Starting phenix.real_space_refine on Thu Jul 2 09:17:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5n_61147/07_2026/9j5n_61147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5n_61147/07_2026/9j5n_61147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j5n_61147/07_2026/9j5n_61147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5n_61147/07_2026/9j5n_61147.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5n_61147/07_2026/9j5n_61147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5n_61147/07_2026/9j5n_61147.cif" } resolution = 4.3 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= 0.002 sd= 0.082 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: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 33 5.16 5 C 5017 2.51 5 N 1365 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7932 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2408 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 14, 'TRANS': 333} Chain breaks: 7 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 487 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'ASN:plan1': 6, 'TYR:plan': 5, 'GLN:plan1': 9, 'HIS:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 221 Chain: "A" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3512 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 25, 'TRANS': 486} Chain breaks: 4 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 425 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'PHE:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 14, 'GLU:plan': 16, 'ARG:plan': 17, 'TRP:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 8, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 321 Chain: "C" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2010 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 3, 'TRP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 1.64, per 1000 atoms: 0.21 Number of scatterers: 7932 At special positions: 0 Unit cell: (85.86, 109.18, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 33 16.00 O 1515 8.00 N 1365 7.00 C 5017 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 479.3 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 3 sheets defined 71.7% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 161 through 177 Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.608A pdb=" N PHE B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.651A pdb=" N GLY B 194 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP B 195 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 197 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 198 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 4.303A pdb=" N ALA B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 250 through 267 Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 292 through 308 removed outlier: 3.721A pdb=" N ASN B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 327 through 336 removed outlier: 3.569A pdb=" N ILE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 360 Processing helix chain 'B' and resid 362 through 370 removed outlier: 3.662A pdb=" N ALA B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 3.603A pdb=" N GLY B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 removed outlier: 3.635A pdb=" N LEU B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 417 through 431 removed outlier: 3.805A pdb=" N ILE B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.929A pdb=" N ALA B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 3.718A pdb=" N VAL B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 492 removed outlier: 3.723A pdb=" N THR B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.765A pdb=" N GLU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 542 Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.903A pdb=" N LEU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 88 through 98 removed outlier: 4.221A pdb=" N GLU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.677A pdb=" N ARG A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 4.054A pdb=" N HIS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 153 removed outlier: 3.951A pdb=" N GLY A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 172 removed outlier: 3.655A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 235 through 251 removed outlier: 3.588A pdb=" N GLN A 240 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 255 through 265 removed outlier: 4.383A pdb=" N ALA A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.953A pdb=" N THR A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 297 through 308 removed outlier: 4.315A pdb=" N ALA A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 Proline residue: A 322 - end of helix removed outlier: 3.504A pdb=" N SER A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 347 removed outlier: 4.261A pdb=" N SER A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 4.216A pdb=" N ILE A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Proline residue: A 361 - end of helix Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.588A pdb=" N LEU A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 407 Proline residue: A 400 - end of helix Processing helix chain 'A' and resid 412 through 419 removed outlier: 3.962A pdb=" N GLU A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.992A pdb=" N LEU A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.680A pdb=" N ASN A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 486 removed outlier: 3.532A pdb=" N HIS A 475 " --> pdb=" O TRP A 471 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 4.720A pdb=" N GLU A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.524A pdb=" N ARG A 492 " --> pdb=" O HIS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 removed outlier: 4.218A pdb=" N VAL A 518 " --> pdb=" O LYS A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 539 removed outlier: 3.521A pdb=" N GLN A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 Proline residue: A 556 - end of helix Processing helix chain 'A' and resid 566 through 580 Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 24 through 42 removed outlier: 3.596A pdb=" N LYS C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 removed outlier: 3.724A pdb=" N THR C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 119 Processing helix chain 'C' and resid 120 through 125 removed outlier: 3.900A pdb=" N GLN C 125 " --> pdb=" O ARG C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 153 removed outlier: 3.927A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 192 through 201 removed outlier: 3.815A pdb=" N CYS C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 3.608A pdb=" N ILE C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.281A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 210 through 211 477 hydrogen bonds defined for protein. 1413 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: 1.06 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: 1.21 - 1.33: 1737 1.33 - 1.45: 1632 1.45 - 1.57: 4641 1.57 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 8060 Sorted by residual: bond pdb=" C TYR A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.333 1.368 -0.035 1.44e-02 4.82e+03 5.83e+00 bond pdb=" CA ASN A 57 " pdb=" CB ASN A 57 " ideal model delta sigma weight residual 1.530 1.554 -0.023 1.69e-02 3.50e+03 1.91e+00 bond pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" C ILE A 421 " pdb=" N PRO A 422 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.41e+00 bond pdb=" C GLU A 275 " pdb=" N PRO A 276 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.38e+00 ... (remaining 8055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10636 1.79 - 3.57: 299 3.57 - 5.36: 69 5.36 - 7.14: 26 7.14 - 8.93: 11 Bond angle restraints: 11041 Sorted by residual: angle pdb=" N VAL A 549 " pdb=" CA VAL A 549 " pdb=" C VAL A 549 " ideal model delta sigma weight residual 113.47 105.10 8.37 1.01e+00 9.80e-01 6.86e+01 angle pdb=" C ASP A 175 " pdb=" CA ASP A 175 " pdb=" CB ASP A 175 " ideal model delta sigma weight residual 116.54 110.24 6.30 1.15e+00 7.56e-01 3.00e+01 angle pdb=" C ASN A 57 " pdb=" CA ASN A 57 " pdb=" CB ASN A 57 " ideal model delta sigma weight residual 110.42 118.64 -8.22 1.99e+00 2.53e-01 1.71e+01 angle pdb=" N LEU C 186 " pdb=" CA LEU C 186 " pdb=" C LEU C 186 " ideal model delta sigma weight residual 110.44 115.23 -4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" C GLN C 187 " pdb=" N GLU C 188 " pdb=" CA GLU C 188 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 ... (remaining 11036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4208 17.91 - 35.81: 480 35.81 - 53.72: 109 53.72 - 71.62: 20 71.62 - 89.53: 11 Dihedral angle restraints: 4828 sinusoidal: 1526 harmonic: 3302 Sorted by residual: dihedral pdb=" CA GLN C 187 " pdb=" C GLN C 187 " pdb=" N GLU C 188 " pdb=" CA GLU C 188 " ideal model delta harmonic sigma weight residual 180.00 134.64 45.36 0 5.00e+00 4.00e-02 8.23e+01 dihedral pdb=" CA VAL A 223 " pdb=" C VAL A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PRO A 177 " pdb=" C PRO A 177 " pdb=" N MET A 178 " pdb=" CA MET A 178 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 4825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 864 0.032 - 0.065: 345 0.065 - 0.097: 113 0.097 - 0.130: 35 0.130 - 0.162: 9 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CB ILE A 421 " pdb=" CA ILE A 421 " pdb=" CG1 ILE A 421 " pdb=" CG2 ILE A 421 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ILE C 275 " pdb=" N ILE C 275 " pdb=" C ILE C 275 " pdb=" CB ILE C 275 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA PRO B 339 " pdb=" N PRO B 339 " pdb=" C PRO B 339 " pdb=" CB PRO B 339 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 1363 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 223 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C VAL A 223 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL A 223 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 224 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 527 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 528 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 528 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 528 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 555 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 556 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 556 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 556 " 0.027 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 138 2.65 - 3.21: 8171 3.21 - 3.77: 13048 3.77 - 4.34: 16031 4.34 - 4.90: 25470 Nonbonded interactions: 62858 Sorted by model distance: nonbonded pdb=" OD1 ASN A 57 " pdb=" N ASP A 58 " model vdw 2.084 3.120 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 2.148 3.060 nonbonded pdb=" O LYS C 36 " pdb=" OG1 THR C 40 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP A 392 " pdb=" N LEU A 393 " model vdw 2.196 3.120 nonbonded pdb=" O MET A 159 " pdb=" OG1 THR A 162 " model vdw 2.198 3.040 ... (remaining 62853 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 group one per residue 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: 2.040 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.960 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4611 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 8060 Z= 0.160 Angle : 0.803 8.929 11041 Z= 0.438 Chirality : 0.041 0.162 1366 Planarity : 0.005 0.050 1435 Dihedral : 16.932 89.528 2660 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.68 % Favored : 90.05 % Rotamer: Outliers : 5.24 % Allowed : 31.59 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.55 (0.26), residues: 1095 helix: -0.05 (0.20), residues: 708 sheet: -3.56 (0.72), residues: 46 loop : -2.65 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 118 TYR 0.015 0.001 TYR A 168 PHE 0.029 0.002 PHE C 260 TRP 0.026 0.002 TRP A 411 HIS 0.006 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 ( 8060) covalent geometry : angle 0.80294 / 0.44 (11041) hydrogen bonds : bond 0.14938 / 9.95 ( 477) hydrogen bonds : angle 6.84675 / 4.93 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 368 THR cc_start: 0.4309 (p) cc_final: 0.3972 (p) REVERT: B 515 MET cc_start: 0.1772 (mmt) cc_final: 0.1395 (tpt) REVERT: A 204 MET cc_start: 0.4663 (ttt) cc_final: 0.3209 (tpt) REVERT: A 350 LEU cc_start: 0.3623 (OUTLIER) cc_final: 0.2864 (tt) REVERT: A 405 LEU cc_start: 0.4024 (OUTLIER) cc_final: 0.3517 (mt) REVERT: A 432 PHE cc_start: 0.3821 (OUTLIER) cc_final: 0.3506 (p90) REVERT: A 520 MET cc_start: 0.3378 (pp-130) cc_final: 0.2832 (tmm) REVERT: C 33 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5664 (mm-30) REVERT: C 113 ILE cc_start: 0.6433 (mt) cc_final: 0.6133 (mt) REVERT: C 121 ARG cc_start: 0.3122 (OUTLIER) cc_final: 0.1797 (tmm160) outliers start: 38 outliers final: 26 residues processed: 116 average time/residue: 0.0672 time to fit residues: 11.2804 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN A 236 GLN A 292 ASN A 319 HIS ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.181972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.165800 restraints weight = 16307.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.167299 restraints weight = 11928.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.168308 restraints weight = 9314.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.169027 restraints weight = 7719.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.169178 restraints weight = 6721.291| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8060 Z= 0.189 Angle : 0.770 8.934 11041 Z= 0.401 Chirality : 0.046 0.251 1366 Planarity : 0.006 0.065 1435 Dihedral : 5.864 42.565 1163 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.86 % Favored : 90.96 % Rotamer: Outliers : 0.41 % Allowed : 6.34 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.71 (0.25), residues: 1095 helix: -0.11 (0.20), residues: 723 sheet: -4.07 (0.69), residues: 44 loop : -2.93 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 49 TYR 0.014 0.002 TYR C 265 PHE 0.016 0.002 PHE B 395 TRP 0.026 0.002 TRP B 265 HIS 0.014 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 8060) covalent geometry : angle 0.76955 / 0.40 (11041) hydrogen bonds : bond 0.04739 / 3.22 ( 477) hydrogen bonds : angle 5.59983 / 3.99 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 116 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6718 (t0) cc_final: 0.5964 (t0) REVERT: A 204 MET cc_start: 0.5136 (ttp) cc_final: 0.3600 (tpt) REVERT: A 350 LEU cc_start: 0.4781 (pt) cc_final: 0.3690 (tt) REVERT: A 520 MET cc_start: 0.4376 (ppp) cc_final: 0.4070 (tmm) REVERT: A 551 GLU cc_start: 0.5469 (pm20) cc_final: 0.5081 (mm-30) REVERT: A 579 SER cc_start: 0.7576 (m) cc_final: 0.6970 (t) REVERT: C 12 GLN cc_start: 0.6709 (tm-30) cc_final: 0.6078 (mt0) outliers start: 3 outliers final: 0 residues processed: 119 average time/residue: 0.0677 time to fit residues: 11.9353 Evaluate side-chains 84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.182895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.166597 restraints weight = 16162.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.168112 restraints weight = 11786.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.168911 restraints weight = 9090.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.169893 restraints weight = 7652.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.170510 restraints weight = 6582.385| |-----------------------------------------------------------------------------| r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4920 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8060 Z= 0.151 Angle : 0.695 8.633 11041 Z= 0.361 Chirality : 0.043 0.197 1366 Planarity : 0.005 0.063 1435 Dihedral : 5.645 39.825 1163 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.86 % Favored : 89.95 % Rotamer: Outliers : 0.28 % Allowed : 4.14 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.53 (0.26), residues: 1095 helix: -0.00 (0.20), residues: 721 sheet: -5.10 (0.69), residues: 29 loop : -2.75 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 256 TYR 0.012 0.001 TYR C 265 PHE 0.012 0.002 PHE B 395 TRP 0.020 0.002 TRP A 444 HIS 0.010 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 8060) covalent geometry : angle 0.69456 / 0.36 (11041) hydrogen bonds : bond 0.04359 / 2.94 ( 477) hydrogen bonds : angle 5.40099 / 3.85 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5074 (ttp) cc_final: 0.3577 (tpt) REVERT: A 350 LEU cc_start: 0.4522 (pt) cc_final: 0.3445 (tt) REVERT: A 520 MET cc_start: 0.4291 (ppp) cc_final: 0.4022 (tmm) REVERT: A 551 GLU cc_start: 0.5278 (pm20) cc_final: 0.5036 (mm-30) REVERT: C 12 GLN cc_start: 0.6675 (tm-30) cc_final: 0.6215 (mt0) outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.0631 time to fit residues: 10.1945 Evaluate side-chains 88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 459 ASN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.183372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.166898 restraints weight = 16604.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.168655 restraints weight = 13061.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.169254 restraints weight = 10065.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.169903 restraints weight = 8577.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.170481 restraints weight = 7279.136| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4916 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8060 Z= 0.139 Angle : 0.671 8.628 11041 Z= 0.347 Chirality : 0.043 0.201 1366 Planarity : 0.005 0.051 1435 Dihedral : 5.515 39.517 1163 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.86 % Favored : 89.95 % Rotamer: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.32 (0.26), residues: 1095 helix: 0.18 (0.20), residues: 712 sheet: -4.33 (0.73), residues: 39 loop : -2.64 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 256 TYR 0.013 0.001 TYR C 265 PHE 0.016 0.002 PHE A 149 TRP 0.013 0.002 TRP A 411 HIS 0.008 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 8060) covalent geometry : angle 0.67061 / 0.35 (11041) hydrogen bonds : bond 0.04151 / 2.79 ( 477) hydrogen bonds : angle 5.20830 / 3.71 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.5853 (t0) cc_final: 0.5648 (t0) REVERT: A 204 MET cc_start: 0.5213 (ttp) cc_final: 0.3673 (tpt) REVERT: A 350 LEU cc_start: 0.4933 (pt) cc_final: 0.3767 (tt) REVERT: A 551 GLU cc_start: 0.5306 (pm20) cc_final: 0.4974 (mm-30) REVERT: A 579 SER cc_start: 0.7537 (m) cc_final: 0.6926 (t) REVERT: C 12 GLN cc_start: 0.6889 (tm-30) cc_final: 0.6258 (mt0) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.0651 time to fit residues: 10.5285 Evaluate side-chains 85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 53 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS A 319 HIS A 443 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.178893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.168987 restraints weight = 158298.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.171155 restraints weight = 107287.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.171251 restraints weight = 87087.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.171361 restraints weight = 86404.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.171414 restraints weight = 80602.274| |-----------------------------------------------------------------------------| r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4932 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8060 Z= 0.149 Angle : 0.700 8.383 11041 Z= 0.362 Chirality : 0.043 0.196 1366 Planarity : 0.005 0.064 1435 Dihedral : 5.585 39.074 1163 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.86 % Favored : 89.95 % Rotamer: Outliers : 0.28 % Allowed : 3.59 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.30 (0.26), residues: 1095 helix: 0.17 (0.20), residues: 712 sheet: -4.47 (0.68), residues: 39 loop : -2.55 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 49 TYR 0.014 0.001 TYR A 83 PHE 0.013 0.002 PHE B 484 TRP 0.014 0.002 TRP A 444 HIS 0.008 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 8060) covalent geometry : angle 0.69980 / 0.36 (11041) hydrogen bonds : bond 0.04133 / 2.80 ( 477) hydrogen bonds : angle 5.24773 / 3.72 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5209 (ttp) cc_final: 0.3822 (tpt) REVERT: A 223 VAL cc_start: 0.5174 (OUTLIER) cc_final: 0.4918 (m) REVERT: A 350 LEU cc_start: 0.4172 (pt) cc_final: 0.3260 (tt) REVERT: A 551 GLU cc_start: 0.5423 (pm20) cc_final: 0.5164 (mm-30) REVERT: A 575 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: A 579 SER cc_start: 0.7194 (m) cc_final: 0.6136 (t) REVERT: C 12 GLN cc_start: 0.7099 (tm-30) cc_final: 0.6518 (mt0) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.0649 time to fit residues: 10.0273 Evaluate side-chains 80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 72 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.182283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.165793 restraints weight = 16178.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.167321 restraints weight = 12032.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.168259 restraints weight = 9411.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.168803 restraints weight = 7847.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.169607 restraints weight = 6933.945| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4939 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8060 Z= 0.141 Angle : 0.683 8.621 11041 Z= 0.351 Chirality : 0.043 0.203 1366 Planarity : 0.005 0.053 1435 Dihedral : 5.510 39.045 1163 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.86 % Favored : 90.05 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.35 (0.26), residues: 1095 helix: 0.13 (0.20), residues: 723 sheet: -4.29 (0.70), residues: 39 loop : -2.66 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 49 TYR 0.014 0.001 TYR C 265 PHE 0.014 0.002 PHE A 149 TRP 0.011 0.001 TRP A 444 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8060) covalent geometry : angle 0.68333 / 0.35 (11041) hydrogen bonds : bond 0.03885 / 2.64 ( 477) hydrogen bonds : angle 5.14011 / 3.67 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6167 (t0) cc_final: 0.5918 (t0) REVERT: A 204 MET cc_start: 0.5225 (ttp) cc_final: 0.3699 (tpt) REVERT: A 350 LEU cc_start: 0.4941 (pt) cc_final: 0.3853 (tt) REVERT: A 579 SER cc_start: 0.7470 (m) cc_final: 0.6545 (t) REVERT: C 12 GLN cc_start: 0.6768 (tm-30) cc_final: 0.6268 (mt0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0638 time to fit residues: 9.3485 Evaluate side-chains 78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN A 446 GLN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.169942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.160851 restraints weight = 174508.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.162936 restraints weight = 114433.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.162520 restraints weight = 92510.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.162702 restraints weight = 93214.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.162753 restraints weight = 87195.128| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5224 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8060 Z= 0.270 Angle : 0.885 12.507 11041 Z= 0.470 Chirality : 0.050 0.230 1366 Planarity : 0.007 0.093 1435 Dihedral : 6.681 37.898 1163 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.32 % Favored : 88.40 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.12 (0.25), residues: 1095 helix: -0.47 (0.19), residues: 710 sheet: -4.76 (0.61), residues: 41 loop : -2.82 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 49 TYR 0.020 0.002 TYR B 232 PHE 0.022 0.003 PHE B 484 TRP 0.044 0.004 TRP A 444 HIS 0.016 0.002 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.27 ( 8060) covalent geometry : angle 0.88547 / 0.47 (11041) hydrogen bonds : bond 0.05453 / 3.82 ( 477) hydrogen bonds : angle 5.88172 / 4.20 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5601 (ttp) cc_final: 0.4093 (tpt) REVERT: A 350 LEU cc_start: 0.4447 (pt) cc_final: 0.3815 (tt) REVERT: A 579 SER cc_start: 0.7059 (m) cc_final: 0.6394 (t) REVERT: C 12 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6530 (mt0) REVERT: C 113 ILE cc_start: 0.7210 (mt) cc_final: 0.6938 (mt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0640 time to fit residues: 9.6331 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.0010 chunk 83 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.0060 chunk 39 optimal weight: 7.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 497 GLN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN A 450 HIS A 459 ASN ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.177465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.167441 restraints weight = 171877.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.169981 restraints weight = 112832.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.169629 restraints weight = 99642.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.169793 restraints weight = 95417.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.169988 restraints weight = 85226.675| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5025 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8060 Z= 0.144 Angle : 0.727 8.796 11041 Z= 0.372 Chirality : 0.043 0.209 1366 Planarity : 0.005 0.055 1435 Dihedral : 5.793 39.505 1163 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.68 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.57 (0.26), residues: 1095 helix: -0.05 (0.20), residues: 724 sheet: -4.31 (0.69), residues: 41 loop : -2.71 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 497 TYR 0.016 0.001 TYR C 265 PHE 0.020 0.002 PHE B 446 TRP 0.018 0.002 TRP A 444 HIS 0.008 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8060) covalent geometry : angle 0.72690 / 0.37 (11041) hydrogen bonds : bond 0.04066 / 2.76 ( 477) hydrogen bonds : angle 5.35438 / 3.84 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5519 (ttp) cc_final: 0.4023 (tpt) REVERT: A 350 LEU cc_start: 0.4287 (pt) cc_final: 0.3769 (tt) REVERT: A 579 SER cc_start: 0.7184 (m) cc_final: 0.6137 (t) REVERT: C 12 GLN cc_start: 0.7020 (tm-30) cc_final: 0.6473 (mt0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0660 time to fit residues: 10.2837 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.174853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.167171 restraints weight = 174215.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.168741 restraints weight = 112897.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.168712 restraints weight = 88979.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.168810 restraints weight = 91532.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.168849 restraints weight = 85687.776| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4980 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8060 Z= 0.162 Angle : 0.745 8.010 11041 Z= 0.385 Chirality : 0.045 0.225 1366 Planarity : 0.005 0.056 1435 Dihedral : 5.835 43.737 1163 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.32 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.49 (0.26), residues: 1095 helix: -0.02 (0.20), residues: 721 sheet: -4.41 (0.66), residues: 41 loop : -2.58 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 49 TYR 0.014 0.001 TYR B 232 PHE 0.017 0.002 PHE B 446 TRP 0.022 0.002 TRP C 13 HIS 0.010 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8060) covalent geometry : angle 0.74478 / 0.38 (11041) hydrogen bonds : bond 0.04245 / 2.89 ( 477) hydrogen bonds : angle 5.33322 / 3.83 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 MET cc_start: 0.6446 (mmm) cc_final: 0.5903 (mmm) REVERT: A 204 MET cc_start: 0.5415 (ttp) cc_final: 0.3988 (tpt) REVERT: A 350 LEU cc_start: 0.4192 (pt) cc_final: 0.3635 (tt) REVERT: A 579 SER cc_start: 0.7088 (m) cc_final: 0.6270 (t) REVERT: C 12 GLN cc_start: 0.7030 (tm-30) cc_final: 0.6375 (mt0) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0580 time to fit residues: 8.6734 Evaluate side-chains 80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 chunk 24 optimal weight: 0.1980 chunk 80 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 486 ASN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.179630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.163697 restraints weight = 16613.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.164875 restraints weight = 12493.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.166000 restraints weight = 9958.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.166783 restraints weight = 8310.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.167071 restraints weight = 7234.421| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4969 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8060 Z= 0.136 Angle : 0.706 8.658 11041 Z= 0.361 Chirality : 0.043 0.189 1366 Planarity : 0.005 0.048 1435 Dihedral : 5.497 43.168 1163 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.59 % Favored : 90.32 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.23 (0.26), residues: 1095 helix: 0.16 (0.20), residues: 726 sheet: -4.36 (0.78), residues: 36 loop : -2.50 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 497 TYR 0.014 0.001 TYR C 86 PHE 0.020 0.002 PHE B 446 TRP 0.020 0.002 TRP C 13 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 8060) covalent geometry : angle 0.70604 / 0.36 (11041) hydrogen bonds : bond 0.03778 / 2.56 ( 477) hydrogen bonds : angle 5.13196 / 3.68 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5516 (ttp) cc_final: 0.3902 (tpt) REVERT: A 350 LEU cc_start: 0.5307 (pt) cc_final: 0.4459 (tt) REVERT: A 560 GLU cc_start: 0.6363 (pt0) cc_final: 0.6111 (pt0) REVERT: A 579 SER cc_start: 0.7314 (m) cc_final: 0.6372 (t) REVERT: C 12 GLN cc_start: 0.6599 (tm-30) cc_final: 0.6217 (mt0) REVERT: C 113 ILE cc_start: 0.6342 (mt) cc_final: 0.6085 (mt) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.0693 time to fit residues: 10.8776 Evaluate side-chains 78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 24 optimal weight: 0.0980 chunk 99 optimal weight: 0.3980 chunk 105 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.179193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.179030 restraints weight = 17142.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.178218 restraints weight = 19808.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.178121 restraints weight = 25588.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.178051 restraints weight = 22844.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.177954 restraints weight = 22866.808| |-----------------------------------------------------------------------------| r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4673 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8060 Z= 0.142 Angle : 0.724 10.230 11041 Z= 0.373 Chirality : 0.043 0.188 1366 Planarity : 0.005 0.048 1435 Dihedral : 5.425 43.359 1163 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.50 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.22 (0.26), residues: 1095 helix: 0.15 (0.20), residues: 726 sheet: -4.26 (0.72), residues: 41 loop : -2.41 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 172 TYR 0.011 0.001 TYR B 232 PHE 0.018 0.002 PHE B 446 TRP 0.022 0.002 TRP C 13 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8060) covalent geometry : angle 0.72437 / 0.37 (11041) hydrogen bonds : bond 0.03898 / 2.64 ( 477) hydrogen bonds : angle 5.17638 / 3.73 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1243.71 seconds wall clock time: 22 minutes 6.74 seconds (1326.74 seconds total)