Starting phenix.real_space_refine on Sat Aug 8 04:27:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hjt_52226/08_2026/9hjt_52226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hjt_52226/08_2026/9hjt_52226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hjt_52226/08_2026/9hjt_52226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hjt_52226/08_2026/9hjt_52226.map" model { file = "/net/cci-nas-00/data/ceres_data/9hjt_52226/08_2026/9hjt_52226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hjt_52226/08_2026/9hjt_52226.cif" } resolution = 3.26 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= -0.000 sd= 0.007 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 62 5.49 5 S 92 5.16 5 C 8252 2.51 5 N 2323 2.21 5 O 2585 1.98 5 H 12764 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26083 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 2529 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "F" Number of atoms: 5849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5849 Classifications: {'peptide': 379} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 359} Chain: "G" Number of atoms: 5849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5849 Classifications: {'peptide': 379} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 359} Chain: "H" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4942 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 19, 'TRANS': 283} Chain: "I" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4942 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 19, 'TRANS': 283} Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 967 Classifications: {'DNA': 31} Modifications used: {'3*END': 1, 'p5*END': 1} Link IDs: {'rna3p': 30} Chain: "L" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 1000 Classifications: {'DNA': 31} Modifications used: {'3*END': 1, 'p5*END': 1} Link IDs: {'rna3p': 30} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1206 SG CYS A 84 54.447 64.073 32.985 1.00108.47 S ATOM 1252 SG CYS A 87 53.845 60.784 31.138 1.00108.30 S ATOM 174 SG CYS A 23 25.061 93.196 34.341 1.00137.92 S ATOM 238 SG CYS A 28 24.796 89.351 35.222 1.00142.71 S ATOM 697 SG CYS A 54 35.867 75.119 13.520 1.00150.02 S ATOM 763 SG CYS A 59 34.047 72.129 15.190 1.00125.49 S ATOM 1648 SG CYS A 112 32.123 60.776 50.162 1.00 85.78 S ATOM 1692 SG CYS A 115 33.144 57.108 50.806 1.00 76.59 S ATOM 2124 SG CYS A 142 19.716 67.788 31.252 1.00146.57 S ATOM 2167 SG CYS A 145 20.028 64.432 29.602 1.00160.05 S Time building chain proxies: 4.37, per 1000 atoms: 0.17 Number of scatterers: 26083 At special positions: 0 Unit cell: (79.376, 125.296, 169.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 92 16.00 P 62 15.00 O 2585 8.00 N 2323 7.00 C 8252 6.00 H 12764 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 709.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 104 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 100 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 41 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 46 " pdb="ZN ZN A 302 " - pdb=" SG CYS A 28 " pdb="ZN ZN A 302 " - pdb=" SG CYS A 23 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 76 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 59 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 54 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 128 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 132 " pdb="ZN ZN A 304 " - pdb=" SG CYS A 115 " pdb="ZN ZN A 304 " - pdb=" SG CYS A 112 " pdb=" ZN A 305 " pdb="ZN ZN A 305 " - pdb=" NE2 HIS A 158 " pdb="ZN ZN A 305 " - pdb=" NE2 HIS A 163 " pdb="ZN ZN A 305 " - pdb=" SG CYS A 145 " pdb="ZN ZN A 305 " - pdb=" SG CYS A 142 " Number of angles added : 10 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 46.1% alpha, 8.8% beta 31 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 36 through 46 removed outlier: 4.080A pdb=" N HIS A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.869A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.911A pdb=" N MET A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS A 104 " --> pdb=" O HIS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.593A pdb=" N LYS A 130 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 131 " --> pdb=" O TRP A 127 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.622A pdb=" N PHE F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 46 removed outlier: 3.846A pdb=" N LEU F 38 " --> pdb=" O PRO F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 58 Processing helix chain 'F' and resid 95 through 113 removed outlier: 4.316A pdb=" N ASP F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 155 removed outlier: 3.549A pdb=" N ASP F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Proline residue: F 142 - end of helix Processing helix chain 'F' and resid 204 through 215 removed outlier: 3.668A pdb=" N GLN F 213 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 225 removed outlier: 4.123A pdb=" N LYS F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.543A pdb=" N VAL F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 258 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 307 through 310 removed outlier: 3.999A pdb=" N PHE F 310 " --> pdb=" O GLY F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 310' Processing helix chain 'F' and resid 329 through 342 removed outlier: 3.801A pdb=" N ALA F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 35 through 46 Processing helix chain 'G' and resid 48 through 58 removed outlier: 3.886A pdb=" N ASP G 53 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU G 54 " --> pdb=" O GLN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 114 removed outlier: 4.083A pdb=" N ASP G 110 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 114 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 156 removed outlier: 3.869A pdb=" N LYS G 139 " --> pdb=" O ARG G 135 " (cutoff:3.500A) Proline residue: G 142 - end of helix Processing helix chain 'G' and resid 181 through 185 removed outlier: 4.085A pdb=" N PHE G 185 " --> pdb=" O PRO G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.739A pdb=" N ALA G 208 " --> pdb=" O GLY G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 228 removed outlier: 3.578A pdb=" N ASN G 222 " --> pdb=" O PRO G 218 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS G 223 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE G 224 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU G 226 " --> pdb=" O ASN G 222 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 245 removed outlier: 3.680A pdb=" N VAL G 233 " --> pdb=" O THR G 229 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU G 234 " --> pdb=" O GLN G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 258 removed outlier: 3.917A pdb=" N HIS G 256 " --> pdb=" O ALA G 252 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR G 257 " --> pdb=" O GLY G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 280 removed outlier: 3.687A pdb=" N ASN G 277 " --> pdb=" O GLY G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 removed outlier: 4.180A pdb=" N VAL G 302 " --> pdb=" O LYS G 298 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA G 305 " --> pdb=" O ALA G 301 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS G 306 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 342 removed outlier: 4.008A pdb=" N ARG G 335 " --> pdb=" O GLU G 331 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 338 " --> pdb=" O ALA G 334 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 497 removed outlier: 3.501A pdb=" N GLY H 478 " --> pdb=" O LYS H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 520 through 535 removed outlier: 3.616A pdb=" N THR H 532 " --> pdb=" O LEU H 528 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG H 533 " --> pdb=" O CYS H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 562 removed outlier: 3.683A pdb=" N TYR H 549 " --> pdb=" O PRO H 545 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR H 550 " --> pdb=" O ASP H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 571 through 573 No H-bonds generated for 'chain 'H' and resid 571 through 573' Processing helix chain 'H' and resid 574 through 587 removed outlier: 4.660A pdb=" N ASP H 587 " --> pdb=" O GLU H 583 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 611 Processing helix chain 'H' and resid 618 through 634 Processing helix chain 'H' and resid 638 through 644 removed outlier: 3.516A pdb=" N LYS H 644 " --> pdb=" O ASP H 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 697 through 700 Processing helix chain 'H' and resid 701 through 713 Processing helix chain 'H' and resid 714 through 718 Processing helix chain 'H' and resid 746 through 759 removed outlier: 3.727A pdb=" N VAL H 759 " --> pdb=" O THR H 755 " (cutoff:3.500A) Processing helix chain 'H' and resid 760 through 773 removed outlier: 3.514A pdb=" N ALA H 770 " --> pdb=" O ALA H 766 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 497 removed outlier: 3.925A pdb=" N GLY I 478 " --> pdb=" O LYS I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 535 removed outlier: 3.523A pdb=" N ASN I 525 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR I 532 " --> pdb=" O LEU I 528 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG I 533 " --> pdb=" O CYS I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 544 through 562 Processing helix chain 'I' and resid 571 through 573 No H-bonds generated for 'chain 'I' and resid 571 through 573' Processing helix chain 'I' and resid 574 through 586 Processing helix chain 'I' and resid 604 through 611 Processing helix chain 'I' and resid 618 through 634 Processing helix chain 'I' and resid 638 through 644 removed outlier: 3.502A pdb=" N HIS I 642 " --> pdb=" O THR I 638 " (cutoff:3.500A) Processing helix chain 'I' and resid 683 through 687 Processing helix chain 'I' and resid 697 through 700 Processing helix chain 'I' and resid 701 through 712 Processing helix chain 'I' and resid 746 through 758 Processing helix chain 'I' and resid 760 through 773 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.515A pdb=" N TYR A 82 " --> pdb=" O PHE A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 71 through 74 removed outlier: 3.961A pdb=" N CYS F 71 " --> pdb=" O GLN F 84 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN F 84 " --> pdb=" O CYS F 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 87 through 89 removed outlier: 3.637A pdb=" N ASP F 87 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY F 174 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 125 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 325 through 328 removed outlier: 6.499A pdb=" N LEU F 197 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N TRP F 352 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N LEU F 293 " --> pdb=" O TRP F 352 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE F 354 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE F 367 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE F 290 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS F 369 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASN F 292 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG F 371 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE F 373 " --> pdb=" O PRO F 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 72 through 74 removed outlier: 3.506A pdb=" N ASN G 121 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 163 through 166 Processing sheet with id=AA9, first strand: chain 'G' and resid 325 through 329 removed outlier: 3.795A pdb=" N ASP G 195 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY G 355 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU G 199 " --> pdb=" O ILE G 353 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE G 353 " --> pdb=" O LEU G 199 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N TRP G 352 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N LEU G 293 " --> pdb=" O TRP G 352 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE G 354 " --> pdb=" O HIS G 291 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N SER G 287 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N ILE G 367 " --> pdb=" O SER G 287 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N VAL G 289 " --> pdb=" O ILE G 367 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N LYS G 369 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS G 291 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 371 " --> pdb=" O HIS G 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 651 through 653 removed outlier: 3.606A pdb=" N LEU H 651 " --> pdb=" O ARG H 669 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG H 669 " --> pdb=" O LEU H 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 726 through 728 removed outlier: 5.875A pdb=" N GLN H 743 " --> pdb=" O THR H 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 651 through 653 removed outlier: 3.613A pdb=" N GLN I 653 " --> pdb=" O SER I 667 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER I 667 " --> pdb=" O GLN I 653 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 726 through 728 removed outlier: 5.789A pdb=" N GLN I 743 " --> pdb=" O THR I 727 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 5.91 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12735 1.03 - 1.23: 60 1.23 - 1.42: 5711 1.42 - 1.62: 7844 1.62 - 1.81: 145 Bond restraints: 26495 Sorted by residual: bond pdb=" C3' DG L 2 " pdb=" C2' DG L 2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.12e+00 bond pdb=" C3' DG L 7 " pdb=" C2' DG L 7 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.27e+00 bond pdb=" C3' DC K 23 " pdb=" C2' DC K 23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.15e+00 bond pdb=" C1' DC K 21 " pdb=" N1 DC K 21 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.07e+00 bond pdb=" C3' DC K 26 " pdb=" C2' DC K 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.62e+00 ... (remaining 26490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 44025 0.99 - 1.98: 3679 1.98 - 2.98: 204 2.98 - 3.97: 103 3.97 - 4.96: 18 Bond angle restraints: 48029 Sorted by residual: angle pdb=" N3 DT K 15 " pdb=" C4 DT K 15 " pdb=" O4 DT K 15 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT L 13 " pdb=" C4 DT L 13 " pdb=" O4 DT L 13 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT K 14 " pdb=" C4 DT K 14 " pdb=" O4 DT K 14 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT K 7 " pdb=" C4 DT K 7 " pdb=" O4 DT K 7 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT L 15 " pdb=" C4 DT L 15 " pdb=" O4 DT L 15 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 48024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.55: 11290 26.55 - 53.09: 730 53.09 - 79.64: 170 79.64 - 106.18: 0 106.18 - 132.73: 1 Dihedral angle restraints: 12191 sinusoidal: 7058 harmonic: 5133 Sorted by residual: dihedral pdb=" CA VAL F 33 " pdb=" C VAL F 33 " pdb=" N PRO F 34 " pdb=" CA PRO F 34 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU H 516 " pdb=" C LEU H 516 " pdb=" N ILE H 517 " pdb=" CA ILE H 517 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DG L 26 " pdb=" C3' DG L 26 " pdb=" O3' DG L 26 " pdb=" P DG L 27 " ideal model delta sinusoidal sigma weight residual 220.00 87.27 132.73 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 12188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1452 0.035 - 0.069: 416 0.069 - 0.104: 121 0.104 - 0.138: 69 0.138 - 0.173: 45 Chirality restraints: 2103 Sorted by residual: chirality pdb=" C3' DT L 16 " pdb=" C4' DT L 16 " pdb=" O3' DT L 16 " pdb=" C2' DT L 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" C3' DA K 19 " pdb=" C4' DA K 19 " pdb=" O3' DA K 19 " pdb=" C2' DA K 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" C3' DC K 6 " pdb=" C4' DC K 6 " pdb=" O3' DC K 6 " pdb=" C2' DC K 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 2100 not shown) Planarity restraints: 3698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 576 " 0.109 9.50e-02 1.11e+02 3.65e-02 1.52e+00 pdb=" NE ARG I 576 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG I 576 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG I 576 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 576 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG I 576 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG I 576 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG I 576 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG I 576 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 163 " -0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO A 164 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 95 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO G 96 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO G 96 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO G 96 " 0.015 5.00e-02 4.00e+02 ... (remaining 3695 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 667 2.13 - 2.75: 47683 2.75 - 3.37: 73452 3.37 - 3.98: 95748 3.98 - 4.60: 147415 Nonbonded interactions: 364965 Sorted by model distance: nonbonded pdb=" HG SER A 154 " pdb=" O3' DT L 15 " model vdw 1.515 2.450 nonbonded pdb=" O MET G 114 " pdb=" H ILE G 186 " model vdw 1.634 2.450 nonbonded pdb=" HD1 HIS A 75 " pdb=" OP1 DA K 17 " model vdw 1.640 2.450 nonbonded pdb=" O CYS I 529 " pdb=" HG1 THR I 532 " model vdw 1.653 2.450 nonbonded pdb=" HZ1 LYS A 161 " pdb=" N3 DA K 17 " model vdw 1.658 2.600 ... (remaining 364960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } 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: 8.850 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: 0.110 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.940 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.004 0.044 13751 Z= 0.260 Angle : 0.570 7.193 18876 Z= 0.371 Chirality : 0.045 0.173 2103 Planarity : 0.003 0.049 2216 Dihedral : 16.965 132.726 5291 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1508 helix: 0.82 (0.22), residues: 597 sheet: -1.38 (0.43), residues: 152 loop : -0.62 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 576 TYR 0.012 0.001 TYR I 550 PHE 0.011 0.001 PHE A 149 TRP 0.016 0.001 TRP I 485 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.26 (13731) covalent geometry : angle 0.56372 / 0.37 (18866) hydrogen bonds : bond 0.19154 / 13.11 ( 560) hydrogen bonds : angle 6.42626 / 4.71 ( 1486) metal coordination : bond 0.00756 / 0.42 ( 20) metal coordination : angle 3.62430 / 1.93 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 ASN cc_start: 0.8636 (t0) cc_final: 0.8429 (t0) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3013 time to fit residues: 124.4839 Evaluate side-chains 160 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 106 ASN F 259 ASN F 314 HIS H 537 ASN I 641 GLN I 743 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.103394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.076022 restraints weight = 106930.917| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 4.20 r_work: 0.3216 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13751 Z= 0.254 Angle : 0.656 8.608 18876 Z= 0.361 Chirality : 0.043 0.201 2103 Planarity : 0.004 0.049 2216 Dihedral : 17.115 130.497 2291 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.06 % Allowed : 7.71 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1508 helix: 0.66 (0.20), residues: 634 sheet: -1.38 (0.43), residues: 152 loop : -0.77 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 500 TYR 0.011 0.002 TYR I 706 PHE 0.023 0.002 PHE I 647 TRP 0.012 0.001 TRP I 485 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (13731) covalent geometry : angle 0.64778 / 0.36 (18866) hydrogen bonds : bond 0.05796 / 3.99 ( 560) hydrogen bonds : angle 5.31398 / 3.89 ( 1486) metal coordination : bond 0.01590 / 0.77 ( 20) metal coordination : angle 4.46406 / 2.26 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8234 (tp30) cc_final: 0.8017 (tp30) REVERT: G 8 ASN cc_start: 0.8705 (t0) cc_final: 0.8339 (t0) REVERT: H 627 MET cc_start: 0.9280 (ttm) cc_final: 0.9011 (ttp) REVERT: H 687 MET cc_start: 0.7607 (pmm) cc_final: 0.7374 (pmm) REVERT: H 771 ASN cc_start: 0.8829 (m110) cc_final: 0.8587 (m-40) REVERT: I 560 PHE cc_start: 0.8258 (m-10) cc_final: 0.8011 (m-10) outliers start: 14 outliers final: 14 residues processed: 169 average time/residue: 0.2598 time to fit residues: 63.7029 Evaluate side-chains 155 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 529 CYS Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 710 LEU Chi-restraints excluded: chain H residue 713 CYS Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 63 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.103038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.076097 restraints weight = 106279.958| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 4.05 r_work: 0.3217 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13751 Z= 0.164 Angle : 0.565 6.327 18876 Z= 0.312 Chirality : 0.040 0.199 2103 Planarity : 0.004 0.037 2216 Dihedral : 17.134 129.376 2291 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.21 % Allowed : 8.16 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1508 helix: 0.95 (0.21), residues: 624 sheet: -1.41 (0.43), residues: 152 loop : -0.70 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 747 TYR 0.010 0.001 TYR F 112 PHE 0.015 0.001 PHE I 647 TRP 0.010 0.001 TRP I 485 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (13731) covalent geometry : angle 0.55947 / 0.31 (18866) hydrogen bonds : bond 0.05045 / 3.45 ( 560) hydrogen bonds : angle 4.89524 / 3.56 ( 1486) metal coordination : bond 0.00878 / 0.45 ( 20) metal coordination : angle 3.51214 / 1.82 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 ASN cc_start: 0.8688 (t0) cc_final: 0.8327 (t0) REVERT: G 122 MET cc_start: 0.8752 (ttp) cc_final: 0.8506 (ttp) REVERT: H 627 MET cc_start: 0.9258 (ttm) cc_final: 0.8989 (ttp) REVERT: H 687 MET cc_start: 0.7689 (pmm) cc_final: 0.7469 (pmm) outliers start: 16 outliers final: 14 residues processed: 161 average time/residue: 0.2451 time to fit residues: 58.4987 Evaluate side-chains 157 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 529 CYS Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 691 GLN Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 710 LEU Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 145 optimal weight: 0.0870 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.103083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.075595 restraints weight = 106348.141| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.08 r_work: 0.3205 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13751 Z= 0.157 Angle : 0.554 9.206 18876 Z= 0.304 Chirality : 0.040 0.196 2103 Planarity : 0.004 0.035 2216 Dihedral : 17.156 128.631 2291 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.44 % Allowed : 8.39 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1508 helix: 1.15 (0.21), residues: 622 sheet: -1.39 (0.43), residues: 152 loop : -0.67 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 536 TYR 0.007 0.001 TYR I 706 PHE 0.017 0.001 PHE F 148 TRP 0.009 0.001 TRP I 485 HIS 0.006 0.001 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (13731) covalent geometry : angle 0.54896 / 0.30 (18866) hydrogen bonds : bond 0.04396 / 2.98 ( 560) hydrogen bonds : angle 4.62674 / 3.36 ( 1486) metal coordination : bond 0.00940 / 0.51 ( 20) metal coordination : angle 3.31241 / 1.72 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 ASN cc_start: 0.8679 (t0) cc_final: 0.8322 (t0) REVERT: G 122 MET cc_start: 0.8781 (ttp) cc_final: 0.8515 (ttp) REVERT: I 560 PHE cc_start: 0.8324 (m-10) cc_final: 0.8026 (m-10) outliers start: 19 outliers final: 15 residues processed: 162 average time/residue: 0.2650 time to fit residues: 63.6955 Evaluate side-chains 156 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 529 CYS Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 119 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 0.0170 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 overall best weight: 1.1626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.103185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075475 restraints weight = 106304.629| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.09 r_work: 0.3228 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13751 Z= 0.131 Angle : 0.535 6.514 18876 Z= 0.293 Chirality : 0.040 0.197 2103 Planarity : 0.004 0.036 2216 Dihedral : 17.164 128.242 2291 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.13 % Allowed : 9.07 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1508 helix: 1.26 (0.21), residues: 623 sheet: -1.65 (0.41), residues: 162 loop : -0.58 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 669 TYR 0.007 0.001 TYR A 82 PHE 0.013 0.001 PHE I 647 TRP 0.009 0.001 TRP I 485 HIS 0.009 0.001 HIS G 314 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (13731) covalent geometry : angle 0.53134 / 0.29 (18866) hydrogen bonds : bond 0.04074 / 2.75 ( 560) hydrogen bonds : angle 4.41547 / 3.20 ( 1486) metal coordination : bond 0.00699 / 0.37 ( 20) metal coordination : angle 2.93343 / 1.54 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8102 (tp30) cc_final: 0.7890 (tp30) REVERT: G 8 ASN cc_start: 0.8698 (t0) cc_final: 0.8345 (t0) REVERT: G 122 MET cc_start: 0.8790 (ttp) cc_final: 0.8566 (ttp) REVERT: H 753 MET cc_start: 0.8522 (mtm) cc_final: 0.8317 (ttm) outliers start: 15 outliers final: 12 residues processed: 155 average time/residue: 0.2436 time to fit residues: 55.5542 Evaluate side-chains 149 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 529 CYS Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.101783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074388 restraints weight = 106594.546| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.08 r_work: 0.3199 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13751 Z= 0.188 Angle : 0.554 6.083 18876 Z= 0.303 Chirality : 0.040 0.194 2103 Planarity : 0.004 0.035 2216 Dihedral : 17.195 127.714 2291 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.28 % Allowed : 9.45 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1508 helix: 1.35 (0.21), residues: 623 sheet: -1.77 (0.42), residues: 158 loop : -0.65 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 747 TYR 0.009 0.001 TYR H 549 PHE 0.016 0.001 PHE I 647 TRP 0.007 0.001 TRP I 485 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (13731) covalent geometry : angle 0.54767 / 0.30 (18866) hydrogen bonds : bond 0.04184 / 2.84 ( 560) hydrogen bonds : angle 4.40192 / 3.19 ( 1486) metal coordination : bond 0.01439 / 0.87 ( 20) metal coordination : angle 3.69755 / 1.88 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 ASN cc_start: 0.8679 (t0) cc_final: 0.8321 (t0) REVERT: I 560 PHE cc_start: 0.8351 (m-10) cc_final: 0.8010 (m-10) outliers start: 17 outliers final: 14 residues processed: 151 average time/residue: 0.2474 time to fit residues: 55.3690 Evaluate side-chains 147 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 124 MET Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 529 CYS Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 131 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 642 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.100636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.073852 restraints weight = 107039.971| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.98 r_work: 0.3195 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13751 Z= 0.224 Angle : 0.562 6.078 18876 Z= 0.310 Chirality : 0.041 0.192 2103 Planarity : 0.004 0.037 2216 Dihedral : 17.260 127.349 2291 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.21 % Allowed : 9.83 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1508 helix: 1.13 (0.20), residues: 638 sheet: -1.61 (0.43), residues: 148 loop : -0.75 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 747 TYR 0.009 0.001 TYR I 549 PHE 0.017 0.002 PHE I 647 TRP 0.008 0.001 TRP I 609 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (13731) covalent geometry : angle 0.55432 / 0.31 (18866) hydrogen bonds : bond 0.04252 / 2.89 ( 560) hydrogen bonds : angle 4.48407 / 3.24 ( 1486) metal coordination : bond 0.01641 / 0.92 ( 20) metal coordination : angle 3.99741 / 2.04 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 164 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8811 (p) REVERT: G 8 ASN cc_start: 0.8664 (t0) cc_final: 0.8317 (t0) outliers start: 16 outliers final: 15 residues processed: 146 average time/residue: 0.2368 time to fit residues: 51.1370 Evaluate side-chains 148 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 529 CYS Chi-restraints excluded: chain H residue 579 GLU Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.101738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074223 restraints weight = 108058.587| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.07 r_work: 0.3206 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13751 Z= 0.139 Angle : 0.529 6.112 18876 Z= 0.290 Chirality : 0.040 0.193 2103 Planarity : 0.004 0.037 2216 Dihedral : 17.265 127.075 2291 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.91 % Allowed : 10.81 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1508 helix: 1.43 (0.21), residues: 625 sheet: -1.53 (0.44), residues: 148 loop : -0.62 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 747 TYR 0.007 0.001 TYR A 52 PHE 0.014 0.001 PHE I 647 TRP 0.008 0.001 TRP I 485 HIS 0.005 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (13731) covalent geometry : angle 0.52361 / 0.29 (18866) hydrogen bonds : bond 0.03815 / 2.56 ( 560) hydrogen bonds : angle 4.27892 / 3.10 ( 1486) metal coordination : bond 0.00962 / 0.54 ( 20) metal coordination : angle 3.38416 / 1.75 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 ASN cc_start: 0.8649 (t0) cc_final: 0.8299 (t0) REVERT: H 494 GLU cc_start: 0.9076 (tp30) cc_final: 0.8755 (tp30) outliers start: 12 outliers final: 12 residues processed: 145 average time/residue: 0.2553 time to fit residues: 54.8980 Evaluate side-chains 145 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.073723 restraints weight = 107269.005| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.98 r_work: 0.3192 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13751 Z= 0.196 Angle : 0.554 6.770 18876 Z= 0.303 Chirality : 0.040 0.192 2103 Planarity : 0.004 0.039 2216 Dihedral : 17.291 126.804 2291 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.06 % Allowed : 10.81 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1508 helix: 1.37 (0.21), residues: 627 sheet: -1.60 (0.44), residues: 148 loop : -0.68 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 700 TYR 0.014 0.001 TYR H 543 PHE 0.017 0.001 PHE I 647 TRP 0.007 0.001 TRP I 609 HIS 0.006 0.001 HIS H 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (13731) covalent geometry : angle 0.54696 / 0.30 (18866) hydrogen bonds : bond 0.04021 / 2.72 ( 560) hydrogen bonds : angle 4.34787 / 3.14 ( 1486) metal coordination : bond 0.01346 / 0.70 ( 20) metal coordination : angle 3.76226 / 1.95 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 164 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8827 (p) outliers start: 14 outliers final: 13 residues processed: 141 average time/residue: 0.2393 time to fit residues: 50.8993 Evaluate side-chains 144 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 568 ILE Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 152 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.100944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073488 restraints weight = 107808.973| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 4.06 r_work: 0.3191 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13751 Z= 0.168 Angle : 0.541 6.098 18876 Z= 0.296 Chirality : 0.040 0.192 2103 Planarity : 0.004 0.058 2216 Dihedral : 17.316 126.649 2291 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.13 % Allowed : 11.04 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.21), residues: 1508 helix: 1.44 (0.21), residues: 626 sheet: -1.59 (0.44), residues: 148 loop : -0.62 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 700 TYR 0.012 0.001 TYR H 543 PHE 0.016 0.001 PHE I 647 TRP 0.007 0.001 TRP I 485 HIS 0.004 0.001 HIS H 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (13731) covalent geometry : angle 0.53471 / 0.30 (18866) hydrogen bonds : bond 0.03907 / 2.65 ( 560) hydrogen bonds : angle 4.28013 / 3.09 ( 1486) metal coordination : bond 0.01182 / 0.63 ( 20) metal coordination : angle 3.68680 / 1.92 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 164 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8833 (p) REVERT: F 304 LYS cc_start: 0.9118 (mptt) cc_final: 0.8727 (mmtm) REVERT: H 494 GLU cc_start: 0.9091 (tp30) cc_final: 0.8779 (tp30) outliers start: 15 outliers final: 13 residues processed: 144 average time/residue: 0.2445 time to fit residues: 52.8645 Evaluate side-chains 145 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 164 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 508 GLN Chi-restraints excluded: chain H residue 568 ILE Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 716 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.101416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.074166 restraints weight = 107229.291| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.11 r_work: 0.3190 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13751 Z= 0.144 Angle : 0.533 6.106 18876 Z= 0.290 Chirality : 0.040 0.193 2103 Planarity : 0.004 0.046 2216 Dihedral : 17.324 126.379 2291 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.06 % Allowed : 10.88 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1508 helix: 1.54 (0.21), residues: 626 sheet: -1.54 (0.44), residues: 148 loop : -0.56 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 101 TYR 0.011 0.001 TYR G 345 PHE 0.015 0.001 PHE I 647 TRP 0.008 0.001 TRP I 485 HIS 0.004 0.001 HIS I 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (13731) covalent geometry : angle 0.52714 / 0.29 (18866) hydrogen bonds : bond 0.03708 / 2.50 ( 560) hydrogen bonds : angle 4.17550 / 3.02 ( 1486) metal coordination : bond 0.00967 / 0.52 ( 20) metal coordination : angle 3.40316 / 1.77 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5921.69 seconds wall clock time: 101 minutes 9.82 seconds (6069.82 seconds total)