Starting phenix.real_space_refine on Wed Aug 5 03:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x5g_66587/08_2026/9x5g_66587.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x5g_66587/08_2026/9x5g_66587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x5g_66587/08_2026/9x5g_66587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x5g_66587/08_2026/9x5g_66587.map" model { file = "/net/cci-nas-00/data/ceres_data/9x5g_66587/08_2026/9x5g_66587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x5g_66587/08_2026/9x5g_66587.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.012 sd= 0.468 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5181 2.51 5 N 1390 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8121 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3265 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 16, 'TRANS': 403} Chain breaks: 3 Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2675 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 315} Chain breaks: 1 Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 905 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "D" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1251 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.29, per 1000 atoms: 0.16 Number of scatterers: 8121 At special positions: 0 Unit cell: (110.4, 100.28, 116.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1509 8.00 N 1390 7.00 C 5181 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: 0.63 Conformation dependent library (CDL) restraints added in 340.8 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 57.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.931A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 93 removed outlier: 3.792A pdb=" N SER A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.621A pdb=" N ILE A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 removed outlier: 4.012A pdb=" N LEU A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 246 through 249 removed outlier: 5.901A pdb=" N THR A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.907A pdb=" N LYS A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 290 removed outlier: 4.485A pdb=" N HIS A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 309 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.262A pdb=" N ALA A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 Processing helix chain 'A' and resid 412 through 418 removed outlier: 4.087A pdb=" N ALA A 418 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.560A pdb=" N LYS A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 471 removed outlier: 3.937A pdb=" N ARG A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 466 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 511 removed outlier: 3.688A pdb=" N TYR A 511 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.818A pdb=" N ASP A 515 " --> pdb=" O GLU A 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 516 " --> pdb=" O GLY A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 512 through 516' Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 541 through 555 removed outlier: 4.109A pdb=" N PHE A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.620A pdb=" N PHE B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.696A pdb=" N THR B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N CYS B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.893A pdb=" N GLU B 160 " --> pdb=" O PRO B 156 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP B 161 " --> pdb=" O CYS B 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 207 removed outlier: 3.844A pdb=" N HIS B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 3.945A pdb=" N MET B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 4.196A pdb=" N ARG B 247 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.859A pdb=" N GLY B 279 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 removed outlier: 3.664A pdb=" N ARG B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 4.030A pdb=" N TYR B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 44 removed outlier: 3.621A pdb=" N VAL C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 59 through 67 Processing helix chain 'C' and resid 69 through 78 removed outlier: 3.547A pdb=" N GLU C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.675A pdb=" N LEU C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.617A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.552A pdb=" N SER C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 139 removed outlier: 3.689A pdb=" N LEU C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 28 through 35 removed outlier: 3.924A pdb=" N MET D 32 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP D 35 " --> pdb=" O HIS D 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 35' Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 76 through 92 removed outlier: 4.182A pdb=" N ASP D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 109 Processing helix chain 'D' and resid 110 through 126 removed outlier: 3.926A pdb=" N MET D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 138 removed outlier: 3.782A pdb=" N THR D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 removed outlier: 4.330A pdb=" N GLU D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN D 155 " --> pdb=" O VAL D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.497A pdb=" N LEU A 205 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 75 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 145 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 190 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL B 185 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ILE B 218 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N MET B 187 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU B 220 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY B 189 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 289 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER B 286 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 317 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL B 288 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU B 319 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 290 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 381 through 385 removed outlier: 3.638A pdb=" N ARG A 382 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 349 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 317 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP A 319 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 439 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 441 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 381 through 385 removed outlier: 3.638A pdb=" N ARG A 382 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 349 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 317 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP A 319 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 439 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 441 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 572 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA A 581 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU A 570 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 15 through 19 removed outlier: 4.052A pdb=" N VAL D 42 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS D 9 " --> pdb=" O VAL D 42 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1433 1.32 - 1.44: 2130 1.44 - 1.57: 4673 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 8300 Sorted by residual: bond pdb=" N VAL A 203 " pdb=" CA VAL A 203 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.22e-02 6.72e+03 9.74e+00 bond pdb=" N VAL A 204 " pdb=" CA VAL A 204 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.55e+00 bond pdb=" N ASP A 207 " pdb=" CA ASP A 207 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.91e+00 bond pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 1.464 1.496 -0.033 1.13e-02 7.83e+03 8.32e+00 bond pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.10e-02 8.26e+03 8.15e+00 ... (remaining 8295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 10894 1.22 - 2.44: 275 2.44 - 3.66: 62 3.66 - 4.88: 13 4.88 - 6.10: 4 Bond angle restraints: 11248 Sorted by residual: angle pdb=" N THR A 211 " pdb=" CA THR A 211 " pdb=" C THR A 211 " ideal model delta sigma weight residual 113.28 108.67 4.61 1.22e+00 6.72e-01 1.43e+01 angle pdb=" CA VAL A 206 " pdb=" C VAL A 206 " pdb=" O VAL A 206 " ideal model delta sigma weight residual 121.09 117.30 3.79 1.06e+00 8.90e-01 1.28e+01 angle pdb=" C LYS A 323 " pdb=" CA LYS A 323 " pdb=" CB LYS A 323 " ideal model delta sigma weight residual 116.63 112.69 3.94 1.16e+00 7.43e-01 1.16e+01 angle pdb=" N THR A 208 " pdb=" CA THR A 208 " pdb=" C THR A 208 " ideal model delta sigma weight residual 112.92 109.04 3.88 1.23e+00 6.61e-01 9.96e+00 angle pdb=" C PHE A 535 " pdb=" CA PHE A 535 " pdb=" CB PHE A 535 " ideal model delta sigma weight residual 109.72 115.02 -5.30 1.73e+00 3.34e-01 9.37e+00 ... (remaining 11243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 4622 14.58 - 29.16: 344 29.16 - 43.74: 62 43.74 - 58.31: 2 58.31 - 72.89: 3 Dihedral angle restraints: 5033 sinusoidal: 2065 harmonic: 2968 Sorted by residual: dihedral pdb=" CA ILE B 196 " pdb=" C ILE B 196 " pdb=" N VAL B 197 " pdb=" CA VAL B 197 " ideal model delta harmonic sigma weight residual -180.00 -162.93 -17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN B 146 " pdb=" CB ASN B 146 " pdb=" CG ASN B 146 " pdb=" OD1 ASN B 146 " ideal model delta sinusoidal sigma weight residual 120.00 -167.11 -72.89 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA TYR B 240 " pdb=" C TYR B 240 " pdb=" N PHE B 241 " pdb=" CA PHE B 241 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 5030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 868 0.036 - 0.071: 275 0.071 - 0.107: 77 0.107 - 0.143: 29 0.143 - 0.178: 2 Chirality restraints: 1251 Sorted by residual: chirality pdb=" CA VAL A 204 " pdb=" N VAL A 204 " pdb=" C VAL A 204 " pdb=" CB VAL A 204 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA ILE A 437 " pdb=" N ILE A 437 " pdb=" C ILE A 437 " pdb=" CB ILE A 437 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 1248 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 16 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 17 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 328 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 329 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 129 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO D 130 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 130 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 130 " -0.020 5.00e-02 4.00e+02 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 829 2.75 - 3.29: 7961 3.29 - 3.83: 12247 3.83 - 4.36: 13381 4.36 - 4.90: 23947 Nonbonded interactions: 58365 Sorted by model distance: nonbonded pdb=" OG SER D 26 " pdb=" O LEU D 108 " model vdw 2.213 3.040 nonbonded pdb=" OD2 ASP A 109 " pdb=" OG SER A 115 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR D 129 " pdb=" OE1 GLU D 131 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASN B 8 " pdb=" OG SER B 10 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP C 48 " pdb=" OG1 THR C 51 " model vdw 2.252 3.040 ... (remaining 58360 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 0.039 8300 Z= 0.192 Angle : 0.500 6.100 11248 Z= 0.302 Chirality : 0.040 0.178 1251 Planarity : 0.004 0.051 1441 Dihedral : 10.237 72.892 3111 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.11 % Allowed : 6.52 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.26), residues: 1006 helix: 0.55 (0.23), residues: 496 sheet: 0.84 (0.49), residues: 108 loop : -1.74 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 117 TYR 0.014 0.001 TYR A 500 PHE 0.009 0.001 PHE A 296 TRP 0.009 0.001 TRP A 328 HIS 0.002 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.19 ( 8300) covalent geometry : angle 0.50037 / 0.30 (11248) hydrogen bonds : bond 0.15821 / 10.47 ( 374) hydrogen bonds : angle 5.90967 / 4.34 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LYS cc_start: 0.9065 (tmmt) cc_final: 0.8827 (tmmt) REVERT: A 243 LEU cc_start: 0.8740 (pp) cc_final: 0.8461 (pp) REVERT: A 496 MET cc_start: 0.6895 (ppp) cc_final: 0.6520 (mtt) REVERT: B 72 ASN cc_start: 0.8173 (m-40) cc_final: 0.7922 (m110) REVERT: B 181 LYS cc_start: 0.8557 (mtmm) cc_final: 0.7402 (tttp) REVERT: C 41 TYR cc_start: 0.8828 (t80) cc_final: 0.7971 (t80) REVERT: C 42 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8215 (mm-30) REVERT: C 46 HIS cc_start: 0.8162 (m90) cc_final: 0.7838 (m90) REVERT: D 1 MET cc_start: 0.2545 (tpt) cc_final: 0.2252 (tpt) REVERT: D 86 TRP cc_start: 0.9375 (t60) cc_final: 0.9148 (t60) REVERT: D 128 LYS cc_start: 0.6725 (ptmm) cc_final: 0.6076 (ptmm) REVERT: D 129 THR cc_start: 0.7918 (t) cc_final: 0.7679 (t) REVERT: D 156 GLN cc_start: 0.8078 (pm20) cc_final: 0.7404 (pm20) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1436 time to fit residues: 34.8531 Evaluate side-chains 147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 221 HIS B 263 HIS C 79 HIS D 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.076156 restraints weight = 27065.436| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.99 r_work: 0.3030 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8300 Z= 0.163 Angle : 0.622 8.874 11248 Z= 0.329 Chirality : 0.043 0.148 1251 Planarity : 0.005 0.049 1441 Dihedral : 4.305 15.383 1180 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.06 % Allowed : 11.44 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.26), residues: 1006 helix: 0.82 (0.23), residues: 508 sheet: 1.16 (0.53), residues: 106 loop : -1.65 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 101 TYR 0.023 0.002 TYR A 463 PHE 0.023 0.002 PHE B 155 TRP 0.013 0.002 TRP A 366 HIS 0.014 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8300) covalent geometry : angle 0.62169 / 0.33 (11248) hydrogen bonds : bond 0.06027 / 4.09 ( 374) hydrogen bonds : angle 4.59954 / 3.37 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.9060 (mp) cc_final: 0.8732 (mt) REVERT: A 496 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6698 (mmm) REVERT: A 577 ARG cc_start: 0.7528 (ttm-80) cc_final: 0.7281 (ttt180) REVERT: B 181 LYS cc_start: 0.8735 (mtmm) cc_final: 0.7591 (tttp) REVERT: B 281 ASP cc_start: 0.7864 (p0) cc_final: 0.7398 (p0) REVERT: C 41 TYR cc_start: 0.8849 (t80) cc_final: 0.8155 (t80) REVERT: C 42 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8253 (mm-30) REVERT: C 46 HIS cc_start: 0.8349 (m90) cc_final: 0.7967 (m90) REVERT: D 1 MET cc_start: 0.0417 (tpt) cc_final: -0.0049 (tpt) REVERT: D 128 LYS cc_start: 0.6467 (ptmm) cc_final: 0.6003 (ptmm) outliers start: 18 outliers final: 9 residues processed: 152 average time/residue: 0.1369 time to fit residues: 25.9677 Evaluate side-chains 148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN C 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.098316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076364 restraints weight = 26522.849| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.96 r_work: 0.3037 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8300 Z= 0.137 Angle : 0.596 14.642 11248 Z= 0.307 Chirality : 0.042 0.137 1251 Planarity : 0.004 0.044 1441 Dihedral : 4.176 14.525 1180 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.29 % Allowed : 12.24 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1006 helix: 0.93 (0.23), residues: 511 sheet: 0.94 (0.50), residues: 116 loop : -1.43 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 102 TYR 0.019 0.001 TYR A 463 PHE 0.019 0.001 PHE B 155 TRP 0.011 0.001 TRP A 328 HIS 0.012 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8300) covalent geometry : angle 0.59629 / 0.31 (11248) hydrogen bonds : bond 0.05204 / 3.53 ( 374) hydrogen bonds : angle 4.31018 / 3.16 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 286 HIS cc_start: 0.8094 (m170) cc_final: 0.7604 (m170) REVERT: A 496 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6464 (mtt) REVERT: A 515 ASP cc_start: 0.8017 (m-30) cc_final: 0.7686 (t70) REVERT: A 577 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.7298 (ttt180) REVERT: B 181 LYS cc_start: 0.8749 (mtmm) cc_final: 0.7736 (tttp) REVERT: B 261 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7265 (ttp-170) REVERT: B 281 ASP cc_start: 0.7785 (p0) cc_final: 0.7405 (p0) REVERT: C 41 TYR cc_start: 0.8883 (t80) cc_final: 0.8226 (t80) REVERT: C 42 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8326 (mm-30) REVERT: D 1 MET cc_start: 0.0338 (tpt) cc_final: -0.0136 (tpt) REVERT: D 52 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9228 (pt) REVERT: D 128 LYS cc_start: 0.6314 (ptmm) cc_final: 0.5900 (ptmm) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 0.1368 time to fit residues: 26.5684 Evaluate side-chains 147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 95 optimal weight: 0.0050 chunk 20 optimal weight: 0.5980 chunk 90 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN C 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.100047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078378 restraints weight = 27141.892| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.98 r_work: 0.3083 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8300 Z= 0.110 Angle : 0.578 11.688 11248 Z= 0.292 Chirality : 0.040 0.135 1251 Planarity : 0.004 0.043 1441 Dihedral : 3.876 14.100 1180 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 13.73 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1006 helix: 1.02 (0.23), residues: 511 sheet: 0.83 (0.49), residues: 118 loop : -1.34 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.017 0.001 TYR A 463 PHE 0.016 0.001 PHE B 155 TRP 0.011 0.001 TRP D 86 HIS 0.010 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8300) covalent geometry : angle 0.57810 / 0.29 (11248) hydrogen bonds : bond 0.03882 / 2.64 ( 374) hydrogen bonds : angle 3.99199 / 2.93 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7331 (tp30) REVERT: A 496 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6154 (mmm) REVERT: B 27 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: B 29 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7068 (mm) REVERT: B 261 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7455 (ttp-170) REVERT: B 281 ASP cc_start: 0.7809 (p0) cc_final: 0.7426 (p0) REVERT: C 41 TYR cc_start: 0.8859 (t80) cc_final: 0.8226 (t80) REVERT: C 42 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 1 MET cc_start: 0.0349 (tpt) cc_final: -0.0105 (tpt) REVERT: D 52 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9248 (pt) REVERT: D 126 LYS cc_start: 0.8768 (ptpt) cc_final: 0.8451 (ptpp) REVERT: D 128 LYS cc_start: 0.6235 (ptmm) cc_final: 0.5854 (ptmm) outliers start: 20 outliers final: 11 residues processed: 150 average time/residue: 0.1360 time to fit residues: 25.2011 Evaluate side-chains 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.094865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.072907 restraints weight = 27067.127| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.97 r_work: 0.2936 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8300 Z= 0.219 Angle : 0.709 14.352 11248 Z= 0.370 Chirality : 0.046 0.169 1251 Planarity : 0.005 0.043 1441 Dihedral : 4.696 16.848 1180 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.55 % Allowed : 14.19 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.26), residues: 1006 helix: 0.70 (0.23), residues: 504 sheet: 0.84 (0.51), residues: 115 loop : -1.49 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 70 TYR 0.016 0.002 TYR B 80 PHE 0.017 0.002 PHE B 64 TRP 0.025 0.002 TRP A 366 HIS 0.014 0.002 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.22 ( 8300) covalent geometry : angle 0.70901 / 0.37 (11248) hydrogen bonds : bond 0.07321 / 4.99 ( 374) hydrogen bonds : angle 4.54168 / 3.32 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LYS cc_start: 0.9158 (tmmt) cc_final: 0.8810 (pptt) REVERT: A 384 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 411 PHE cc_start: 0.8584 (m-10) cc_final: 0.8382 (m-10) REVERT: A 496 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7022 (mmm) REVERT: B 29 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7431 (mm) REVERT: B 181 LYS cc_start: 0.8818 (mtmm) cc_final: 0.7876 (tttp) REVERT: B 261 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7279 (ttp-170) REVERT: B 281 ASP cc_start: 0.8034 (p0) cc_final: 0.7653 (p0) REVERT: C 41 TYR cc_start: 0.8919 (t80) cc_final: 0.8245 (t80) REVERT: C 42 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8306 (mm-30) REVERT: D 1 MET cc_start: 0.0354 (tpt) cc_final: -0.0093 (tpt) REVERT: D 52 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9228 (pt) REVERT: D 128 LYS cc_start: 0.6588 (ptmm) cc_final: 0.6188 (ptmm) outliers start: 31 outliers final: 15 residues processed: 161 average time/residue: 0.1374 time to fit residues: 27.4096 Evaluate side-chains 155 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 0.0570 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.093146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.071381 restraints weight = 27312.526| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.91 r_work: 0.2969 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8300 Z= 0.165 Angle : 0.668 14.491 11248 Z= 0.345 Chirality : 0.043 0.154 1251 Planarity : 0.004 0.045 1441 Dihedral : 4.496 15.520 1180 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.86 % Allowed : 15.22 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.26), residues: 1006 helix: 0.70 (0.23), residues: 512 sheet: 0.81 (0.51), residues: 116 loop : -1.44 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 70 TYR 0.015 0.001 TYR A 463 PHE 0.014 0.002 PHE B 155 TRP 0.021 0.002 TRP A 366 HIS 0.005 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 8300) covalent geometry : angle 0.66751 / 0.34 (11248) hydrogen bonds : bond 0.05882 / 4.03 ( 374) hydrogen bonds : angle 4.33606 / 3.17 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7876 (t80) REVERT: A 496 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6537 (mmm) REVERT: B 29 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7395 (mm) REVERT: B 181 LYS cc_start: 0.8795 (mtmm) cc_final: 0.7897 (tttp) REVERT: B 261 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7331 (ttp-170) REVERT: B 281 ASP cc_start: 0.8058 (p0) cc_final: 0.7673 (p0) REVERT: C 41 TYR cc_start: 0.8857 (t80) cc_final: 0.8203 (t80) REVERT: C 42 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8338 (mm-30) REVERT: C 50 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8430 (tppt) REVERT: D 1 MET cc_start: 0.0404 (tpt) cc_final: -0.0058 (tpt) REVERT: D 52 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9228 (pt) outliers start: 25 outliers final: 13 residues processed: 156 average time/residue: 0.1374 time to fit residues: 26.4851 Evaluate side-chains 149 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.096678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.075024 restraints weight = 26955.159| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.97 r_work: 0.3000 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8300 Z= 0.137 Angle : 0.665 15.358 11248 Z= 0.340 Chirality : 0.042 0.163 1251 Planarity : 0.004 0.046 1441 Dihedral : 4.286 16.134 1180 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.52 % Allowed : 16.70 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1006 helix: 0.79 (0.23), residues: 515 sheet: 0.87 (0.51), residues: 116 loop : -1.45 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 70 TYR 0.016 0.001 TYR A 463 PHE 0.014 0.001 PHE B 155 TRP 0.019 0.001 TRP A 366 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8300) covalent geometry : angle 0.66534 / 0.34 (11248) hydrogen bonds : bond 0.04936 / 3.38 ( 374) hydrogen bonds : angle 4.17743 / 3.06 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 PHE cc_start: 0.8535 (m-10) cc_final: 0.8257 (m-10) REVERT: A 496 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6371 (mmm) REVERT: B 29 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 181 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8037 (tttm) REVERT: B 261 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7380 (ttp-170) REVERT: B 281 ASP cc_start: 0.8081 (p0) cc_final: 0.7700 (p0) REVERT: C 41 TYR cc_start: 0.8870 (t80) cc_final: 0.8264 (t80) REVERT: C 42 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8417 (mm-30) REVERT: D 1 MET cc_start: 0.0503 (tpt) cc_final: 0.0048 (tpt) REVERT: D 52 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9219 (pt) REVERT: D 91 MET cc_start: 0.8948 (mpp) cc_final: 0.8490 (tpp) outliers start: 22 outliers final: 14 residues processed: 151 average time/residue: 0.1357 time to fit residues: 25.5280 Evaluate side-chains 150 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.097310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075586 restraints weight = 26628.857| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.96 r_work: 0.3018 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8300 Z= 0.133 Angle : 0.682 15.937 11248 Z= 0.341 Chirality : 0.042 0.170 1251 Planarity : 0.004 0.046 1441 Dihedral : 4.196 14.735 1180 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.06 % Allowed : 17.16 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 1006 helix: 0.85 (0.23), residues: 517 sheet: 0.90 (0.52), residues: 116 loop : -1.35 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 70 TYR 0.015 0.001 TYR A 463 PHE 0.014 0.001 PHE B 155 TRP 0.018 0.001 TRP D 86 HIS 0.004 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8300) covalent geometry : angle 0.68177 / 0.34 (11248) hydrogen bonds : bond 0.04716 / 3.24 ( 374) hydrogen bonds : angle 4.14107 / 3.05 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 PHE cc_start: 0.8524 (m-10) cc_final: 0.8285 (m-10) REVERT: A 496 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6336 (mmm) REVERT: B 29 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7226 (mm) REVERT: B 181 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8044 (tttm) REVERT: B 261 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7368 (ttp-170) REVERT: B 281 ASP cc_start: 0.8061 (p0) cc_final: 0.7694 (p0) REVERT: C 41 TYR cc_start: 0.8871 (t80) cc_final: 0.8282 (t80) REVERT: C 42 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8451 (mm-30) REVERT: D 52 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9229 (pt) REVERT: D 91 MET cc_start: 0.8908 (mpp) cc_final: 0.8462 (tpp) outliers start: 18 outliers final: 13 residues processed: 155 average time/residue: 0.1166 time to fit residues: 22.3792 Evaluate side-chains 156 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 119 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.098602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.076912 restraints weight = 26736.294| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.95 r_work: 0.3050 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8300 Z= 0.128 Angle : 0.694 16.588 11248 Z= 0.347 Chirality : 0.042 0.163 1251 Planarity : 0.004 0.046 1441 Dihedral : 4.021 14.953 1180 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.06 % Allowed : 17.51 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.27), residues: 1006 helix: 0.96 (0.23), residues: 522 sheet: 0.81 (0.51), residues: 118 loop : -1.36 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 70 TYR 0.016 0.001 TYR A 463 PHE 0.013 0.001 PHE B 155 TRP 0.020 0.001 TRP D 86 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8300) covalent geometry : angle 0.69434 / 0.35 (11248) hydrogen bonds : bond 0.04129 / 2.83 ( 374) hydrogen bonds : angle 3.96580 / 2.91 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 LYS cc_start: 0.9124 (tmmt) cc_final: 0.8897 (tmmt) REVERT: A 253 ARG cc_start: 0.8174 (mmm-85) cc_final: 0.7892 (mmm-85) REVERT: A 411 PHE cc_start: 0.8448 (m-10) cc_final: 0.8223 (m-10) REVERT: A 496 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6204 (mmm) REVERT: B 29 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7205 (mm) REVERT: B 181 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8055 (tttm) REVERT: B 261 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.7566 (ttp-170) REVERT: B 281 ASP cc_start: 0.7999 (p0) cc_final: 0.7625 (p0) REVERT: C 41 TYR cc_start: 0.8853 (t80) cc_final: 0.8299 (t80) REVERT: C 42 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8448 (mm-30) REVERT: D 52 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9230 (pt) outliers start: 18 outliers final: 13 residues processed: 154 average time/residue: 0.1103 time to fit residues: 21.2656 Evaluate side-chains 152 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 119 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 0.0570 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.098847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077193 restraints weight = 26800.712| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.94 r_work: 0.3041 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8300 Z= 0.131 Angle : 0.701 16.787 11248 Z= 0.352 Chirality : 0.042 0.154 1251 Planarity : 0.004 0.046 1441 Dihedral : 3.997 15.939 1180 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.29 % Allowed : 17.85 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.27), residues: 1006 helix: 1.04 (0.23), residues: 520 sheet: 0.81 (0.51), residues: 118 loop : -1.30 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 70 TYR 0.034 0.001 TYR D 107 PHE 0.014 0.001 PHE B 155 TRP 0.024 0.001 TRP D 86 HIS 0.004 0.001 HIS D 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8300) covalent geometry : angle 0.70135 / 0.35 (11248) hydrogen bonds : bond 0.04327 / 2.97 ( 374) hydrogen bonds : angle 3.95901 / 2.89 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7964 (mmm-85) REVERT: A 411 PHE cc_start: 0.8467 (m-10) cc_final: 0.8226 (m-10) REVERT: A 496 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6321 (mmm) REVERT: B 29 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7209 (mm) REVERT: B 181 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8078 (tttm) REVERT: B 261 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: B 281 ASP cc_start: 0.7983 (p0) cc_final: 0.7620 (p0) REVERT: C 41 TYR cc_start: 0.8843 (t80) cc_final: 0.8301 (t80) REVERT: C 42 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8515 (mm-30) REVERT: D 52 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9236 (pt) outliers start: 20 outliers final: 13 residues processed: 151 average time/residue: 0.1009 time to fit residues: 18.9458 Evaluate side-chains 155 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.098397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076553 restraints weight = 26581.049| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.93 r_work: 0.3031 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8300 Z= 0.140 Angle : 0.731 14.958 11248 Z= 0.371 Chirality : 0.043 0.224 1251 Planarity : 0.004 0.045 1441 Dihedral : 4.076 15.700 1180 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.95 % Allowed : 18.31 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 1006 helix: 1.01 (0.23), residues: 520 sheet: 0.88 (0.51), residues: 118 loop : -1.24 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 70 TYR 0.032 0.001 TYR D 107 PHE 0.014 0.001 PHE B 155 TRP 0.028 0.001 TRP D 86 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8300) covalent geometry : angle 0.73052 / 0.37 (11248) hydrogen bonds : bond 0.04609 / 3.16 ( 374) hydrogen bonds : angle 4.04618 / 2.95 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.56 seconds wall clock time: 34 minutes 25.41 seconds (2065.41 seconds total)