Starting phenix.real_space_refine on Thu Jul 2 04:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_34730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_34730.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_34730.cif" model { file = "/net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_34730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_34730.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_34730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hg0_34730/07_2026/8hg0_34730.map" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 chiralities: 1 Time building chain proxies: 1.30, per 1000 atoms: 0.20 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: 0.56 Conformation dependent library (CDL) restraints added in 363.0 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: 0.17 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: 0.81 Time building geometry restraints manager: 0.76 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 - 17.49: 3325 17.49 - 34.97: 460 34.97 - 52.46: 103 52.46 - 69.94: 22 69.94 - 87.43: 4 Dihedral angle restraints: 3914 sinusoidal: 1587 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=" CA ASP A 368 " pdb=" CB ASP A 368 " pdb=" CG ASP A 368 " pdb=" OD1 ASP A 368 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 3911 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: 5.380 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.005 0.200 6659 Z= 0.185 Angle : 0.615 9.367 9041 Z= 0.347 Chirality : 0.038 0.179 945 Planarity : 0.005 0.062 1160 Dihedral : 16.531 87.426 2404 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (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 ARG 0.002 0.000 ARG B 355 TYR 0.015 0.001 TYR A 429 PHE 0.019 0.001 PHE A 428 TRP 0.029 0.001 TRP A 610 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 6648) covalent geometry : angle 0.61200 / 0.35 ( 9020) SS BOND : bond 0.00410 / 0.24 ( 6) SS BOND : angle 1.01198 / 0.60 ( 12) hydrogen bonds : bond 0.30868 / 20.60 ( 264) hydrogen bonds : angle 8.41019 / 6.04 ( 759) metal coordination : bond 0.20009 / 10.04 ( 2) link_NAG-ASN : bond 0.00260 / 0.13 ( 3) link_NAG-ASN : angle 1.71163 / 0.90 ( 9) *********************** 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 : 0.289 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: 0.0724 time to fit residues: 6.0144 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 : 0.162 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0030 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3065 r_free = 0.3065 target = 0.041054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.031148 restraints weight = 39262.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.032280 restraints weight = 21854.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.033037 restraints weight = 14923.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033537 restraints weight = 11534.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.033917 restraints weight = 9718.466| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 6659 Z= 0.136 Angle : 0.560 7.508 9041 Z= 0.291 Chirality : 0.041 0.201 945 Planarity : 0.005 0.058 1160 Dihedral : 4.588 50.249 875 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.95 % Rotamer: Outliers : 3.31 % Allowed : 23.02 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.31), residues: 786 helix: 0.84 (0.27), residues: 377 sheet: 1.21 (0.80), residues: 49 loop : -0.24 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.020 0.001 TYR A 429 PHE 0.010 0.001 PHE A 369 TRP 0.012 0.001 TRP A 610 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 6648) covalent geometry : angle 0.55754 / 0.29 ( 9020) SS BOND : bond 0.00284 / 0.17 ( 6) SS BOND : angle 1.03782 / 0.61 ( 12) hydrogen bonds : bond 0.04964 / 3.22 ( 264) hydrogen bonds : angle 5.35761 / 3.79 ( 759) metal coordination : bond 0.06883 / 3.62 ( 2) link_NAG-ASN : bond 0.00383 / 0.19 ( 3) link_NAG-ASN : angle 1.56390 / 0.81 ( 9) *********************** 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 71 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ILE cc_start: 0.9868 (OUTLIER) cc_final: 0.9657 (mm) REVERT: A 249 MET cc_start: 0.9321 (mmm) cc_final: 0.9047 (mmm) REVERT: A 297 MET cc_start: 0.9230 (mtt) cc_final: 0.9021 (ttm) REVERT: A 347 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8915 (p) REVERT: A 401 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8612 (t-90) REVERT: A 429 TYR cc_start: 0.8530 (t80) cc_final: 0.8256 (t80) REVERT: A 462 MET cc_start: 0.9547 (mmm) cc_final: 0.8898 (tpp) REVERT: A 498 CYS cc_start: 0.8511 (t) cc_final: 0.6930 (p) REVERT: B 406 GLU cc_start: 0.8985 (tp30) cc_final: 0.8715 (tp30) outliers start: 23 outliers final: 6 residues processed: 67 average time/residue: 0.0608 time to fit residues: 5.5361 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 : 0.157 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain A residue 579 MET 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 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3073 r_free = 0.3073 target = 0.041114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.031273 restraints weight = 39454.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.032414 restraints weight = 21925.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.033194 restraints weight = 14936.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.033726 restraints weight = 11504.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.034018 restraints weight = 9588.017| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6659 Z= 0.102 Angle : 0.507 8.119 9041 Z= 0.260 Chirality : 0.040 0.188 945 Planarity : 0.004 0.060 1160 Dihedral : 3.893 21.315 870 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 3.02 % Allowed : 21.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.31), residues: 786 helix: 1.23 (0.28), residues: 372 sheet: 1.29 (0.80), residues: 49 loop : -0.34 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.011 0.001 TYR A 429 PHE 0.009 0.001 PHE A 369 TRP 0.010 0.001 TRP A 478 HIS 0.004 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 6648) covalent geometry : angle 0.50432 / 0.26 ( 9020) SS BOND : bond 0.00301 / 0.19 ( 6) SS BOND : angle 0.97672 / 0.58 ( 12) hydrogen bonds : bond 0.03986 / 2.60 ( 264) hydrogen bonds : angle 4.78641 / 3.39 ( 759) metal coordination : bond 0.00074 / 0.04 ( 2) link_NAG-ASN : bond 0.00252 / 0.12 ( 3) link_NAG-ASN : angle 1.52756 / 0.80 ( 9) *********************** 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 66 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7705 (p) REVERT: A 80 MET cc_start: 0.9499 (mtp) cc_final: 0.9285 (ttt) REVERT: A 347 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8806 (p) REVERT: A 418 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9441 (tp) REVERT: A 429 TYR cc_start: 0.8611 (t80) cc_final: 0.8289 (t80) REVERT: A 462 MET cc_start: 0.9602 (mmm) cc_final: 0.8943 (tpp) REVERT: B 406 GLU cc_start: 0.9115 (tp30) cc_final: 0.8528 (tp30) REVERT: B 417 LYS cc_start: 0.9010 (tppt) cc_final: 0.8773 (tppt) outliers start: 21 outliers final: 7 residues processed: 62 average time/residue: 0.0629 time to fit residues: 5.3177 Evaluate side-chains 56 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 299 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.4980 chunk 11 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 0.0570 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030706 restraints weight = 39828.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.031835 restraints weight = 22449.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.032593 restraints weight = 15335.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.033070 restraints weight = 11862.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.033438 restraints weight = 10023.376| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6659 Z= 0.111 Angle : 0.498 8.217 9041 Z= 0.254 Chirality : 0.040 0.186 945 Planarity : 0.004 0.060 1160 Dihedral : 3.798 15.265 868 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.31), residues: 786 helix: 1.42 (0.29), residues: 366 sheet: 1.14 (0.77), residues: 49 loop : -0.25 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.007 0.001 TYR A 429 PHE 0.008 0.001 PHE A 523 TRP 0.007 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6648) covalent geometry : angle 0.49482 / 0.25 ( 9020) SS BOND : bond 0.00283 / 0.18 ( 6) SS BOND : angle 0.90967 / 0.54 ( 12) hydrogen bonds : bond 0.03587 / 2.34 ( 264) hydrogen bonds : angle 4.59368 / 3.26 ( 759) metal coordination : bond 0.00242 / 0.12 ( 2) link_NAG-ASN : bond 0.00218 / 0.11 ( 3) link_NAG-ASN : angle 1.53906 / 0.80 ( 9) *********************** 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 64 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9233 (mmm) cc_final: 0.9019 (mmp) REVERT: A 429 TYR cc_start: 0.8587 (t80) cc_final: 0.8285 (t80) REVERT: A 462 MET cc_start: 0.9609 (mmm) cc_final: 0.8982 (tpp) REVERT: B 406 GLU cc_start: 0.9093 (tp30) cc_final: 0.8880 (tp30) outliers start: 20 outliers final: 12 residues processed: 57 average time/residue: 0.0620 time to fit residues: 4.8967 Evaluate side-chains 51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 299 ASN 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 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 29 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.039702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.029845 restraints weight = 41913.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.030944 restraints weight = 23130.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.031715 restraints weight = 15791.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.032262 restraints weight = 12181.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.032619 restraints weight = 10161.588| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6659 Z= 0.141 Angle : 0.521 8.338 9041 Z= 0.265 Chirality : 0.040 0.186 945 Planarity : 0.004 0.059 1160 Dihedral : 3.864 15.650 868 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.07 % Rotamer: Outliers : 3.74 % Allowed : 23.02 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.31), residues: 786 helix: 1.56 (0.29), residues: 366 sheet: 0.98 (0.75), residues: 49 loop : -0.20 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.008 0.001 TYR A 51 PHE 0.011 0.001 PHE A 523 TRP 0.007 0.001 TRP A 478 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6648) covalent geometry : angle 0.51786 / 0.26 ( 9020) SS BOND : bond 0.00293 / 0.18 ( 6) SS BOND : angle 0.95713 / 0.56 ( 12) hydrogen bonds : bond 0.03574 / 2.34 ( 264) hydrogen bonds : angle 4.52599 / 3.23 ( 759) metal coordination : bond 0.00363 / 0.18 ( 2) link_NAG-ASN : bond 0.00151 / 0.07 ( 3) link_NAG-ASN : angle 1.65005 / 0.86 ( 9) *********************** 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 66 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7608 (p) REVERT: A 249 MET cc_start: 0.9263 (mmm) cc_final: 0.9045 (mmm) REVERT: A 347 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.8752 (p) REVERT: A 462 MET cc_start: 0.9617 (mmm) cc_final: 0.8996 (tpp) REVERT: B 340 GLU cc_start: 0.8990 (tp30) cc_final: 0.8763 (tp30) REVERT: B 406 GLU cc_start: 0.9115 (tp30) cc_final: 0.8641 (mm-30) outliers start: 26 outliers final: 12 residues processed: 62 average time/residue: 0.0685 time to fit residues: 6.1896 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.039985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.030199 restraints weight = 41182.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.031319 restraints weight = 22749.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.032090 restraints weight = 15509.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032630 restraints weight = 11926.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.032962 restraints weight = 9952.178| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6659 Z= 0.109 Angle : 0.506 8.823 9041 Z= 0.254 Chirality : 0.040 0.189 945 Planarity : 0.004 0.058 1160 Dihedral : 3.813 15.751 868 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 2.88 % Allowed : 23.88 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.31), residues: 786 helix: 1.60 (0.28), residues: 368 sheet: 0.96 (0.74), residues: 49 loop : -0.19 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.009 0.001 TYR A 51 PHE 0.008 0.001 PHE A 438 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 6648) covalent geometry : angle 0.50294 / 0.25 ( 9020) SS BOND : bond 0.00286 / 0.18 ( 6) SS BOND : angle 0.87149 / 0.51 ( 12) hydrogen bonds : bond 0.03270 / 2.15 ( 264) hydrogen bonds : angle 4.40834 / 3.13 ( 759) metal coordination : bond 0.00280 / 0.14 ( 2) link_NAG-ASN : bond 0.00238 / 0.12 ( 3) link_NAG-ASN : angle 1.51968 / 0.79 ( 9) *********************** 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 62 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7581 (p) REVERT: A 249 MET cc_start: 0.9263 (mmm) cc_final: 0.9022 (mmm) REVERT: A 347 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8740 (p) REVERT: A 462 MET cc_start: 0.9622 (mmm) cc_final: 0.9082 (mmm) REVERT: A 474 MET cc_start: 0.9237 (mmt) cc_final: 0.8669 (mpp) outliers start: 20 outliers final: 12 residues processed: 56 average time/residue: 0.0772 time to fit residues: 6.1406 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 542 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.040001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030081 restraints weight = 41175.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.031194 restraints weight = 23041.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031955 restraints weight = 15791.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032507 restraints weight = 12218.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.032879 restraints weight = 10174.036| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6659 Z= 0.115 Angle : 0.516 9.122 9041 Z= 0.259 Chirality : 0.040 0.190 945 Planarity : 0.004 0.058 1160 Dihedral : 3.777 13.777 868 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 3.02 % Allowed : 24.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.31), residues: 786 helix: 1.63 (0.28), residues: 369 sheet: 0.93 (0.73), residues: 49 loop : -0.14 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.020 0.001 TYR A 51 PHE 0.008 0.001 PHE A 438 TRP 0.007 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 6648) covalent geometry : angle 0.51354 / 0.26 ( 9020) SS BOND : bond 0.00323 / 0.20 ( 6) SS BOND : angle 0.88009 / 0.52 ( 12) hydrogen bonds : bond 0.03285 / 2.15 ( 264) hydrogen bonds : angle 4.34927 / 3.09 ( 759) metal coordination : bond 0.00274 / 0.14 ( 2) link_NAG-ASN : bond 0.00206 / 0.10 ( 3) link_NAG-ASN : angle 1.53252 / 0.80 ( 9) *********************** 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 62 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 249 MET cc_start: 0.9248 (mmm) cc_final: 0.9032 (mmm) REVERT: A 347 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8795 (p) REVERT: A 462 MET cc_start: 0.9597 (mmm) cc_final: 0.8991 (tpp) REVERT: A 474 MET cc_start: 0.9250 (mmt) cc_final: 0.8677 (mpp) outliers start: 21 outliers final: 14 residues processed: 56 average time/residue: 0.0772 time to fit residues: 6.0325 Evaluate side-chains 56 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 181 GLU 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 498 CYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.040020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.030087 restraints weight = 41771.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.031202 restraints weight = 23294.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031983 restraints weight = 15899.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.032537 restraints weight = 12290.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.032907 restraints weight = 10262.283| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 0.033 6659 Z= 0.110 Angle : 0.526 9.381 9041 Z= 0.262 Chirality : 0.040 0.190 945 Planarity : 0.004 0.058 1160 Dihedral : 3.751 14.135 868 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.71 % Rotamer: Outliers : 2.73 % Allowed : 24.03 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.31), residues: 786 helix: 1.64 (0.28), residues: 369 sheet: 0.93 (0.73), residues: 49 loop : -0.14 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.009 0.001 TYR A 51 PHE 0.009 0.001 PHE A 438 TRP 0.007 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6648) covalent geometry : angle 0.52340 / 0.26 ( 9020) SS BOND : bond 0.00316 / 0.20 ( 6) SS BOND : angle 0.83935 / 0.50 ( 12) hydrogen bonds : bond 0.03345 / 2.26 ( 264) hydrogen bonds : angle 4.31083 / 3.07 ( 759) metal coordination : bond 0.00258 / 0.13 ( 2) link_NAG-ASN : bond 0.00226 / 0.11 ( 3) link_NAG-ASN : angle 1.51223 / 0.78 ( 9) *********************** 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 61 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7822 (OUTLIER) cc_final: 0.7408 (p) REVERT: A 162 LEU cc_start: 0.9746 (tp) cc_final: 0.9475 (pp) REVERT: A 347 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8775 (p) REVERT: A 462 MET cc_start: 0.9619 (mmm) cc_final: 0.9018 (tpp) REVERT: A 474 MET cc_start: 0.9240 (mmt) cc_final: 0.8812 (mpp) REVERT: B 406 GLU cc_start: 0.8981 (tp30) cc_final: 0.8389 (tp30) outliers start: 19 outliers final: 9 residues processed: 57 average time/residue: 0.0805 time to fit residues: 6.5074 Evaluate side-chains 51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 55 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.030302 restraints weight = 41948.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.031419 restraints weight = 23410.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.032202 restraints weight = 15973.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.032738 restraints weight = 12304.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.033127 restraints weight = 10247.260| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6659 Z= 0.109 Angle : 0.545 9.663 9041 Z= 0.269 Chirality : 0.040 0.189 945 Planarity : 0.004 0.058 1160 Dihedral : 3.751 13.883 868 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.42 % Favored : 97.46 % Rotamer: Outliers : 2.01 % Allowed : 25.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.31), residues: 786 helix: 1.65 (0.28), residues: 372 sheet: 0.99 (0.73), residues: 49 loop : -0.16 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 346 TYR 0.010 0.001 TYR A 51 PHE 0.007 0.001 PHE A 523 TRP 0.007 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6648) covalent geometry : angle 0.54266 / 0.27 ( 9020) SS BOND : bond 0.00315 / 0.20 ( 6) SS BOND : angle 0.78173 / 0.46 ( 12) hydrogen bonds : bond 0.03266 / 2.19 ( 264) hydrogen bonds : angle 4.38504 / 3.12 ( 759) metal coordination : bond 0.00246 / 0.12 ( 2) link_NAG-ASN : bond 0.00219 / 0.11 ( 3) link_NAG-ASN : angle 1.47848 / 0.77 ( 9) *********************** 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 55 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7811 (OUTLIER) cc_final: 0.7399 (p) REVERT: A 162 LEU cc_start: 0.9735 (tp) cc_final: 0.9472 (pp) REVERT: A 347 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 462 MET cc_start: 0.9617 (mmm) cc_final: 0.9022 (tpp) REVERT: A 474 MET cc_start: 0.9277 (mmt) cc_final: 0.8884 (mpp) REVERT: B 406 GLU cc_start: 0.8933 (tp30) cc_final: 0.8153 (tp30) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.0819 time to fit residues: 6.0220 Evaluate side-chains 53 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain B residue 367 VAL 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 9 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 67 optimal weight: 0.0030 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.040255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.030396 restraints weight = 41368.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031520 restraints weight = 22869.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.032305 restraints weight = 15647.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.032799 restraints weight = 12089.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.033194 restraints weight = 10196.054| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6659 Z= 0.104 Angle : 0.558 9.860 9041 Z= 0.273 Chirality : 0.040 0.192 945 Planarity : 0.004 0.058 1160 Dihedral : 3.724 13.804 868 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.16 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 25.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.31), residues: 786 helix: 1.63 (0.28), residues: 369 sheet: 1.05 (0.73), residues: 49 loop : -0.12 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 346 TYR 0.008 0.001 TYR A 51 PHE 0.007 0.001 PHE A 438 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 6648) covalent geometry : angle 0.55651 / 0.27 ( 9020) SS BOND : bond 0.00298 / 0.19 ( 6) SS BOND : angle 0.74608 / 0.44 ( 12) hydrogen bonds : bond 0.03226 / 2.16 ( 264) hydrogen bonds : angle 4.33828 / 3.09 ( 759) metal coordination : bond 0.00221 / 0.11 ( 2) link_NAG-ASN : bond 0.00240 / 0.12 ( 3) link_NAG-ASN : angle 1.46365 / 0.76 ( 9) ********************** 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 54 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7283 (p) REVERT: A 162 LEU cc_start: 0.9719 (tp) cc_final: 0.9464 (pp) REVERT: A 249 MET cc_start: 0.9021 (mmp) cc_final: 0.8758 (mmt) REVERT: A 347 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8804 (p) REVERT: A 462 MET cc_start: 0.9612 (mmm) cc_final: 0.9075 (mmm) REVERT: A 474 MET cc_start: 0.9288 (mmt) cc_final: 0.8927 (mpp) outliers start: 15 outliers final: 11 residues processed: 52 average time/residue: 0.0750 time to fit residues: 5.6149 Evaluate side-chains 50 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 503 LEU Chi-restraints excluded: chain B residue 367 VAL 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 24 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.030588 restraints weight = 41529.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.031709 restraints weight = 22789.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.032505 restraints weight = 15555.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.033053 restraints weight = 11982.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.033417 restraints weight = 9981.129| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6659 Z= 0.105 Angle : 0.550 9.856 9041 Z= 0.269 Chirality : 0.040 0.192 945 Planarity : 0.004 0.059 1160 Dihedral : 3.724 14.134 868 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 25.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.31), residues: 786 helix: 1.53 (0.28), residues: 374 sheet: 1.03 (0.73), residues: 49 loop : -0.11 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.007 0.001 TYR A 51 PHE 0.007 0.001 PHE A 438 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 6648) covalent geometry : angle 0.54811 / 0.27 ( 9020) SS BOND : bond 0.00294 / 0.18 ( 6) SS BOND : angle 0.74445 / 0.44 ( 12) hydrogen bonds : bond 0.03201 / 2.14 ( 264) hydrogen bonds : angle 4.36336 / 3.10 ( 759) metal coordination : bond 0.00212 / 0.11 ( 2) link_NAG-ASN : bond 0.00244 / 0.12 ( 3) link_NAG-ASN : angle 1.44910 / 0.75 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1203.78 seconds wall clock time: 21 minutes 37.15 seconds (1297.15 seconds total)