Starting phenix.real_space_refine on Fri Dec 27 19:38:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hg0_34730/12_2024/8hg0_34730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg0_34730/12_2024/8hg0_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_34730/12_2024/8hg0_34730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg0_34730/12_2024/8hg0_34730.map" model { file = "/net/cci-nas-00/data/ceres_data/8hg0_34730/12_2024/8hg0_34730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg0_34730/12_2024/8hg0_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-5532/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: 5.92, per 1000 atoms: 0.91 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: 1.67 Conformation dependent library (CDL) restraints added in 981.5 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: 0.84 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: 1.96 Time building geometry restraints manager: 1.93 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.770 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.570 ------------------------------------------------------------------------------- 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 : 0.774 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: 0.1982 time to fit residues: 16.1559 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 : 0.743 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8347 (mmm) cc_final: 0.8117 (tpp) REVERT: A 498 CYS cc_start: 0.7441 (t) cc_final: 0.6861 (p) outliers start: 24 outliers final: 5 residues processed: 66 average time/residue: 0.2326 time to fit residues: 20.9756 Evaluate side-chains 47 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 299 ASN 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 39 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.0050 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6648 Z= 0.162 Angle : 0.525 7.971 9020 Z= 0.268 Chirality : 0.040 0.187 945 Planarity : 0.004 0.060 1160 Dihedral : 4.615 27.424 933 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 2.59 % Allowed : 21.58 % Favored : 75.83 % 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: 0.73 (0.31), residues: 786 helix: 1.20 (0.28), residues: 372 sheet: 1.21 (0.78), residues: 49 loop : -0.31 (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 0.009 0.001 TYR A 202 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 62 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7936 (mtp) cc_final: 0.7724 (ttt) REVERT: A 462 MET cc_start: 0.8347 (mmm) cc_final: 0.8106 (tpp) outliers start: 18 outliers final: 8 residues processed: 59 average time/residue: 0.2053 time to fit residues: 16.6550 Evaluate side-chains 51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6648 Z= 0.156 Angle : 0.508 8.140 9020 Z= 0.259 Chirality : 0.040 0.185 945 Planarity : 0.004 0.059 1160 Dihedral : 4.127 18.364 932 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 2.88 % Allowed : 22.45 % Favored : 74.68 % 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: 0.82 (0.31), residues: 786 helix: 1.35 (0.28), residues: 371 sheet: 1.04 (0.75), residues: 49 loop : -0.30 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.008 0.001 PHE A 438 TYR 0.017 0.001 TYR A 429 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 63 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 462 MET cc_start: 0.8410 (mmm) cc_final: 0.8145 (tpp) outliers start: 20 outliers final: 12 residues processed: 58 average time/residue: 0.2001 time to fit residues: 15.8542 Evaluate side-chains 52 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER 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 360 MET 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 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 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2964 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= 0.182 Angle : 0.522 8.534 9020 Z= 0.265 Chirality : 0.040 0.186 945 Planarity : 0.004 0.059 1160 Dihedral : 4.032 18.268 931 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 3.02 % Allowed : 23.60 % Favored : 73.38 % 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: 0.94 (0.31), residues: 786 helix: 1.51 (0.29), residues: 366 sheet: 0.91 (0.73), residues: 49 loop : -0.27 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 523 TYR 0.024 0.001 TYR A 51 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 62 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.793 Fit side-chains REVERT: A 462 MET cc_start: 0.8444 (mmm) cc_final: 0.8179 (tpp) outliers start: 21 outliers final: 10 residues processed: 58 average time/residue: 0.1984 time to fit residues: 16.0665 Evaluate side-chains 49 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER 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 439 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 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 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6648 Z= 0.287 Angle : 0.587 8.963 9020 Z= 0.300 Chirality : 0.041 0.192 945 Planarity : 0.004 0.060 1160 Dihedral : 4.316 21.728 931 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 3.60 % Allowed : 23.45 % Favored : 72.95 % 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: 1.03 (0.31), residues: 786 helix: 1.52 (0.28), residues: 368 sheet: 0.88 (0.73), residues: 49 loop : -0.15 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 606 HIS 0.003 0.001 HIS A 378 PHE 0.014 0.001 PHE A 523 TYR 0.018 0.001 TYR A 429 ARG 0.005 0.001 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 68 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 462 MET cc_start: 0.8473 (mmm) cc_final: 0.8209 (tpp) REVERT: A 474 MET cc_start: 0.8566 (mmt) cc_final: 0.8313 (mpp) outliers start: 25 outliers final: 16 residues processed: 60 average time/residue: 0.1902 time to fit residues: 16.6550 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 : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 376 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 542 CYS Chi-restraints excluded: chain A residue 604 VAL 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 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3340 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= 0.184 Angle : 0.544 9.013 9020 Z= 0.275 Chirality : 0.040 0.203 945 Planarity : 0.004 0.059 1160 Dihedral : 4.071 18.738 931 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 3.31 % Allowed : 23.88 % Favored : 72.81 % 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: 1.02 (0.31), residues: 786 helix: 1.55 (0.28), residues: 369 sheet: 0.76 (0.72), residues: 49 loop : -0.18 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 438 TYR 0.018 0.001 TYR A 51 ARG 0.006 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 64 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8456 (mmm) cc_final: 0.8234 (tpp) outliers start: 23 outliers final: 17 residues processed: 57 average time/residue: 0.1981 time to fit residues: 15.7533 Evaluate side-chains 57 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 376 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 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 14 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 42 optimal weight: 0.0570 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6648 Z= 0.158 Angle : 0.550 10.301 9020 Z= 0.275 Chirality : 0.040 0.201 945 Planarity : 0.004 0.058 1160 Dihedral : 3.901 17.461 931 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 2.45 % Allowed : 25.32 % Favored : 72.23 % 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: 373 sheet: 0.71 (0.71), residues: 49 loop : -0.19 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 PHE 0.010 0.001 PHE A 438 TYR 0.017 0.001 TYR A 429 ARG 0.005 0.000 ARG B 346 *********************** 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 59 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8452 (mmm) cc_final: 0.8251 (tpp) REVERT: A 474 MET cc_start: 0.8384 (mpp) cc_final: 0.8033 (mpp) outliers start: 17 outliers final: 13 residues processed: 54 average time/residue: 0.1764 time to fit residues: 13.4082 Evaluate side-chains 52 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 360 MET Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 503 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6648 Z= 0.153 Angle : 0.573 16.480 9020 Z= 0.278 Chirality : 0.040 0.195 945 Planarity : 0.004 0.058 1160 Dihedral : 3.761 15.967 931 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 2.45 % Allowed : 25.04 % Favored : 72.52 % 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: 1.09 (0.31), residues: 786 helix: 1.64 (0.28), residues: 372 sheet: 0.75 (0.72), residues: 49 loop : -0.19 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 PHE 0.009 0.001 PHE A 438 TYR 0.016 0.001 TYR A 51 ARG 0.007 0.000 ARG A 160 *********************** 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 59 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 55 average time/residue: 0.1830 time to fit residues: 14.2144 Evaluate side-chains 52 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 366 MET Chi-restraints excluded: chain A residue 503 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6648 Z= 0.213 Angle : 0.582 9.648 9020 Z= 0.288 Chirality : 0.041 0.193 945 Planarity : 0.004 0.059 1160 Dihedral : 3.894 19.311 931 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 2.30 % Allowed : 25.04 % 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: 1.14 (0.31), residues: 786 helix: 1.68 (0.28), residues: 371 sheet: 0.85 (0.72), residues: 49 loop : -0.16 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 378 PHE 0.010 0.001 PHE A 523 TYR 0.016 0.001 TYR A 429 ARG 0.004 0.000 ARG B 346 ********************** 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 58 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.9544 (tp) cc_final: 0.9334 (pp) REVERT: A 474 MET cc_start: 0.8373 (mpp) cc_final: 0.7959 (mpp) outliers start: 16 outliers final: 14 residues processed: 53 average time/residue: 0.1766 time to fit residues: 13.5080 Evaluate side-chains 54 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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 366 MET Chi-restraints excluded: chain A residue 503 LEU 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 17 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.0000 chunk 41 optimal weight: 2.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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 = 0.3063 r_free = 0.3063 target = 0.040206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.030495 restraints weight = 40003.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031614 restraints weight = 22465.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.032386 restraints weight = 15435.694| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6648 Z= 0.152 Angle : 0.570 9.909 9020 Z= 0.278 Chirality : 0.040 0.195 945 Planarity : 0.004 0.058 1160 Dihedral : 3.757 16.614 931 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 1.87 % Allowed : 25.61 % Favored : 72.52 % 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: 1.09 (0.31), residues: 786 helix: 1.64 (0.28), residues: 367 sheet: 0.79 (0.72), residues: 49 loop : -0.16 (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 241 PHE 0.008 0.001 PHE A 438 TYR 0.016 0.001 TYR A 51 ARG 0.004 0.000 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.86 seconds wall clock time: 33 minutes 31.44 seconds (2011.44 seconds total)