Starting phenix.real_space_refine on Mon Jun 9 17:36:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c6b_45243/06_2025/9c6b_45243.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c6b_45243/06_2025/9c6b_45243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c6b_45243/06_2025/9c6b_45243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c6b_45243/06_2025/9c6b_45243.map" model { file = "/net/cci-nas-00/data/ceres_data/9c6b_45243/06_2025/9c6b_45243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c6b_45243/06_2025/9c6b_45243.cif" } resolution = 2.6 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= 0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 S 61 5.16 5 C 6783 2.51 5 N 1841 2.21 5 O 2050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10737 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4527 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 554} Chain: "B" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3553 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 15, 'TRANS': 418} Chain breaks: 1 Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2498 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 294} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'MLL%COO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 157 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 18} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.52, per 1000 atoms: 0.61 Number of scatterers: 10737 At special positions: 0 Unit cell: (102.498, 103.325, 123.163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 61 16.00 O 2050 8.00 N 1841 7.00 C 6783 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: 3.04 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 " 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 53.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.537A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 50 through 57 removed outlier: 4.546A pdb=" N ASP A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.722A pdb=" N GLY A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 4.953A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.892A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.936A pdb=" N CYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.585A pdb=" N SER A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 4.659A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.712A pdb=" N ALA A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.509A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.796A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.888A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.560A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.908A pdb=" N LEU A 368 " --> pdb=" O HIS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.721A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 removed outlier: 4.212A pdb=" N GLU A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 413 removed outlier: 4.497A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.509A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'A' and resid 442 through 451 removed outlier: 4.543A pdb=" N LEU A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.648A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 494 through 521 removed outlier: 3.569A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 533 through 547 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 145 through 149 removed outlier: 4.024A pdb=" N VAL B 149 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 4.001A pdb=" N GLU B 224 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.754A pdb=" N LEU B 329 " --> pdb=" O HIS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.753A pdb=" N ASN B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.628A pdb=" N PHE B 343 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP B 344 " --> pdb=" O CYS B 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 344' Processing helix chain 'B' and resid 382 through 386 removed outlier: 4.126A pdb=" N ASN B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.886A pdb=" N GLU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 41 removed outlier: 4.416A pdb=" N LYS C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.746A pdb=" N VAL C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.618A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.669A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 4.003A pdb=" N CYS C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'D' and resid 619 through 631 Processing sheet with id=AA1, first strand: chain 'B' and resid 390 through 391 removed outlier: 4.166A pdb=" N THR B 390 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 441 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 17 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 439 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N HIS B 421 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.403A pdb=" N GLY B 46 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 34 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE B 36 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU B 42 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 47 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 52 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 76 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 54 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.699A pdb=" N LYS B 98 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 119 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE B 171 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 121 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LYS B 129 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASP B 161 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.769A pdb=" N ILE B 200 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N HIS B 204 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ARG B 210 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.818A pdb=" N ALA B 231 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.564A pdb=" N ASP B 290 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 321 " --> pdb=" O ILE B 310 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 350 Processing sheet with id=AA9, first strand: chain 'B' and resid 396 through 398 removed outlier: 6.867A pdb=" N LYS B 396 " --> pdb=" O ILE B 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.315A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.516A pdb=" N VAL C 52 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.728A pdb=" N ASP C 202 " --> pdb=" O PHE C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 501 hydrogen bonds defined for protein. 1434 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: 3.72 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3582 1.34 - 1.46: 2100 1.46 - 1.58: 5178 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 10949 Sorted by residual: bond pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 1.231 1.364 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" CA VAL B 149 " pdb=" CB VAL B 149 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.05e-02 9.07e+03 2.49e+00 bond pdb=" CD GLU C 15 " pdb=" OE1 GLU C 15 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.33e-01 bond pdb=" C ASP C 290 " pdb=" N PRO C 291 " ideal model delta sigma weight residual 1.332 1.343 -0.011 1.30e-02 5.92e+03 7.30e-01 bond pdb=" CG GLU C 15 " pdb=" CD GLU C 15 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.13e-01 ... (remaining 10944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 14614 1.47 - 2.94: 169 2.94 - 4.41: 33 4.41 - 5.88: 19 5.88 - 7.36: 3 Bond angle restraints: 14838 Sorted by residual: angle pdb=" N VAL C 58 " pdb=" CA VAL C 58 " pdb=" C VAL C 58 " ideal model delta sigma weight residual 111.90 108.87 3.03 8.10e-01 1.52e+00 1.40e+01 angle pdb=" C ARG A 537 " pdb=" N PHE A 538 " pdb=" CA PHE A 538 " ideal model delta sigma weight residual 121.14 115.85 5.29 1.75e+00 3.27e-01 9.13e+00 angle pdb=" N GLU C 15 " pdb=" CA GLU C 15 " pdb=" CB GLU C 15 " ideal model delta sigma weight residual 110.28 114.73 -4.45 1.55e+00 4.16e-01 8.26e+00 angle pdb=" CA GLY B 401 " pdb=" C GLY B 401 " pdb=" O GLY B 401 " ideal model delta sigma weight residual 122.57 120.10 2.47 9.20e-01 1.18e+00 7.19e+00 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 112.29 115.15 -2.86 1.12e+00 7.97e-01 6.51e+00 ... (remaining 14833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6207 17.94 - 35.88: 393 35.88 - 53.82: 58 53.82 - 71.76: 3 71.76 - 89.71: 8 Dihedral angle restraints: 6669 sinusoidal: 2712 harmonic: 3957 Sorted by residual: dihedral pdb=" CA GLU C 297 " pdb=" C GLU C 297 " pdb=" N PRO C 298 " pdb=" CA PRO C 298 " ideal model delta harmonic sigma weight residual -180.00 -138.08 -41.92 0 5.00e+00 4.00e-02 7.03e+01 dihedral pdb=" CA TYR C 127 " pdb=" C TYR C 127 " pdb=" N GLY C 128 " pdb=" CA GLY C 128 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " pdb=" CD GLU A 110 " pdb=" OE1 GLU A 110 " ideal model delta sinusoidal sigma weight residual 0.00 -89.71 89.71 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 972 0.027 - 0.055: 424 0.055 - 0.082: 161 0.082 - 0.109: 96 0.109 - 0.136: 22 Chirality restraints: 1675 Sorted by residual: chirality pdb=" CA PHE A 538 " pdb=" N PHE A 538 " pdb=" C PHE A 538 " pdb=" CB PHE A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA GLU C 15 " pdb=" N GLU C 15 " pdb=" C GLU C 15 " pdb=" CB GLU C 15 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL B 154 " pdb=" N VAL B 154 " pdb=" C VAL B 154 " pdb=" CB VAL B 154 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1672 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 297 " 0.059 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO C 298 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 90 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 91 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 548 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 549 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 549 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 549 " -0.022 5.00e-02 4.00e+02 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 5 2.12 - 2.82: 3095 2.82 - 3.51: 14736 3.51 - 4.21: 25399 4.21 - 4.90: 46496 Nonbonded interactions: 89731 Sorted by model distance: nonbonded pdb=" OXT MLL C 309 " pdb=" C10 MLL C 309 " model vdw 1.427 3.460 nonbonded pdb=" OD2 ASP C 85 " pdb="FE FE2 C 401 " model vdw 1.940 3.000 nonbonded pdb=" ND1 HIS C 241 " pdb="FE FE2 C 401 " model vdw 1.998 3.080 nonbonded pdb=" NE2 HIS C 167 " pdb="FE FE2 C 401 " model vdw 2.015 3.080 nonbonded pdb=" OD2 ASP C 85 " pdb="ZN ZN C 402 " model vdw 2.066 2.230 ... (remaining 89726 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: 2.450 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 0.133 10950 Z= 0.141 Angle : 0.474 7.356 14838 Z= 0.253 Chirality : 0.041 0.136 1675 Planarity : 0.004 0.090 1922 Dihedral : 11.993 89.706 4093 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.40 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.89 (0.24), residues: 1333 helix: 1.32 (0.22), residues: 604 sheet: 0.24 (0.36), residues: 227 loop : 0.01 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 424 HIS 0.003 0.001 HIS C 241 PHE 0.019 0.001 PHE A 538 TYR 0.009 0.001 TYR B 244 ARG 0.001 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.19646 ( 501) hydrogen bonds : angle 6.10739 ( 1434) metal coordination : bond 0.00099 ( 1) covalent geometry : bond 0.00316 (10949) covalent geometry : angle 0.47450 (14838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.305 Fit side-chains REVERT: B 396 LYS cc_start: 0.8931 (tppp) cc_final: 0.8662 (ttmm) REVERT: C 15 GLU cc_start: 0.8397 (mp0) cc_final: 0.8170 (mp0) REVERT: C 131 ASP cc_start: 0.8449 (t70) cc_final: 0.8173 (t0) REVERT: C 179 HIS cc_start: 0.9231 (m90) cc_final: 0.8774 (m170) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.8998 time to fit residues: 146.6536 Evaluate side-chains 54 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS D 619 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.057888 restraints weight = 21833.919| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.08 r_work: 0.2746 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10950 Z= 0.150 Angle : 0.515 6.590 14838 Z= 0.273 Chirality : 0.042 0.138 1675 Planarity : 0.004 0.063 1922 Dihedral : 4.123 39.189 1461 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.58 % Allowed : 4.50 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.84 (0.23), residues: 1333 helix: 1.27 (0.22), residues: 628 sheet: 0.42 (0.37), residues: 216 loop : -0.19 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 203 HIS 0.004 0.001 HIS C 241 PHE 0.032 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.004 0.000 ARG C 121 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 501) hydrogen bonds : angle 4.72452 ( 1434) metal coordination : bond 0.00124 ( 1) covalent geometry : bond 0.00349 (10949) covalent geometry : angle 0.51467 (14838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.239 Fit side-chains REVERT: A 323 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8307 (mpp) REVERT: C 131 ASP cc_start: 0.8866 (t70) cc_final: 0.8621 (t0) REVERT: C 179 HIS cc_start: 0.9327 (m90) cc_final: 0.9105 (m-70) outliers start: 7 outliers final: 0 residues processed: 58 average time/residue: 1.6752 time to fit residues: 105.4101 Evaluate side-chains 50 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058402 restraints weight = 21977.404| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.02 r_work: 0.2759 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10950 Z= 0.132 Angle : 0.489 8.759 14838 Z= 0.256 Chirality : 0.041 0.138 1675 Planarity : 0.004 0.052 1922 Dihedral : 4.066 36.877 1461 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.50 % Allowed : 6.17 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.86 (0.23), residues: 1333 helix: 1.36 (0.22), residues: 631 sheet: 0.18 (0.36), residues: 226 loop : -0.16 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.016 0.001 HIS C 230 PHE 0.027 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 501) hydrogen bonds : angle 4.40861 ( 1434) metal coordination : bond 0.00170 ( 1) covalent geometry : bond 0.00307 (10949) covalent geometry : angle 0.48938 (14838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.218 Fit side-chains REVERT: B 358 MET cc_start: 0.9639 (ttp) cc_final: 0.9314 (ttp) REVERT: C 131 ASP cc_start: 0.8859 (t70) cc_final: 0.8569 (t0) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 1.4343 time to fit residues: 82.5912 Evaluate side-chains 49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 HIS C 179 HIS C 191 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.057903 restraints weight = 21795.897| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.02 r_work: 0.2738 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10950 Z= 0.158 Angle : 0.497 7.305 14838 Z= 0.258 Chirality : 0.041 0.140 1675 Planarity : 0.004 0.042 1922 Dihedral : 4.094 35.728 1461 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.75 % Allowed : 7.09 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.88 (0.23), residues: 1333 helix: 1.44 (0.22), residues: 629 sheet: 0.24 (0.37), residues: 216 loop : -0.28 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.003 0.001 HIS C 179 PHE 0.026 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.003 0.000 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 501) hydrogen bonds : angle 4.35191 ( 1434) metal coordination : bond 0.00211 ( 1) covalent geometry : bond 0.00375 (10949) covalent geometry : angle 0.49728 (14838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 2.881 Fit side-chains REVERT: C 131 ASP cc_start: 0.8829 (t70) cc_final: 0.8529 (t0) outliers start: 9 outliers final: 3 residues processed: 55 average time/residue: 2.5689 time to fit residues: 154.6849 Evaluate side-chains 50 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 64 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058483 restraints weight = 21786.749| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.08 r_work: 0.2767 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10950 Z= 0.111 Angle : 0.479 7.297 14838 Z= 0.248 Chirality : 0.040 0.135 1675 Planarity : 0.003 0.041 1922 Dihedral : 3.986 33.529 1461 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.42 % Allowed : 8.51 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.97 (0.23), residues: 1333 helix: 1.52 (0.22), residues: 631 sheet: 0.18 (0.36), residues: 226 loop : -0.20 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.015 0.001 HIS C 230 PHE 0.023 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.004 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 501) hydrogen bonds : angle 4.21619 ( 1434) metal coordination : bond 0.00106 ( 1) covalent geometry : bond 0.00258 (10949) covalent geometry : angle 0.47887 (14838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 1.462 Fit side-chains REVERT: B 377 ILE cc_start: 0.8618 (pt) cc_final: 0.8380 (pt) REVERT: B 389 ARG cc_start: 0.8098 (mmp80) cc_final: 0.7555 (mmp-170) REVERT: C 131 ASP cc_start: 0.8831 (t70) cc_final: 0.8553 (t0) REVERT: C 281 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9084 (p) outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 1.7909 time to fit residues: 109.3197 Evaluate side-chains 49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 90 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.086167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.057392 restraints weight = 21784.453| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.07 r_work: 0.2735 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10950 Z= 0.163 Angle : 0.514 8.486 14838 Z= 0.266 Chirality : 0.041 0.139 1675 Planarity : 0.003 0.042 1922 Dihedral : 4.070 34.675 1461 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.58 % Allowed : 9.01 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.98 (0.23), residues: 1333 helix: 1.53 (0.22), residues: 631 sheet: 0.34 (0.37), residues: 216 loop : -0.27 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 350 HIS 0.005 0.001 HIS B 326 PHE 0.024 0.001 PHE A 538 TYR 0.011 0.001 TYR B 74 ARG 0.005 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 501) hydrogen bonds : angle 4.28591 ( 1434) metal coordination : bond 0.00191 ( 1) covalent geometry : bond 0.00389 (10949) covalent geometry : angle 0.51408 (14838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 1.375 Fit side-chains REVERT: C 131 ASP cc_start: 0.8850 (t70) cc_final: 0.8560 (t0) REVERT: C 281 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9158 (p) outliers start: 7 outliers final: 2 residues processed: 53 average time/residue: 1.4013 time to fit residues: 80.5555 Evaluate side-chains 49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 95 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.058763 restraints weight = 21976.220| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.02 r_work: 0.2754 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10950 Z= 0.118 Angle : 0.500 9.627 14838 Z= 0.256 Chirality : 0.040 0.139 1675 Planarity : 0.003 0.041 1922 Dihedral : 4.016 35.086 1461 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.58 % Allowed : 9.34 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 1.02 (0.24), residues: 1333 helix: 1.58 (0.22), residues: 631 sheet: 0.23 (0.37), residues: 226 loop : -0.22 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.004 0.001 HIS B 326 PHE 0.022 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 501) hydrogen bonds : angle 4.18748 ( 1434) metal coordination : bond 0.00116 ( 1) covalent geometry : bond 0.00277 (10949) covalent geometry : angle 0.50042 (14838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 1.234 Fit side-chains REVERT: A 323 MET cc_start: 0.9043 (mpp) cc_final: 0.8827 (mmt) REVERT: B 377 ILE cc_start: 0.8531 (pt) cc_final: 0.8323 (pt) REVERT: B 389 ARG cc_start: 0.8042 (mmp80) cc_final: 0.7328 (mmp-170) REVERT: C 131 ASP cc_start: 0.8853 (t70) cc_final: 0.8570 (t0) outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 1.4170 time to fit residues: 80.0405 Evaluate side-chains 49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.084509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055452 restraints weight = 21712.262| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.07 r_work: 0.2683 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10950 Z= 0.204 Angle : 0.549 11.355 14838 Z= 0.281 Chirality : 0.043 0.201 1675 Planarity : 0.004 0.043 1922 Dihedral : 4.192 40.345 1461 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.25 % Allowed : 9.67 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.92 (0.23), residues: 1333 helix: 1.50 (0.22), residues: 631 sheet: 0.43 (0.38), residues: 206 loop : -0.40 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 350 HIS 0.006 0.001 HIS B 326 PHE 0.025 0.001 PHE A 538 TYR 0.011 0.001 TYR B 74 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 501) hydrogen bonds : angle 4.38621 ( 1434) metal coordination : bond 0.00246 ( 1) covalent geometry : bond 0.00489 (10949) covalent geometry : angle 0.54898 (14838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 3.406 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.9194 (mpp) cc_final: 0.8962 (mmt) REVERT: C 131 ASP cc_start: 0.8791 (t70) cc_final: 0.8490 (t0) REVERT: D 628 ASP cc_start: 0.8654 (m-30) cc_final: 0.8368 (m-30) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 2.4303 time to fit residues: 134.6623 Evaluate side-chains 49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058121 restraints weight = 21915.244| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.07 r_work: 0.2770 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10950 Z= 0.123 Angle : 0.518 12.268 14838 Z= 0.263 Chirality : 0.041 0.240 1675 Planarity : 0.003 0.042 1922 Dihedral : 4.100 39.394 1461 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.50 % Allowed : 9.42 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 1.00 (0.23), residues: 1333 helix: 1.58 (0.22), residues: 629 sheet: 0.35 (0.37), residues: 216 loop : -0.32 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.004 0.001 HIS B 326 PHE 0.022 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 501) hydrogen bonds : angle 4.21186 ( 1434) metal coordination : bond 0.00132 ( 1) covalent geometry : bond 0.00288 (10949) covalent geometry : angle 0.51816 (14838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 2.667 Fit side-chains revert: symmetry clash REVERT: B 340 ASP cc_start: 0.8848 (m-30) cc_final: 0.8599 (OUTLIER) REVERT: C 131 ASP cc_start: 0.8856 (t70) cc_final: 0.8563 (t0) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 2.2490 time to fit residues: 134.8322 Evaluate side-chains 49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 128 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.084661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.055671 restraints weight = 21606.499| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.06 r_work: 0.2690 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10950 Z= 0.197 Angle : 0.565 12.950 14838 Z= 0.285 Chirality : 0.043 0.300 1675 Planarity : 0.004 0.043 1922 Dihedral : 4.234 43.287 1461 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.33 % Allowed : 9.67 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.90 (0.23), residues: 1333 helix: 1.48 (0.22), residues: 631 sheet: 0.43 (0.38), residues: 206 loop : -0.41 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 350 HIS 0.006 0.001 HIS B 326 PHE 0.025 0.001 PHE A 538 TYR 0.011 0.001 TYR B 74 ARG 0.004 0.000 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.03910 ( 501) hydrogen bonds : angle 4.36106 ( 1434) metal coordination : bond 0.00224 ( 1) covalent geometry : bond 0.00475 (10949) covalent geometry : angle 0.56472 (14838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 2.192 Fit side-chains revert: symmetry clash REVERT: B 41 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8450 (pm20) REVERT: C 131 ASP cc_start: 0.8805 (t70) cc_final: 0.8504 (t0) REVERT: D 624 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7937 (tm-30) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 1.7627 time to fit residues: 97.4870 Evaluate side-chains 51 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN C 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057538 restraints weight = 21570.206| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.08 r_work: 0.2736 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10950 Z= 0.103 Angle : 0.521 12.891 14838 Z= 0.261 Chirality : 0.040 0.136 1675 Planarity : 0.003 0.040 1922 Dihedral : 4.049 40.508 1461 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.25 % Allowed : 9.92 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.08 (0.24), residues: 1333 helix: 1.63 (0.22), residues: 629 sheet: 0.44 (0.37), residues: 223 loop : -0.29 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 203 HIS 0.003 0.001 HIS B 326 PHE 0.020 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.005 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 501) hydrogen bonds : angle 4.10754 ( 1434) metal coordination : bond 0.00124 ( 1) covalent geometry : bond 0.00238 (10949) covalent geometry : angle 0.52108 (14838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8070.95 seconds wall clock time: 144 minutes 27.98 seconds (8667.98 seconds total)