Starting phenix.real_space_refine on Fri Sep 19 12:30:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hjt_52226/09_2025/9hjt_52226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hjt_52226/09_2025/9hjt_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 { model { file = "/net/cci-nas-00/data/ceres_data/9hjt_52226/09_2025/9hjt_52226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hjt_52226/09_2025/9hjt_52226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hjt_52226/09_2025/9hjt_52226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hjt_52226/09_2025/9hjt_52226.map" } 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-2.0-5805/lib/python3.9/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: 4.85, per 1000 atoms: 0.19 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: 2.35 Conformation dependent library (CDL) restraints added in 781.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.12 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: 3.25 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=" CB PRO G 34 " pdb=" CG PRO G 34 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.58e-01 bond pdb=" C3' DG L 26 " pdb=" O3' DG L 26 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.53e-01 bond pdb=" C ASN H 697 " pdb=" O ASN H 697 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.23e-01 bond pdb=" C3' DG L 2 " pdb=" C2' DG L 2 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.00e-02 2.50e+03 5.74e-01 bond pdb=" CG PRO I 475 " pdb=" CD PRO I 475 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 5.08e-01 ... (remaining 26490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 44209 0.99 - 1.98: 3550 1.98 - 2.98: 173 2.98 - 3.97: 80 3.97 - 4.96: 17 Bond angle restraints: 48029 Sorted by residual: angle pdb=" N GLY G 162 " pdb=" CA GLY G 162 " pdb=" C GLY G 162 " ideal model delta sigma weight residual 110.38 113.80 -3.42 1.28e+00 6.10e-01 7.12e+00 angle pdb=" N GLY F 67 " pdb=" CA GLY F 67 " pdb=" C GLY F 67 " ideal model delta sigma weight residual 114.67 111.00 3.67 1.41e+00 5.03e-01 6.78e+00 angle pdb=" C3' DT L 16 " pdb=" C2' DT L 16 " pdb=" C1' DT L 16 " ideal model delta sigma weight residual 101.60 105.46 -3.86 1.50e+00 4.44e-01 6.61e+00 angle pdb=" C PHE F 269 " pdb=" CA PHE F 269 " pdb=" CB PHE F 269 " ideal model delta sigma weight residual 110.42 115.19 -4.77 1.99e+00 2.53e-01 5.74e+00 angle pdb=" C3' DG K 3 " pdb=" C2' DG K 3 " pdb=" C1' DG K 3 " ideal model delta sigma weight residual 101.60 105.16 -3.56 1.50e+00 4.44e-01 5.62e+00 ... (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 - 0.027: 1268 0.027 - 0.054: 520 0.054 - 0.081: 164 0.081 - 0.108: 112 0.108 - 0.135: 39 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA ILE F 353 " pdb=" N ILE F 353 " pdb=" C ILE F 353 " pdb=" CB ILE F 353 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE G 373 " pdb=" N ILE G 373 " pdb=" C ILE G 373 " pdb=" CB ILE G 373 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE G 353 " pdb=" N ILE G 353 " pdb=" C ILE G 353 " pdb=" CB ILE G 353 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-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: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 32.810 Find NCS groups from input model: 0.240 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 : 0.003 0.044 13751 Z= 0.140 Angle : 0.530 7.193 18876 Z= 0.288 Chirality : 0.040 0.135 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 aren 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 covalent geometry : bond 0.00306 (13731) covalent geometry : angle 0.52366 (18866) hydrogen bonds : bond 0.19154 ( 560) hydrogen bonds : angle 6.42626 ( 1486) metal coordination : bond 0.00756 ( 20) metal coordination : angle 3.62430 ( 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 : 0.746 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: 0.3147 time to fit residues: 127.6403 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 : 0.691 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 259 ASN F 314 HIS H 537 ASN I 641 GLN I 743 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.102673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.075302 restraints weight = 107000.062| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.20 r_work: 0.3215 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13751 Z= 0.246 Angle : 0.626 5.947 18876 Z= 0.339 Chirality : 0.043 0.156 2103 Planarity : 0.005 0.056 2216 Dihedral : 16.991 130.640 2291 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.13 % Allowed : 8.16 % Favored : 90.70 % 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 aren not related in a simple way. whole: -0.33 (0.21), residues: 1508 helix: 0.79 (0.21), residues: 636 sheet: -1.43 (0.43), residues: 152 loop : -0.80 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 500 TYR 0.012 0.002 TYR F 88 PHE 0.020 0.002 PHE F 336 TRP 0.011 0.001 TRP I 485 HIS 0.009 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00536 (13731) covalent geometry : angle 0.61938 (18866) hydrogen bonds : bond 0.05250 ( 560) hydrogen bonds : angle 5.13369 ( 1486) metal coordination : bond 0.01302 ( 20) metal coordination : angle 4.05824 ( 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 174 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.623 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: A 107 GLU cc_start: 0.8310 (tp30) cc_final: 0.8089 (tp30) REVERT: F 124 MET cc_start: 0.8966 (ttp) cc_final: 0.8722 (ttm) REVERT: G 8 ASN cc_start: 0.8683 (t0) cc_final: 0.8319 (t0) REVERT: H 771 ASN cc_start: 0.8765 (m110) cc_final: 0.8517 (m110) REVERT: I 560 PHE cc_start: 0.8302 (m-10) cc_final: 0.8017 (m-10) outliers start: 15 outliers final: 13 residues processed: 169 average time/residue: 0.2747 time to fit residues: 66.3443 Evaluate side-chains 154 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 140 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 143 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.103614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.076216 restraints weight = 107186.362| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 4.16 r_work: 0.3231 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13751 Z= 0.125 Angle : 0.543 5.476 18876 Z= 0.290 Chirality : 0.040 0.157 2103 Planarity : 0.004 0.040 2216 Dihedral : 16.910 130.014 2291 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.28 % Allowed : 8.62 % Favored : 90.10 % 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 aren not related in a simple way. whole: 0.03 (0.21), residues: 1508 helix: 1.20 (0.21), residues: 622 sheet: -1.37 (0.43), residues: 152 loop : -0.65 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 500 TYR 0.011 0.001 TYR F 112 PHE 0.013 0.001 PHE I 647 TRP 0.011 0.001 TRP I 485 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00279 (13731) covalent geometry : angle 0.53907 (18866) hydrogen bonds : bond 0.04269 ( 560) hydrogen bonds : angle 4.56460 ( 1486) metal coordination : bond 0.00627 ( 20) metal coordination : angle 2.86933 ( 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 174 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.720 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: 0.8702 (t0) cc_final: 0.8341 (t0) REVERT: G 122 MET cc_start: 0.8787 (ttp) cc_final: 0.8523 (ttp) REVERT: I 560 PHE cc_start: 0.8291 (m-10) cc_final: 0.7995 (m-10) REVERT: I 753 MET cc_start: 0.9179 (mtp) cc_final: 0.8967 (mtp) outliers start: 17 outliers final: 14 residues processed: 168 average time/residue: 0.2782 time to fit residues: 67.4734 Evaluate side-chains 159 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 H residue 508 GLN Chi-restraints excluded: chain H residue 529 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 705 LEU Chi-restraints excluded: chain H residue 757 ILE Chi-restraints excluded: chain H residue 760 ILE 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: 5.9990 chunk 44 optimal weight: 0.2980 chunk 126 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 0.0050 chunk 11 optimal weight: 0.7980 chunk 154 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.104343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.076989 restraints weight = 105850.385| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.03 r_work: 0.3237 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13751 Z= 0.107 Angle : 0.519 7.456 18876 Z= 0.276 Chirality : 0.039 0.133 2103 Planarity : 0.003 0.033 2216 Dihedral : 16.832 129.698 2291 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.06 % Allowed : 9.30 % Favored : 89.64 % 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 aren not related in a simple way. whole: 0.27 (0.22), residues: 1508 helix: 1.44 (0.21), residues: 625 sheet: -1.30 (0.43), residues: 152 loop : -0.55 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 747 TYR 0.006 0.001 TYR A 82 PHE 0.011 0.001 PHE I 647 TRP 0.009 0.001 TRP I 485 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00243 (13731) covalent geometry : angle 0.51649 (18866) hydrogen bonds : bond 0.03518 ( 560) hydrogen bonds : angle 4.21486 ( 1486) metal coordination : bond 0.00464 ( 20) metal coordination : angle 2.44416 ( 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 171 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.580 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: 0.8682 (t0) cc_final: 0.8324 (t0) REVERT: H 494 GLU cc_start: 0.9035 (tp30) cc_final: 0.8720 (tp30) REVERT: H 627 MET cc_start: 0.9243 (ttm) cc_final: 0.9027 (ttp) REVERT: H 643 MET cc_start: 0.8245 (mtm) cc_final: 0.7516 (mtp) REVERT: I 560 PHE cc_start: 0.8313 (m-10) cc_final: 0.8006 (m-10) REVERT: I 727 THR cc_start: 0.9329 (m) cc_final: 0.9109 (p) REVERT: I 740 TYR cc_start: 0.9061 (m-80) cc_final: 0.8754 (m-80) REVERT: I 753 MET cc_start: 0.9180 (mtp) cc_final: 0.8967 (mtp) outliers start: 14 outliers final: 9 residues processed: 166 average time/residue: 0.2820 time to fit residues: 66.9871 Evaluate side-chains 152 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain G residue 48 ASN 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 757 ILE Chi-restraints excluded: chain H residue 760 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 119 optimal weight: 0.0070 chunk 87 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.101752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073991 restraints weight = 107118.930| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 4.12 r_work: 0.3197 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13751 Z= 0.187 Angle : 0.559 7.896 18876 Z= 0.297 Chirality : 0.041 0.136 2103 Planarity : 0.004 0.057 2216 Dihedral : 16.862 129.176 2291 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.36 % Allowed : 9.45 % Favored : 89.19 % 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 aren not related in a simple way. whole: 0.17 (0.21), residues: 1508 helix: 1.41 (0.21), residues: 629 sheet: -1.43 (0.43), residues: 148 loop : -0.66 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 747 TYR 0.008 0.001 TYR I 549 PHE 0.018 0.001 PHE F 148 TRP 0.007 0.001 TRP I 485 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00411 (13731) covalent geometry : angle 0.55235 (18866) hydrogen bonds : bond 0.03989 ( 560) hydrogen bonds : angle 4.32517 ( 1486) metal coordination : bond 0.01282 ( 20) metal coordination : angle 3.75666 ( 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: 18 poor density : 141 time to evaluate : 0.800 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: A 107 GLU cc_start: 0.8264 (tp30) cc_final: 0.8051 (tp30) REVERT: F 118 GLU cc_start: 0.7998 (mp0) cc_final: 0.7791 (mp0) REVERT: G 8 ASN cc_start: 0.8669 (t0) cc_final: 0.8301 (t0) REVERT: I 560 PHE cc_start: 0.8365 (m-10) cc_final: 0.8046 (m-10) REVERT: I 753 MET cc_start: 0.9227 (mtp) cc_final: 0.9026 (mtp) outliers start: 18 outliers final: 15 residues processed: 153 average time/residue: 0.2929 time to fit residues: 63.6561 Evaluate side-chains 146 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 153 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 0.0470 chunk 101 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 642 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.101037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073701 restraints weight = 108503.133| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.11 r_work: 0.3201 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3585 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= 0.167 Angle : 0.533 5.035 18876 Z= 0.286 Chirality : 0.040 0.137 2103 Planarity : 0.004 0.036 2216 Dihedral : 16.886 128.465 2291 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.06 % Allowed : 10.43 % Favored : 88.51 % 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 aren not related in a simple way. whole: 0.28 (0.21), residues: 1508 helix: 1.53 (0.21), residues: 625 sheet: -1.45 (0.44), residues: 148 loop : -0.60 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 747 TYR 0.008 0.001 TYR I 549 PHE 0.012 0.001 PHE H 577 TRP 0.007 0.001 TRP I 609 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00368 (13731) covalent geometry : angle 0.52711 (18866) hydrogen bonds : bond 0.03645 ( 560) hydrogen bonds : angle 4.22527 ( 1486) metal coordination : bond 0.01119 ( 20) metal coordination : angle 3.37398 ( 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 147 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.755 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 118 GLU cc_start: 0.7990 (mp0) cc_final: 0.7778 (mp0) REVERT: F 164 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8830 (p) REVERT: H 494 GLU cc_start: 0.9072 (tp30) cc_final: 0.8748 (tp30) REVERT: I 753 MET cc_start: 0.9226 (mtp) cc_final: 0.9008 (mtp) outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 0.2672 time to fit residues: 56.4870 Evaluate side-chains 145 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 97 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.100207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073701 restraints weight = 106715.392| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.96 r_work: 0.3170 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13751 Z= 0.200 Angle : 0.554 6.336 18876 Z= 0.297 Chirality : 0.041 0.139 2103 Planarity : 0.004 0.064 2216 Dihedral : 16.936 127.693 2291 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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 aren not related in a simple way. whole: 0.20 (0.21), residues: 1508 helix: 1.47 (0.21), residues: 625 sheet: -1.59 (0.43), residues: 148 loop : -0.64 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 101 TYR 0.015 0.001 TYR G 345 PHE 0.019 0.001 PHE I 647 TRP 0.007 0.001 TRP I 609 HIS 0.005 0.001 HIS I 642 Details of bonding type rmsd covalent geometry : bond 0.00438 (13731) covalent geometry : angle 0.54535 (18866) hydrogen bonds : bond 0.03969 ( 560) hydrogen bonds : angle 4.30466 ( 1486) metal coordination : bond 0.01509 ( 20) metal coordination : angle 4.31998 ( 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 146 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.778 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: F 118 GLU cc_start: 0.8024 (mp0) cc_final: 0.7799 (mp0) REVERT: F 124 MET cc_start: 0.9055 (ttm) cc_final: 0.8833 (ttm) REVERT: F 164 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8833 (p) REVERT: H 494 GLU cc_start: 0.9100 (tp30) cc_final: 0.8792 (tp30) REVERT: I 753 MET cc_start: 0.9217 (mtp) cc_final: 0.8999 (mtp) outliers start: 15 outliers final: 13 residues processed: 142 average time/residue: 0.2601 time to fit residues: 55.1880 Evaluate side-chains 143 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 2 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 25 optimal weight: 0.0020 chunk 134 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.100952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073728 restraints weight = 107826.562| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.13 r_work: 0.3181 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13751 Z= 0.148 Angle : 0.534 5.141 18876 Z= 0.285 Chirality : 0.040 0.137 2103 Planarity : 0.004 0.039 2216 Dihedral : 16.933 127.015 2291 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.98 % Allowed : 11.49 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.22), residues: 1508 helix: 1.56 (0.21), residues: 630 sheet: -1.51 (0.44), residues: 148 loop : -0.60 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 101 TYR 0.007 0.001 TYR I 549 PHE 0.015 0.001 PHE I 647 TRP 0.007 0.001 TRP I 485 HIS 0.004 0.001 HIS I 642 Details of bonding type rmsd covalent geometry : bond 0.00331 (13731) covalent geometry : angle 0.52787 (18866) hydrogen bonds : bond 0.03544 ( 560) hydrogen bonds : angle 4.15156 ( 1486) metal coordination : bond 0.00981 ( 20) metal coordination : angle 3.41724 ( 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: 13 poor density : 135 time to evaluate : 0.674 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: F 118 GLU cc_start: 0.8028 (mp0) cc_final: 0.7806 (mp0) REVERT: F 164 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8822 (p) REVERT: H 494 GLU cc_start: 0.9082 (tp30) cc_final: 0.8778 (tp30) REVERT: H 508 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7932 (pt0) outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.2428 time to fit residues: 52.2914 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 : 0.706 ------------------------------------------------------------------------------- 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 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 760 ILE Chi-restraints excluded: chain I residue 716 SER Chi-restraints excluded: chain I residue 758 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.100791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074020 restraints weight = 106500.867| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.04 r_work: 0.3186 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13751 Z= 0.133 Angle : 0.525 5.146 18876 Z= 0.279 Chirality : 0.039 0.132 2103 Planarity : 0.004 0.038 2216 Dihedral : 16.925 126.187 2291 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.06 % Allowed : 11.79 % Favored : 87.15 % 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 aren not related in a simple way. whole: 0.41 (0.22), residues: 1508 helix: 1.70 (0.21), residues: 628 sheet: -1.49 (0.44), residues: 148 loop : -0.58 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 101 TYR 0.007 0.001 TYR A 52 PHE 0.014 0.001 PHE I 647 TRP 0.007 0.001 TRP I 485 HIS 0.004 0.001 HIS I 642 Details of bonding type rmsd covalent geometry : bond 0.00298 (13731) covalent geometry : angle 0.51937 (18866) hydrogen bonds : bond 0.03407 ( 560) hydrogen bonds : angle 4.04042 ( 1486) metal coordination : bond 0.00956 ( 20) metal coordination : angle 3.31233 ( 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 147 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.540 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: F 118 GLU cc_start: 0.7993 (mp0) cc_final: 0.7774 (mp0) REVERT: F 164 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8830 (p) REVERT: G 345 TYR cc_start: 0.8119 (p90) cc_final: 0.7496 (p90) REVERT: H 494 GLU cc_start: 0.9093 (tp30) cc_final: 0.8805 (tp30) REVERT: H 508 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: I 643 MET cc_start: 0.8791 (tpt) cc_final: 0.8557 (tpt) outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 0.2409 time to fit residues: 51.7536 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 : 0.685 ------------------------------------------------------------------------------- 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 760 ILE Chi-restraints excluded: chain I residue 716 SER Chi-restraints excluded: chain I residue 758 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 152 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 137 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 106 ASN H 630 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.101178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074347 restraints weight = 106255.630| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.01 r_work: 0.3201 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13751 Z= 0.117 Angle : 0.517 5.758 18876 Z= 0.274 Chirality : 0.039 0.131 2103 Planarity : 0.004 0.038 2216 Dihedral : 16.891 125.169 2291 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.76 % Allowed : 12.32 % Favored : 86.92 % 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 aren not related in a simple way. whole: 0.51 (0.22), residues: 1508 helix: 1.83 (0.21), residues: 628 sheet: -1.70 (0.43), residues: 158 loop : -0.48 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 101 TYR 0.006 0.001 TYR A 52 PHE 0.012 0.001 PHE I 647 TRP 0.008 0.001 TRP I 485 HIS 0.003 0.001 HIS I 642 Details of bonding type rmsd covalent geometry : bond 0.00264 (13731) covalent geometry : angle 0.51261 (18866) hydrogen bonds : bond 0.03226 ( 560) hydrogen bonds : angle 3.92447 ( 1486) metal coordination : bond 0.00737 ( 20) metal coordination : angle 2.94443 ( 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 142 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.703 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: F 112 TYR cc_start: 0.8782 (m-10) cc_final: 0.8516 (m-10) REVERT: F 118 GLU cc_start: 0.7957 (mp0) cc_final: 0.7738 (mp0) REVERT: G 99 MET cc_start: 0.8631 (tpp) cc_final: 0.8385 (tpp) REVERT: H 494 GLU cc_start: 0.9075 (tp30) cc_final: 0.8807 (tp30) REVERT: H 508 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: I 643 MET cc_start: 0.8778 (tpt) cc_final: 0.8538 (tpt) outliers start: 10 outliers final: 9 residues processed: 140 average time/residue: 0.2405 time to fit residues: 50.2128 Evaluate side-chains 139 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 H residue 508 GLN Chi-restraints excluded: chain H residue 651 LEU Chi-restraints excluded: chain H residue 760 ILE Chi-restraints excluded: chain I residue 758 LEU 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: 0.7980 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 148 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.100991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074264 restraints weight = 106397.713| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.00 r_work: 0.3199 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13751 Z= 0.125 Angle : 0.524 9.127 18876 Z= 0.277 Chirality : 0.039 0.132 2103 Planarity : 0.004 0.038 2216 Dihedral : 16.875 124.467 2291 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.91 % Allowed : 12.40 % Favored : 86.70 % 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 aren not related in a simple way. whole: 0.56 (0.22), residues: 1508 helix: 1.87 (0.21), residues: 628 sheet: -1.70 (0.43), residues: 158 loop : -0.45 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 101 TYR 0.007 0.001 TYR A 52 PHE 0.012 0.001 PHE I 647 TRP 0.008 0.001 TRP I 485 HIS 0.003 0.001 HIS I 642 Details of bonding type rmsd covalent geometry : bond 0.00280 (13731) covalent geometry : angle 0.51945 (18866) hydrogen bonds : bond 0.03285 ( 560) hydrogen bonds : angle 3.89356 ( 1486) metal coordination : bond 0.00865 ( 20) metal coordination : angle 3.10819 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6498.01 seconds wall clock time: 110 minutes 54.06 seconds (6654.06 seconds total)