Starting phenix.real_space_refine on Tue Mar 11 19:00:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hg0_34730/03_2025/8hg0_34730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg0_34730/03_2025/8hg0_34730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hg0_34730/03_2025/8hg0_34730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg0_34730/03_2025/8hg0_34730.map" model { file = "/net/cci-nas-00/data/ceres_data/8hg0_34730/03_2025/8hg0_34730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg0_34730/03_2025/8hg0_34730.cif" } resolution = 3.51 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= -0.003 sd= 0.017 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 Zn 1 6.06 5 S 38 5.16 5 C 4132 2.51 5 N 1064 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6470 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4884 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.20, per 1000 atoms: 0.80 Number of scatterers: 6470 At special positions: 0 Unit cell: (77.35, 90.95, 119.85, 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) Zn 1 29.99 S 38 16.00 O 1235 8.00 N 1064 7.00 C 4132 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 299 " " NAG A 702 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 931.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 374 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 55.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.625A pdb=" N THR A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.524A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.560A pdb=" N LEU A 101 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.825A pdb=" N ARG A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.526A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.550A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.649A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.253A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 252 removed outlier: 4.256A pdb=" N GLU A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.596A pdb=" N TYR A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.671A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 299 through 302 removed outlier: 4.144A pdb=" N TRP A 302 " --> pdb=" O ASN A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.786A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.835A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.580A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 removed outlier: 3.629A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.610A pdb=" N LEU A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.851A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.244A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.533A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.336A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.625A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.917A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 600 Proline residue: A 590 - end of helix removed outlier: 3.811A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.210A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.511A pdb=" N LEU A 142 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.694A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.450A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.606A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.818A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 264 hydrogen bonds defined for protein. 759 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: 1.54 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2068 1.35 - 1.46: 1734 1.46 - 1.58: 2786 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6648 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" CA LEU B 518 " pdb=" CB LEU B 518 " ideal model delta sigma weight residual 1.535 1.519 0.016 1.32e-02 5.74e+03 1.49e+00 bond pdb=" CG LYS B 417 " pdb=" CD LYS B 417 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C LYS A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.334 1.352 -0.018 1.51e-02 4.39e+03 1.40e+00 ... (remaining 6643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8851 1.87 - 3.75: 140 3.75 - 5.62: 23 5.62 - 7.49: 3 7.49 - 9.37: 3 Bond angle restraints: 9020 Sorted by residual: angle pdb=" CB LYS B 417 " pdb=" CG LYS B 417 " pdb=" CD LYS B 417 " ideal model delta sigma weight residual 111.30 120.67 -9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 112.83 108.82 4.01 9.90e-01 1.02e+00 1.64e+01 angle pdb=" N SER A 104 " pdb=" CA SER A 104 " pdb=" C SER A 104 " ideal model delta sigma weight residual 112.13 108.27 3.86 1.37e+00 5.33e-01 7.94e+00 angle pdb=" N SER B 375 " pdb=" CA SER B 375 " pdb=" C SER B 375 " ideal model delta sigma weight residual 114.56 111.11 3.45 1.27e+00 6.20e-01 7.36e+00 angle pdb=" CB MET A 455 " pdb=" CG MET A 455 " pdb=" SD MET A 455 " ideal model delta sigma weight residual 112.70 120.76 -8.06 3.00e+00 1.11e-01 7.21e+00 ... (remaining 9015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 3494 20.96 - 41.92: 399 41.92 - 62.88: 71 62.88 - 83.84: 4 83.84 - 104.80: 9 Dihedral angle restraints: 3977 sinusoidal: 1650 harmonic: 2327 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -143.61 57.61 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -128.35 42.35 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" C2 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" C4 NAG A 701 " pdb=" O4 NAG A 701 " ideal model delta sinusoidal sigma weight residual 175.11 70.31 104.80 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 3974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 681 0.036 - 0.072: 191 0.072 - 0.107: 63 0.107 - 0.143: 9 0.143 - 0.179: 1 Chirality restraints: 945 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ILE A 468 " pdb=" N ILE A 468 " pdb=" C ILE A 468 " pdb=" CB ILE A 468 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 942 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO A 258 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO A 146 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 235 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.027 5.00e-02 4.00e+02 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 96 2.66 - 3.22: 6013 3.22 - 3.78: 9451 3.78 - 4.34: 13113 4.34 - 4.90: 21292 Nonbonded interactions: 49965 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 703 " model vdw 2.098 2.230 nonbonded pdb=" O THR A 123 " pdb=" OG1 THR A 126 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP B 467 " pdb=" OG SER B 469 " model vdw 2.270 3.040 nonbonded pdb=" O THR A 119 " pdb=" OG1 THR A 123 " model vdw 2.300 3.040 nonbonded pdb=" O THR A 126 " pdb=" OG1 THR A 130 " model vdw 2.302 3.040 ... (remaining 49960 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: 3.660 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.400 Find NCS groups from input model: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 0.054 6648 Z= 0.200 Angle : 0.612 9.367 9020 Z= 0.346 Chirality : 0.038 0.179 945 Planarity : 0.005 0.062 1160 Dihedral : 17.579 104.802 2467 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 1.15 % Allowed : 26.19 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.06 (0.30), residues: 786 helix: 0.27 (0.28), residues: 334 sheet: 1.49 (0.84), residues: 49 loop : -0.24 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 610 HIS 0.003 0.001 HIS A 241 PHE 0.019 0.001 PHE A 428 TYR 0.015 0.001 TYR A 429 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 498 CYS cc_start: 0.7594 (t) cc_final: 0.7364 (p) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.1945 time to fit residues: 16.0173 Evaluate side-chains 50 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 52 ASN A 97 GLN A 103 GLN A 118 ASN A 122 ASN A 194 ASN A 239 GLN A 374 HIS A 493 HIS A 522 GLN A 599 ASN B 409 GLN B 498 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.030772 restraints weight = 38341.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031888 restraints weight = 21655.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032662 restraints weight = 14907.940| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6648 Z= 0.189 Angle : 0.577 7.843 9020 Z= 0.298 Chirality : 0.041 0.188 945 Planarity : 0.005 0.059 1160 Dihedral : 7.258 60.524 938 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 3.45 % Allowed : 23.02 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.58 (0.31), residues: 786 helix: 0.91 (0.27), residues: 376 sheet: 1.20 (0.80), residues: 49 loop : -0.19 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 610 HIS 0.005 0.000 HIS A 241 PHE 0.010 0.001 PHE A 438 TYR 0.018 0.001 TYR A 429 ARG 0.007 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.9400 (mmm) cc_final: 0.9191 (mmm) REVERT: A 233 ILE cc_start: 0.9871 (OUTLIER) cc_final: 0.9662 (mm) REVERT: A 249 MET cc_start: 0.9351 (mmm) cc_final: 0.9063 (mmm) REVERT: A 297 MET cc_start: 0.9233 (mtt) cc_final: 0.9020 (ttm) REVERT: A 347 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.8936 (p) REVERT: A 366 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8713 (mtp) REVERT: A 401 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8652 (t-90) REVERT: A 429 TYR cc_start: 0.8584 (t80) cc_final: 0.8315 (t80) REVERT: A 462 MET cc_start: 0.9553 (mmm) cc_final: 0.8969 (tpp) REVERT: A 498 CYS cc_start: 0.8555 (t) cc_final: 0.6964 (p) REVERT: B 406 GLU cc_start: 0.9021 (tp30) cc_final: 0.8740 (tp30) outliers start: 24 outliers final: 5 residues processed: 66 average time/residue: 0.4365 time to fit residues: 38.4311 Evaluate side-chains 51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS A 552 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.040537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.030932 restraints weight = 37506.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.032023 restraints weight = 21279.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.032761 restraints weight = 14742.359| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6648 Z= 0.163 Angle : 0.520 7.973 9020 Z= 0.266 Chirality : 0.040 0.183 945 Planarity : 0.004 0.060 1160 Dihedral : 4.536 25.635 933 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 2.73 % Allowed : 21.87 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.76 (0.31), residues: 786 helix: 1.23 (0.28), residues: 372 sheet: 1.24 (0.79), residues: 49 loop : -0.29 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.004 0.000 HIS A 241 PHE 0.008 0.001 PHE A 369 TYR 0.011 0.001 TYR A 429 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7770 (p) REVERT: A 80 MET cc_start: 0.9511 (mtp) cc_final: 0.9260 (ttt) REVERT: A 124 MET cc_start: 0.9382 (mmm) cc_final: 0.9136 (mmm) REVERT: A 366 MET cc_start: 0.8865 (tpp) cc_final: 0.8638 (mtt) REVERT: A 429 TYR cc_start: 0.8635 (t80) cc_final: 0.8338 (t80) REVERT: A 462 MET cc_start: 0.9602 (mmm) cc_final: 0.8945 (tpp) REVERT: B 406 GLU cc_start: 0.9118 (tp30) cc_final: 0.8495 (tp30) REVERT: B 417 LYS cc_start: 0.9032 (tppt) cc_final: 0.8800 (tppt) outliers start: 19 outliers final: 8 residues processed: 60 average time/residue: 0.2014 time to fit residues: 16.6409 Evaluate side-chains 52 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 611 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS A 522 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.038371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.028692 restraints weight = 40453.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.029717 restraints weight = 22984.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.030422 restraints weight = 15908.304| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6648 Z= 0.316 Angle : 0.585 8.132 9020 Z= 0.303 Chirality : 0.042 0.184 945 Planarity : 0.004 0.060 1160 Dihedral : 4.516 22.236 932 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 3.74 % Allowed : 22.73 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.87 (0.31), residues: 786 helix: 1.33 (0.28), residues: 371 sheet: 1.01 (0.76), residues: 49 loop : -0.21 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 606 HIS 0.003 0.001 HIS A 378 PHE 0.014 0.001 PHE A 523 TYR 0.011 0.001 TYR A 381 ARG 0.004 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 42 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.9394 (mmm) cc_final: 0.9145 (mmm) REVERT: A 347 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8733 (p) REVERT: A 367 ASP cc_start: 0.9169 (OUTLIER) cc_final: 0.8900 (p0) REVERT: A 462 MET cc_start: 0.9615 (mmm) cc_final: 0.9018 (tpp) REVERT: B 340 GLU cc_start: 0.9002 (tp30) cc_final: 0.8797 (tp30) REVERT: B 406 GLU cc_start: 0.9140 (tp30) cc_final: 0.8594 (mm-30) outliers start: 26 outliers final: 14 residues processed: 64 average time/residue: 0.1898 time to fit residues: 16.9223 Evaluate side-chains 55 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 24 optimal weight: 0.0770 chunk 45 optimal weight: 0.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.039965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030465 restraints weight = 38749.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031520 restraints weight = 21609.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032254 restraints weight = 14877.753| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6648 Z= 0.140 Angle : 0.510 8.572 9020 Z= 0.257 Chirality : 0.040 0.189 945 Planarity : 0.004 0.060 1160 Dihedral : 3.979 15.891 931 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 2.88 % Allowed : 24.03 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.95 (0.31), residues: 786 helix: 1.51 (0.28), residues: 367 sheet: 0.92 (0.75), residues: 49 loop : -0.25 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 PHE 0.009 0.001 PHE A 438 TYR 0.006 0.001 TYR A 252 ARG 0.005 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7695 (p) REVERT: A 124 MET cc_start: 0.9404 (mmm) cc_final: 0.9150 (mmm) REVERT: A 249 MET cc_start: 0.9244 (mmm) cc_final: 0.9007 (mmp) REVERT: A 347 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 462 MET cc_start: 0.9610 (mmm) cc_final: 0.9031 (tpp) REVERT: B 346 ARG cc_start: 0.8423 (ptm-80) cc_final: 0.8096 (ptm-80) REVERT: B 406 GLU cc_start: 0.9079 (tp30) cc_final: 0.8863 (tp30) outliers start: 20 outliers final: 10 residues processed: 56 average time/residue: 0.1951 time to fit residues: 15.0126 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.038890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.029320 restraints weight = 39473.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030334 restraints weight = 22230.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.031039 restraints weight = 15461.762| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6648 Z= 0.224 Angle : 0.539 8.761 9020 Z= 0.272 Chirality : 0.040 0.188 945 Planarity : 0.004 0.060 1160 Dihedral : 4.061 19.775 931 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 3.31 % Allowed : 24.75 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.07 (0.31), residues: 786 helix: 1.63 (0.28), residues: 367 sheet: 0.90 (0.74), residues: 49 loop : -0.19 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS A 378 PHE 0.012 0.001 PHE A 523 TYR 0.008 0.001 TYR A 381 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 124 MET cc_start: 0.9404 (mmm) cc_final: 0.9125 (mmm) REVERT: A 249 MET cc_start: 0.9268 (mmm) cc_final: 0.9044 (mmm) REVERT: A 347 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8814 (p) REVERT: A 366 MET cc_start: 0.8987 (ttm) cc_final: 0.8687 (mtt) REVERT: A 462 MET cc_start: 0.9634 (mmm) cc_final: 0.9079 (tpp) REVERT: A 474 MET cc_start: 0.9174 (mmt) cc_final: 0.8789 (mpp) REVERT: B 406 GLU cc_start: 0.9092 (tp30) cc_final: 0.8603 (mm-30) outliers start: 23 outliers final: 16 residues processed: 59 average time/residue: 0.1945 time to fit residues: 15.8334 Evaluate side-chains 59 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.039270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.029704 restraints weight = 39369.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.030743 restraints weight = 22252.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031467 restraints weight = 15412.115| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6648 Z= 0.180 Angle : 0.533 9.088 9020 Z= 0.266 Chirality : 0.040 0.190 945 Planarity : 0.004 0.059 1160 Dihedral : 3.967 18.487 931 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % Rotamer: Outliers : 3.45 % Allowed : 24.46 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.31), residues: 786 helix: 1.63 (0.28), residues: 367 sheet: 0.84 (0.74), residues: 49 loop : -0.19 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.002 0.001 HIS A 378 PHE 0.009 0.001 PHE A 523 TYR 0.006 0.001 TYR A 381 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7677 (p) REVERT: A 124 MET cc_start: 0.9395 (mmm) cc_final: 0.9119 (mmm) REVERT: A 249 MET cc_start: 0.9290 (mmm) cc_final: 0.9057 (mmm) REVERT: A 347 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8821 (p) REVERT: A 366 MET cc_start: 0.8977 (ttm) cc_final: 0.8673 (mtt) REVERT: A 462 MET cc_start: 0.9632 (mmm) cc_final: 0.9088 (tpp) REVERT: A 474 MET cc_start: 0.9157 (mmt) cc_final: 0.8785 (mpp) outliers start: 24 outliers final: 17 residues processed: 58 average time/residue: 0.1903 time to fit residues: 15.2929 Evaluate side-chains 60 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029611 restraints weight = 38995.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.030652 restraints weight = 22551.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031376 restraints weight = 15552.357| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6648 Z= 0.173 Angle : 0.535 9.442 9020 Z= 0.267 Chirality : 0.040 0.190 945 Planarity : 0.004 0.059 1160 Dihedral : 3.919 18.166 931 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 3.31 % Allowed : 24.75 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.11 (0.31), residues: 786 helix: 1.66 (0.28), residues: 367 sheet: 0.87 (0.74), residues: 49 loop : -0.17 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.002 0.000 HIS A 378 PHE 0.008 0.001 PHE A 438 TYR 0.009 0.001 TYR A 51 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7626 (p) REVERT: A 124 MET cc_start: 0.9402 (mmm) cc_final: 0.9178 (mmm) REVERT: A 162 LEU cc_start: 0.9737 (tp) cc_final: 0.9466 (pp) REVERT: A 249 MET cc_start: 0.9280 (mmm) cc_final: 0.9051 (mmm) REVERT: A 347 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8834 (p) REVERT: A 366 MET cc_start: 0.8973 (ttm) cc_final: 0.8702 (mtt) REVERT: A 462 MET cc_start: 0.9635 (mmm) cc_final: 0.9084 (mmm) REVERT: A 474 MET cc_start: 0.9179 (mmt) cc_final: 0.8789 (mpp) REVERT: B 406 GLU cc_start: 0.8935 (tp30) cc_final: 0.8676 (tp30) outliers start: 23 outliers final: 17 residues processed: 58 average time/residue: 0.1934 time to fit residues: 15.5633 Evaluate side-chains 60 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.029543 restraints weight = 39856.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.030591 restraints weight = 22504.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.031314 restraints weight = 15634.286| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6648 Z= 0.179 Angle : 0.531 9.568 9020 Z= 0.265 Chirality : 0.040 0.191 945 Planarity : 0.004 0.059 1160 Dihedral : 3.864 18.479 931 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % Rotamer: Outliers : 3.45 % Allowed : 24.17 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.31), residues: 786 helix: 1.64 (0.28), residues: 372 sheet: 0.90 (0.74), residues: 49 loop : -0.17 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.000 HIS A 378 PHE 0.008 0.001 PHE A 523 TYR 0.009 0.001 TYR A 51 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7490 (p) REVERT: A 124 MET cc_start: 0.9383 (mmm) cc_final: 0.9087 (mmm) REVERT: A 162 LEU cc_start: 0.9733 (tp) cc_final: 0.9468 (pp) REVERT: A 249 MET cc_start: 0.9263 (mmm) cc_final: 0.9032 (mmm) REVERT: A 347 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8845 (p) REVERT: A 366 MET cc_start: 0.8963 (ttm) cc_final: 0.8707 (mtt) REVERT: A 462 MET cc_start: 0.9638 (mmm) cc_final: 0.9083 (mmm) REVERT: A 474 MET cc_start: 0.9183 (mmt) cc_final: 0.8787 (mpp) outliers start: 24 outliers final: 17 residues processed: 61 average time/residue: 0.1826 time to fit residues: 15.4857 Evaluate side-chains 59 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 0.0570 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.039530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.029909 restraints weight = 39692.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030953 restraints weight = 22409.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.031680 restraints weight = 15583.145| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6648 Z= 0.170 Angle : 0.536 9.768 9020 Z= 0.267 Chirality : 0.040 0.189 945 Planarity : 0.004 0.059 1160 Dihedral : 3.823 18.065 931 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.73 % Allowed : 24.17 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.31), residues: 786 helix: 1.57 (0.28), residues: 372 sheet: 0.97 (0.74), residues: 49 loop : -0.15 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.002 0.000 HIS A 378 PHE 0.007 0.001 PHE A 438 TYR 0.009 0.001 TYR A 51 ARG 0.003 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7410 (p) REVERT: A 124 MET cc_start: 0.9349 (mmm) cc_final: 0.9078 (mmm) REVERT: A 162 LEU cc_start: 0.9727 (tp) cc_final: 0.9464 (pp) REVERT: A 347 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 366 MET cc_start: 0.8946 (ttm) cc_final: 0.8718 (mtt) REVERT: A 462 MET cc_start: 0.9639 (mmm) cc_final: 0.9079 (mmm) REVERT: A 474 MET cc_start: 0.9154 (mmt) cc_final: 0.8880 (mpp) REVERT: B 406 GLU cc_start: 0.9044 (tp30) cc_final: 0.8527 (tp30) outliers start: 19 outliers final: 14 residues processed: 55 average time/residue: 0.1898 time to fit residues: 14.5751 Evaluate side-chains 57 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 498 CYS Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.0370 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.039827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.030179 restraints weight = 39957.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031241 restraints weight = 22592.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031978 restraints weight = 15631.854| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6648 Z= 0.155 Angle : 0.527 9.927 9020 Z= 0.262 Chirality : 0.040 0.191 945 Planarity : 0.004 0.059 1160 Dihedral : 3.698 16.970 931 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.59 % Allowed : 24.32 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.10 (0.31), residues: 786 helix: 1.59 (0.28), residues: 367 sheet: 1.06 (0.75), residues: 49 loop : -0.14 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.002 0.000 HIS A 322 PHE 0.007 0.001 PHE A 438 TYR 0.009 0.001 TYR A 51 ARG 0.002 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.69 seconds wall clock time: 40 minutes 18.23 seconds (2418.23 seconds total)