm-80) REVERT: C 205 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7649 (mttm) REVERT: C 411 MET cc_start: 0.5839 (OUTLIER) cc_final: 0.4619 (tmt) REVERT: D 102 PHE cc_start: 0.7169 (m-80) cc_final: 0.6562 (m-80) REVERT: D 411 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.4631 (tmt) outliers start: 34 outliers final: 18 residues processed: 217 average time/residue: 0.6752 time to fit residues: 159.9439 Evaluate side-chains 218 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 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 64 ASN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 136 ARG 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 64 ASN Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 205 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 29 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 104 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 186 HIS C 133 GLN C 186 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131280 restraints weight = 13170.868| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.93 r_work: 0.3094 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16228 Z= 0.167 Angle : 0.583 5.410 22028 Z= 0.311 Chirality : 0.044 0.145 2344 Planarity : 0.005 0.037 2816 Dihedral : 9.824 58.525 2272 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.86 % Allowed : 19.24 % Favored : 78.90 % 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: 0.47 (0.19), residues: 1888 helix: 0.85 (0.20), residues: 712 sheet: -0.48 (0.27), residues: 388 loop : 0.47 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 136 TYR 0.017 0.002 TYR A 118 PHE 0.021 0.002 PHE C 88 TRP 0.015 0.001 TRP D 164 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (16228) covalent geometry : angle 0.58344 / 0.31 (22028) hydrogen bonds : bond 0.04873 / 3.11 ( 703) hydrogen bonds : angle 5.65542 / 4.13 ( 2007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7017.57 seconds wall clock time: 119 minutes 57.21 seconds (7197.21 seconds total)