Starting phenix.real_space_refine on Fri Jun 20 01:23:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfh_25872/06_2025/7tfh_25872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfh_25872/06_2025/7tfh_25872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfh_25872/06_2025/7tfh_25872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfh_25872/06_2025/7tfh_25872.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfh_25872/06_2025/7tfh_25872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfh_25872/06_2025/7tfh_25872.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 370 atoms to isotropic. 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 Se 18 7.20 5 P 77 5.49 5 Mg 4 5.21 5 S 86 5.16 5 C 14225 2.51 5 N 3895 2.21 5 O 4526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22831 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4925 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 24, 'TRANS': 603} Chain breaks: 3 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2694 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2014 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "I" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.55, per 1000 atoms: 0.59 Number of scatterers: 22831 At special positions: 0 Unit cell: (125.028, 146.556, 139.104, 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) Se 18 33.99 S 86 16.00 P 77 15.00 Mg 4 11.99 O 4526 8.00 N 3895 7.00 C 14225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 2.8 seconds 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5156 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 17 sheets defined 52.9% alpha, 13.8% beta 25 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 8.05 Creating SS restraints... Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.502A pdb=" N LYS A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 206 through 217 removed outlier: 3.846A pdb=" N LYS A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.892A pdb=" N GLN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.602A pdb=" N GLY A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 281 removed outlier: 3.946A pdb=" N GLU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.695A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.597A pdb=" N LEU A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 removed outlier: 3.697A pdb=" N TYR A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 479 through 494 removed outlier: 4.090A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 3.961A pdb=" N ARG A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.806A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.312A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.674A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 657 removed outlier: 5.250A pdb=" N TYR A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Proline residue: A 652 - end of helix removed outlier: 3.535A pdb=" N LYS A 655 " --> pdb=" O TYR A 651 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 690 Processing helix chain 'A' and resid 697 through 704 removed outlier: 3.629A pdb=" N ARG A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 removed outlier: 3.913A pdb=" N THR A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 738 through 747 removed outlier: 3.578A pdb=" N ASP A 743 " --> pdb=" O LYS A 739 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 746 " --> pdb=" O TRP A 742 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 749 No H-bonds generated for 'chain 'A' and resid 748 through 749' Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 763 through 777 removed outlier: 3.521A pdb=" N GLY A 769 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 770 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 771 " --> pdb=" O LYS A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 67 removed outlier: 3.735A pdb=" N SER B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 4.084A pdb=" N GLN B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.808A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.532A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.817A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.677A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.698A pdb=" N MET C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 78' Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.019A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.540A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.847A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.821A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.810A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.591A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.091A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 313 removed outlier: 4.400A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.744A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 43 through 55 removed outlier: 3.898A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 86 through 91 removed outlier: 4.439A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 4.005A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.387A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.614A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 removed outlier: 3.579A pdb=" N SER D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 296 through 309 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.758A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.972A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 104 through 117 removed outlier: 4.398A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 149 through 161 removed outlier: 4.170A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.558A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 3.959A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 removed outlier: 4.184A pdb=" N GLY F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 23 " --> pdb=" O PHE F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.555A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 3.508A pdb=" N ARG G 80 " --> pdb=" O SER G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.809A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.537A pdb=" N LEU G 221 " --> pdb=" O GLY G 218 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER G 222 " --> pdb=" O SER G 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 218 through 222' Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 162 through 166 removed outlier: 3.549A pdb=" N GLU H 165 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 216 Processing helix chain 'H' and resid 217 through 219 No H-bonds generated for 'chain 'H' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188 removed outlier: 5.825A pdb=" N THR A 162 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 200 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL A 164 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 377 removed outlier: 6.850A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP A 424 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN A 377 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA A 348 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 473 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N MET A 350 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.980A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.175A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.049A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.024A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.388A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.085A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 71 through 76 removed outlier: 3.601A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 57 through 62 removed outlier: 3.909A pdb=" N GLU F 59 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 112 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 51 through 53 removed outlier: 4.047A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.681A pdb=" N ALA F 39 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 48 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY F 244 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 236 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS F 196 " --> pdb=" O SER F 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.836A pdb=" N VAL F 203 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR G 114 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.087A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.939A pdb=" N SER G 157 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP G 172 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU H 88 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLU H 3 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR H 60 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS H 5 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 67 through 71 removed outlier: 3.684A pdb=" N VAL H 26 " --> pdb=" O MSE H 70 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN H 38 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE H 237 " --> pdb=" O PHE H 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU H 236 " --> pdb=" O ARG H 228 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 238 " --> pdb=" O GLY H 226 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 139 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 136 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 138 " --> pdb=" O LYS H 196 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS H 196 " --> pdb=" O SER H 138 " (cutoff:3.500A) 1125 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 9.46 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 7500 1.37 - 1.52: 8078 1.52 - 1.67: 7579 1.67 - 1.82: 124 1.82 - 1.97: 40 Bond restraints: 23321 Sorted by residual: bond pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" C4 ADP E 500 " pdb=" C5 ADP E 500 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" CG ARG E 106 " pdb=" CD ARG E 106 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB PRO G 184 " pdb=" CG PRO G 184 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 1.00e+00 bond pdb=" CB GLN E 32 " pdb=" CG GLN E 32 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.28e-01 ... (remaining 23316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 31106 1.66 - 3.31: 552 3.31 - 4.97: 87 4.97 - 6.63: 28 6.63 - 8.28: 7 Bond angle restraints: 31780 Sorted by residual: angle pdb=" N MSE G 199 " pdb=" CA MSE G 199 " pdb=" C MSE G 199 " ideal model delta sigma weight residual 108.52 113.63 -5.11 1.63e+00 3.76e-01 9.81e+00 angle pdb=" N MSE G 188 " pdb=" CA MSE G 188 " pdb=" C MSE G 188 " ideal model delta sigma weight residual 112.89 109.01 3.88 1.24e+00 6.50e-01 9.79e+00 angle pdb=" CG ARG D 115 " pdb=" CD ARG D 115 " pdb=" NE ARG D 115 " ideal model delta sigma weight residual 112.00 118.24 -6.24 2.20e+00 2.07e-01 8.05e+00 angle pdb=" N MSE G 70 " pdb=" CA MSE G 70 " pdb=" C MSE G 70 " ideal model delta sigma weight residual 109.50 113.73 -4.23 1.58e+00 4.01e-01 7.18e+00 angle pdb=" C LYS D 80 " pdb=" N GLU D 81 " pdb=" CA GLU D 81 " ideal model delta sigma weight residual 122.65 118.53 4.12 1.60e+00 3.91e-01 6.63e+00 ... (remaining 31775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.02: 13441 30.02 - 60.04: 706 60.04 - 90.05: 34 90.05 - 120.07: 1 120.07 - 150.09: 2 Dihedral angle restraints: 14184 sinusoidal: 6258 harmonic: 7926 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -171.67 111.67 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 82.36 -150.09 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" CA LEU B 103 " pdb=" C LEU B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 14181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2915 0.046 - 0.092: 607 0.092 - 0.138: 169 0.138 - 0.184: 3 0.184 - 0.230: 4 Chirality restraints: 3698 Sorted by residual: chirality pdb=" CB ILE H 111 " pdb=" CA ILE H 111 " pdb=" CG1 ILE H 111 " pdb=" CG2 ILE H 111 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU B 67 " pdb=" CB LEU B 67 " pdb=" CD1 LEU B 67 " pdb=" CD2 LEU B 67 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE B 86 " pdb=" CA ILE B 86 " pdb=" CG1 ILE B 86 " pdb=" CG2 ILE B 86 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3695 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 97 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO E 98 " -0.208 5.00e-02 4.00e+02 pdb=" CA PRO E 98 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 98 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 353 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 354 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 354 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 354 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 232 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO B 233 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.028 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 272 2.63 - 3.20: 19919 3.20 - 3.77: 36069 3.77 - 4.33: 50063 4.33 - 4.90: 82174 Nonbonded interactions: 188497 Sorted by model distance: nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.074 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.078 2.170 nonbonded pdb=" O3G AGS A 901 " pdb="MG MG A 902 " model vdw 2.080 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.095 2.170 ... (remaining 188492 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' and resid 1 through 254) selection = (chain 'G' and resid 1 through 254) selection = chain 'H' } 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: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 56.910 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 0.050 23321 Z= 0.124 Angle : 0.567 8.282 31780 Z= 0.293 Chirality : 0.040 0.230 3698 Planarity : 0.004 0.120 3814 Dihedral : 16.177 150.091 9028 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.04 % Allowed : 0.29 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2693 helix: 0.98 (0.15), residues: 1275 sheet: -0.35 (0.25), residues: 505 loop : -0.89 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 4 HIS 0.005 0.001 HIS D 124 PHE 0.026 0.001 PHE A 443 TYR 0.017 0.001 TYR H 60 ARG 0.010 0.000 ARG E 106 Details of bonding type rmsd hydrogen bonds : bond 0.19093 ( 1182) hydrogen bonds : angle 6.80708 ( 3350) covalent geometry : bond 0.00271 (23321) covalent geometry : angle 0.56678 (31780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 ASP cc_start: 0.7098 (m-30) cc_final: 0.6788 (m-30) REVERT: D 115 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7531 (ttp80) REVERT: E 106 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7651 (ptt90) REVERT: E 212 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7453 (tp40) REVERT: F 46 LEU cc_start: 0.4781 (tt) cc_final: 0.4475 (tt) REVERT: F 87 THR cc_start: 0.7155 (p) cc_final: 0.6897 (t) REVERT: F 217 LYS cc_start: 0.7043 (tttt) cc_final: 0.6756 (tptt) REVERT: H 61 ARG cc_start: 0.6639 (tmm-80) cc_final: 0.6425 (ttt90) REVERT: H 199 MSE cc_start: 0.4091 (ttp) cc_final: 0.3886 (ttp) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.3420 time to fit residues: 196.4751 Evaluate side-chains 296 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 160 optimal weight: 0.0980 chunk 249 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 202 ASN C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 103 ASN H 238 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.153719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113011 restraints weight = 32674.583| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.06 r_work: 0.3405 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 23321 Z= 0.147 Angle : 0.560 7.282 31780 Z= 0.294 Chirality : 0.041 0.145 3698 Planarity : 0.004 0.097 3814 Dihedral : 15.299 139.433 3675 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.71 % Allowed : 8.37 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2693 helix: 1.28 (0.15), residues: 1288 sheet: -0.27 (0.24), residues: 508 loop : -0.67 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 327 HIS 0.005 0.001 HIS D 124 PHE 0.019 0.001 PHE H 19 TYR 0.023 0.001 TYR E 92 ARG 0.008 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 1182) hydrogen bonds : angle 5.09401 ( 3350) covalent geometry : bond 0.00331 (23321) covalent geometry : angle 0.56004 (31780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 312 time to evaluate : 3.231 Fit side-chains revert: symmetry clash REVERT: A 190 LYS cc_start: 0.9064 (mmmt) cc_final: 0.8862 (tttm) REVERT: A 393 LYS cc_start: 0.6933 (ttmm) cc_final: 0.6635 (pptt) REVERT: A 560 ASP cc_start: 0.7624 (m-30) cc_final: 0.7261 (m-30) REVERT: A 628 GLU cc_start: 0.8516 (tp30) cc_final: 0.8269 (tm-30) REVERT: C 135 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7981 (mt-10) REVERT: E 32 GLN cc_start: 0.7861 (tp40) cc_final: 0.7642 (tp40) REVERT: E 212 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7352 (tp40) REVERT: F 17 ASP cc_start: 0.6951 (m-30) cc_final: 0.6720 (m-30) REVERT: F 217 LYS cc_start: 0.7312 (tttt) cc_final: 0.6713 (tptt) REVERT: F 228 ARG cc_start: 0.6126 (ptp90) cc_final: 0.5918 (ptp90) REVERT: F 248 PHE cc_start: 0.3879 (m-80) cc_final: 0.3194 (m-80) REVERT: G 101 LEU cc_start: 0.8911 (mm) cc_final: 0.8627 (mt) outliers start: 17 outliers final: 13 residues processed: 319 average time/residue: 0.3653 time to fit residues: 183.2135 Evaluate side-chains 305 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 292 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 136 optimal weight: 0.1980 chunk 225 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 166 optimal weight: 0.0980 chunk 220 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 221 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS C 202 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN H 238 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.154305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113610 restraints weight = 32805.385| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.05 r_work: 0.3414 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23321 Z= 0.117 Angle : 0.506 7.069 31780 Z= 0.264 Chirality : 0.039 0.137 3698 Planarity : 0.004 0.089 3814 Dihedral : 15.257 139.804 3675 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.04 % Allowed : 10.70 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2693 helix: 1.45 (0.15), residues: 1297 sheet: -0.29 (0.24), residues: 517 loop : -0.62 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 327 HIS 0.005 0.001 HIS D 124 PHE 0.017 0.001 PHE H 19 TYR 0.016 0.001 TYR E 92 ARG 0.008 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 1182) hydrogen bonds : angle 4.64030 ( 3350) covalent geometry : bond 0.00258 (23321) covalent geometry : angle 0.50639 (31780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 305 time to evaluate : 2.561 Fit side-chains REVERT: A 190 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8860 (tttm) REVERT: A 393 LYS cc_start: 0.6976 (ttmm) cc_final: 0.6707 (pptt) REVERT: A 445 ARG cc_start: 0.7725 (mmp80) cc_final: 0.7449 (mpt180) REVERT: A 560 ASP cc_start: 0.7602 (m-30) cc_final: 0.7262 (m-30) REVERT: A 628 GLU cc_start: 0.8463 (tp30) cc_final: 0.8227 (tm-30) REVERT: A 686 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7172 (mp) REVERT: B 146 GLN cc_start: 0.8405 (tp40) cc_final: 0.7992 (tp40) REVERT: B 282 GLU cc_start: 0.8122 (tp30) cc_final: 0.7723 (tp30) REVERT: C 87 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: D 81 GLU cc_start: 0.8454 (pm20) cc_final: 0.8226 (pm20) REVERT: E 1 MET cc_start: 0.6161 (mtm) cc_final: 0.5891 (mtm) REVERT: E 50 LYS cc_start: 0.8597 (mttm) cc_final: 0.8296 (mtmt) REVERT: E 212 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7373 (tp40) REVERT: F 17 ASP cc_start: 0.6973 (m-30) cc_final: 0.6707 (m-30) REVERT: F 217 LYS cc_start: 0.7261 (tttt) cc_final: 0.6705 (tptt) REVERT: F 248 PHE cc_start: 0.3801 (m-80) cc_final: 0.3152 (m-80) outliers start: 25 outliers final: 16 residues processed: 318 average time/residue: 0.3551 time to fit residues: 173.7379 Evaluate side-chains 306 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 288 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 30 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 49 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 156 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 148 ASN B 317 HIS C 202 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN D 338 ASN ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.153184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.112153 restraints weight = 32757.084| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.07 r_work: 0.3371 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23321 Z= 0.140 Angle : 0.523 7.422 31780 Z= 0.271 Chirality : 0.040 0.138 3698 Planarity : 0.004 0.086 3814 Dihedral : 15.304 143.747 3675 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.46 % Allowed : 12.57 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2693 helix: 1.53 (0.15), residues: 1296 sheet: -0.30 (0.24), residues: 516 loop : -0.63 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 4 HIS 0.004 0.001 HIS D 124 PHE 0.017 0.001 PHE H 19 TYR 0.014 0.001 TYR E 92 ARG 0.012 0.000 ARG G 110 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 1182) hydrogen bonds : angle 4.47157 ( 3350) covalent geometry : bond 0.00324 (23321) covalent geometry : angle 0.52275 (31780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 2.528 Fit side-chains REVERT: A 393 LYS cc_start: 0.7066 (ttmm) cc_final: 0.6772 (pptt) REVERT: A 398 ASN cc_start: 0.5731 (t0) cc_final: 0.5485 (t0) REVERT: A 445 ARG cc_start: 0.7709 (mmp80) cc_final: 0.7421 (mpt180) REVERT: A 560 ASP cc_start: 0.7611 (m-30) cc_final: 0.7280 (m-30) REVERT: A 686 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7140 (mp) REVERT: B 282 GLU cc_start: 0.8148 (tp30) cc_final: 0.7715 (tp30) REVERT: C 87 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: C 132 ARG cc_start: 0.8427 (tpm170) cc_final: 0.8193 (tpm170) REVERT: D 81 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: E 1 MET cc_start: 0.6209 (mtm) cc_final: 0.5920 (mtm) REVERT: E 50 LYS cc_start: 0.8633 (mttm) cc_final: 0.8314 (mtmt) REVERT: E 212 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7360 (tp40) REVERT: E 354 ASP cc_start: 0.6679 (t0) cc_final: 0.6410 (t0) REVERT: F 17 ASP cc_start: 0.6942 (m-30) cc_final: 0.6637 (m-30) REVERT: F 217 LYS cc_start: 0.7278 (tttt) cc_final: 0.6761 (tptt) REVERT: F 248 PHE cc_start: 0.3481 (m-80) cc_final: 0.2842 (m-80) outliers start: 35 outliers final: 21 residues processed: 316 average time/residue: 0.3951 time to fit residues: 191.8165 Evaluate side-chains 311 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 161 MSE Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 30 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 235 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS C 202 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110900 restraints weight = 32146.292| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.07 r_work: 0.3362 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23321 Z= 0.146 Angle : 0.522 7.248 31780 Z= 0.271 Chirality : 0.040 0.138 3698 Planarity : 0.004 0.086 3814 Dihedral : 15.351 144.237 3675 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.46 % Allowed : 13.82 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2693 helix: 1.54 (0.15), residues: 1296 sheet: -0.27 (0.24), residues: 516 loop : -0.65 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 PHE 0.016 0.001 PHE H 19 TYR 0.020 0.001 TYR E 92 ARG 0.007 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 1182) hydrogen bonds : angle 4.41341 ( 3350) covalent geometry : bond 0.00341 (23321) covalent geometry : angle 0.52228 (31780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 302 time to evaluate : 2.420 Fit side-chains REVERT: A 393 LYS cc_start: 0.7040 (ttmm) cc_final: 0.6772 (pptt) REVERT: A 398 ASN cc_start: 0.5787 (t0) cc_final: 0.5527 (t0) REVERT: A 445 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7385 (mpt180) REVERT: A 560 ASP cc_start: 0.7646 (m-30) cc_final: 0.7310 (m-30) REVERT: A 686 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7144 (mp) REVERT: C 87 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: D 81 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: D 88 MET cc_start: 0.7778 (mtp) cc_final: 0.7541 (mtm) REVERT: D 243 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7754 (mp-120) REVERT: E 1 MET cc_start: 0.6212 (mtm) cc_final: 0.5882 (mtm) REVERT: E 106 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.7842 (ptt90) REVERT: E 212 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7360 (tp40) REVERT: F 17 ASP cc_start: 0.7055 (m-30) cc_final: 0.6755 (m-30) REVERT: F 217 LYS cc_start: 0.7244 (tttt) cc_final: 0.6774 (tptt) REVERT: F 248 PHE cc_start: 0.3656 (m-80) cc_final: 0.3039 (m-80) REVERT: G 27 ASN cc_start: 0.8773 (t0) cc_final: 0.7980 (p0) REVERT: G 70 MSE cc_start: 0.8010 (OUTLIER) cc_final: 0.7411 (mtt) outliers start: 35 outliers final: 23 residues processed: 317 average time/residue: 0.3601 time to fit residues: 175.4428 Evaluate side-chains 319 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 161 MSE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 70 MSE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 30 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 239 optimal weight: 0.7980 chunk 180 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 146 GLN B 317 HIS C 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.152392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111403 restraints weight = 31865.615| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.02 r_work: 0.3363 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23321 Z= 0.127 Angle : 0.516 7.205 31780 Z= 0.268 Chirality : 0.039 0.168 3698 Planarity : 0.004 0.082 3814 Dihedral : 15.331 143.353 3675 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.46 % Allowed : 15.07 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2693 helix: 1.61 (0.15), residues: 1296 sheet: -0.16 (0.24), residues: 519 loop : -0.65 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS D 124 PHE 0.013 0.001 PHE H 19 TYR 0.017 0.001 TYR E 92 ARG 0.007 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 1182) hydrogen bonds : angle 4.31206 ( 3350) covalent geometry : bond 0.00291 (23321) covalent geometry : angle 0.51618 (31780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 4.202 Fit side-chains REVERT: A 184 TYR cc_start: 0.7962 (m-80) cc_final: 0.7618 (m-80) REVERT: A 393 LYS cc_start: 0.7068 (ttmm) cc_final: 0.6764 (pptt) REVERT: A 398 ASN cc_start: 0.5763 (t0) cc_final: 0.5482 (t0) REVERT: A 445 ARG cc_start: 0.7607 (mmp80) cc_final: 0.7345 (mpt180) REVERT: A 686 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6936 (mp) REVERT: C 87 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: D 81 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: D 88 MET cc_start: 0.7682 (mtp) cc_final: 0.7432 (mtm) REVERT: D 243 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7751 (mp-120) REVERT: E 1 MET cc_start: 0.6178 (mtm) cc_final: 0.5824 (mtm) REVERT: E 212 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7317 (tp40) REVERT: F 17 ASP cc_start: 0.6958 (m-30) cc_final: 0.6592 (m-30) REVERT: F 217 LYS cc_start: 0.7255 (tttt) cc_final: 0.6744 (tptt) REVERT: F 248 PHE cc_start: 0.3418 (m-80) cc_final: 0.2854 (m-80) outliers start: 35 outliers final: 24 residues processed: 316 average time/residue: 0.4561 time to fit residues: 225.2392 Evaluate side-chains 316 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 161 MSE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain H residue 30 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 208 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 244 optimal weight: 0.3980 chunk 184 optimal weight: 0.0370 chunk 200 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS C 202 ASN C 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.152441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111526 restraints weight = 31935.099| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.01 r_work: 0.3363 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23321 Z= 0.129 Angle : 0.515 7.172 31780 Z= 0.266 Chirality : 0.039 0.145 3698 Planarity : 0.004 0.080 3814 Dihedral : 15.333 143.934 3675 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.50 % Allowed : 15.15 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2693 helix: 1.65 (0.15), residues: 1296 sheet: -0.13 (0.24), residues: 521 loop : -0.64 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 PHE 0.013 0.001 PHE F 237 TYR 0.018 0.001 TYR E 92 ARG 0.008 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 1182) hydrogen bonds : angle 4.25024 ( 3350) covalent geometry : bond 0.00297 (23321) covalent geometry : angle 0.51465 (31780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 300 time to evaluate : 2.670 Fit side-chains REVERT: A 184 TYR cc_start: 0.7972 (m-80) cc_final: 0.7624 (m-80) REVERT: A 398 ASN cc_start: 0.5741 (t0) cc_final: 0.5459 (t0) REVERT: A 445 ARG cc_start: 0.7608 (mmp80) cc_final: 0.7314 (mpt180) REVERT: A 686 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6985 (mp) REVERT: B 301 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8033 (mt-10) REVERT: C 87 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: D 81 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: D 243 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7730 (mp-120) REVERT: E 1 MET cc_start: 0.6272 (mtm) cc_final: 0.5901 (mtm) REVERT: E 106 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.7845 (ptt90) REVERT: E 277 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7325 (t0) REVERT: F 17 ASP cc_start: 0.6984 (m-30) cc_final: 0.6677 (m-30) REVERT: F 217 LYS cc_start: 0.7270 (tttt) cc_final: 0.6768 (tptt) REVERT: F 248 PHE cc_start: 0.3423 (m-80) cc_final: 0.2976 (m-80) outliers start: 36 outliers final: 27 residues processed: 317 average time/residue: 0.4380 time to fit residues: 216.4657 Evaluate side-chains 318 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 161 MSE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 317 HIS C 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110594 restraints weight = 31804.683| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.99 r_work: 0.3347 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23321 Z= 0.154 Angle : 0.534 8.618 31780 Z= 0.275 Chirality : 0.040 0.181 3698 Planarity : 0.004 0.078 3814 Dihedral : 15.375 145.620 3675 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.62 % Allowed : 15.57 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2693 helix: 1.59 (0.15), residues: 1292 sheet: -0.12 (0.24), residues: 521 loop : -0.68 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.006 0.001 HIS E 18 PHE 0.014 0.001 PHE H 249 TYR 0.016 0.001 TYR E 92 ARG 0.008 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1182) hydrogen bonds : angle 4.26185 ( 3350) covalent geometry : bond 0.00365 (23321) covalent geometry : angle 0.53414 (31780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 2.471 Fit side-chains REVERT: A 184 TYR cc_start: 0.7995 (m-80) cc_final: 0.7652 (m-80) REVERT: A 398 ASN cc_start: 0.5693 (t0) cc_final: 0.5418 (t0) REVERT: A 445 ARG cc_start: 0.7581 (mmp80) cc_final: 0.7351 (mpt180) REVERT: A 447 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7455 (m) REVERT: A 686 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7056 (mp) REVERT: C 87 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: D 81 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: D 88 MET cc_start: 0.7626 (mtp) cc_final: 0.7418 (mtm) REVERT: D 243 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7742 (mp-120) REVERT: E 1 MET cc_start: 0.6183 (mtm) cc_final: 0.5756 (mtm) REVERT: E 32 GLN cc_start: 0.7958 (tp40) cc_final: 0.7710 (tp40) REVERT: E 106 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.7888 (ptt90) REVERT: E 277 ASN cc_start: 0.7838 (OUTLIER) cc_final: 0.7453 (t0) REVERT: F 17 ASP cc_start: 0.7050 (m-30) cc_final: 0.6742 (m-30) REVERT: F 217 LYS cc_start: 0.7261 (tttt) cc_final: 0.6776 (tptt) REVERT: F 248 PHE cc_start: 0.3536 (m-80) cc_final: 0.2951 (m-80) REVERT: H 8 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7287 (pp20) outliers start: 39 outliers final: 30 residues processed: 317 average time/residue: 0.3645 time to fit residues: 178.7745 Evaluate side-chains 333 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 161 MSE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 173 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 181 optimal weight: 0.0470 chunk 271 optimal weight: 9.9990 chunk 254 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 317 HIS C 140 ASN C 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.152870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111939 restraints weight = 31950.810| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.03 r_work: 0.3370 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23321 Z= 0.118 Angle : 0.519 11.855 31780 Z= 0.267 Chirality : 0.039 0.188 3698 Planarity : 0.004 0.077 3814 Dihedral : 15.313 143.043 3675 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.46 % Allowed : 15.99 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.17), residues: 2693 helix: 1.70 (0.15), residues: 1296 sheet: -0.10 (0.24), residues: 521 loop : -0.66 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 669 HIS 0.005 0.001 HIS D 124 PHE 0.018 0.001 PHE H 245 TYR 0.016 0.001 TYR E 92 ARG 0.008 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 1182) hydrogen bonds : angle 4.19283 ( 3350) covalent geometry : bond 0.00267 (23321) covalent geometry : angle 0.51870 (31780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 312 time to evaluate : 2.441 Fit side-chains REVERT: A 184 TYR cc_start: 0.7953 (m-80) cc_final: 0.7599 (m-80) REVERT: A 398 ASN cc_start: 0.5683 (t0) cc_final: 0.5387 (t0) REVERT: A 447 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7359 (m) REVERT: A 686 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7016 (mp) REVERT: C 87 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: D 81 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: D 243 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7710 (mp-120) REVERT: E 1 MET cc_start: 0.6145 (mtm) cc_final: 0.5692 (mtm) REVERT: E 32 GLN cc_start: 0.7923 (tp40) cc_final: 0.7653 (tp40) REVERT: E 73 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7270 (mtp-110) REVERT: E 106 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.7860 (ptt90) REVERT: F 17 ASP cc_start: 0.7015 (m-30) cc_final: 0.6682 (m-30) REVERT: F 217 LYS cc_start: 0.7229 (tttt) cc_final: 0.6716 (tptt) REVERT: F 248 PHE cc_start: 0.3427 (m-80) cc_final: 0.2789 (m-80) REVERT: H 8 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7260 (pp20) outliers start: 35 outliers final: 26 residues processed: 330 average time/residue: 0.3682 time to fit residues: 187.1433 Evaluate side-chains 333 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 301 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 161 MSE Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 124 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 198 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 720 GLN B 317 HIS C 140 ASN C 202 ASN G 64 HIS H 153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.150934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109693 restraints weight = 31948.266| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.02 r_work: 0.3333 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23321 Z= 0.184 Angle : 0.566 11.435 31780 Z= 0.289 Chirality : 0.041 0.218 3698 Planarity : 0.004 0.077 3814 Dihedral : 15.431 148.031 3675 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.58 % Allowed : 16.32 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2693 helix: 1.55 (0.15), residues: 1292 sheet: -0.08 (0.24), residues: 518 loop : -0.72 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 4 HIS 0.007 0.001 HIS E 18 PHE 0.018 0.002 PHE H 249 TYR 0.014 0.001 TYR C 75 ARG 0.008 0.001 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 1182) hydrogen bonds : angle 4.29375 ( 3350) covalent geometry : bond 0.00444 (23321) covalent geometry : angle 0.56601 (31780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5386 Ramachandran restraints generated. 2693 Oldfield, 0 Emsley, 2693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 305 time to evaluate : 2.782 Fit side-chains REVERT: A 184 TYR cc_start: 0.8000 (m-80) cc_final: 0.7645 (m-80) REVERT: A 398 ASN cc_start: 0.5748 (t0) cc_final: 0.5438 (t0) REVERT: A 686 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7096 (mp) REVERT: C 87 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: D 81 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: D 88 MET cc_start: 0.7502 (mtm) cc_final: 0.7300 (mtm) REVERT: D 243 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7761 (mp-120) REVERT: E 1 MET cc_start: 0.6209 (mtm) cc_final: 0.5757 (mtm) REVERT: E 32 GLN cc_start: 0.8040 (tp40) cc_final: 0.7796 (tp40) REVERT: E 73 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.7382 (mtp-110) REVERT: E 106 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.7890 (ptt90) REVERT: F 17 ASP cc_start: 0.7081 (m-30) cc_final: 0.6762 (m-30) REVERT: F 217 LYS cc_start: 0.7256 (tttt) cc_final: 0.6757 (tptt) REVERT: F 248 PHE cc_start: 0.3364 (m-80) cc_final: 0.2800 (m-80) REVERT: G 20 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8209 (ttpt) outliers start: 38 outliers final: 30 residues processed: 322 average time/residue: 0.3658 time to fit residues: 183.3074 Evaluate side-chains 333 residues out of total 2402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 161 MSE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 263 optimal weight: 0.5980 chunk 247 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 150 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS C 140 ASN C 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.151939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110959 restraints weight = 31960.479| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.00 r_work: 0.3356 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23321 Z= 0.133 Angle : 0.535 11.341 31780 Z= 0.275 Chirality : 0.039 0.185 3698 Planarity : 0.004 0.077 3814 Dihedral : 15.377 144.953 3675 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.54 % Allowed : 16.40 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2693 helix: 1.64 (0.15), residues: 1296 sheet: -0.13 (0.24), residues: 520 loop : -0.69 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 4 HIS 0.005 0.001 HIS E 18 PHE 0.015 0.001 PHE H 249 TYR 0.018 0.001 TYR E 92 ARG 0.008 0.000 ARG C 136 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 1182) hydrogen bonds : angle 4.20730 ( 3350) covalent geometry : bond 0.00309 (23321) covalent geometry : angle 0.53529 (31780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15529.03 seconds wall clock time: 270 minutes 44.88 seconds (16244.88 seconds total)