Starting phenix.real_space_refine on Wed May 14 07:32:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qa5_18299/05_2025/8qa5_18299_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qa5_18299/05_2025/8qa5_18299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qa5_18299/05_2025/8qa5_18299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qa5_18299/05_2025/8qa5_18299.map" model { file = "/net/cci-nas-00/data/ceres_data/8qa5_18299/05_2025/8qa5_18299_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qa5_18299/05_2025/8qa5_18299_trim.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1148 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 10 5.16 5 C 3426 2.51 5 N 1013 2.21 5 O 1116 1.98 5 H 4771 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 6547 Classifications: {'peptide': 582} Link IDs: {'PTRANS': 35, 'TRANS': 546} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1173 Unresolved non-hydrogen angles: 1685 Unresolved non-hydrogen dihedrals: 765 Unresolved non-hydrogen chiralities: 342 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 10, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 16, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 554 Chain: "B" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3686 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 14, 'TRANS': 215} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'FAD': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 6.58, per 1000 atoms: 0.64 Number of scatterers: 10338 At special positions: 0 Unit cell: (106.19, 114.8, 76.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 P 2 15.00 O 1116 8.00 N 1013 7.00 C 3426 6.00 H 4771 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 760.9 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 46.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.095A pdb=" N MET A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 removed outlier: 4.147A pdb=" N ALA A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.639A pdb=" N GLY A 99 " --> pdb=" O HIS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 134 through 148 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.510A pdb=" N LEU A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 removed outlier: 3.673A pdb=" N GLY A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.982A pdb=" N PHE A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 273 removed outlier: 3.986A pdb=" N LEU A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 290 through 313 removed outlier: 4.073A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 366 through 369 removed outlier: 4.620A pdb=" N SER A 369 " --> pdb=" O PHE A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 370 through 379 removed outlier: 4.214A pdb=" N TYR A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.619A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 468 through 476 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.735A pdb=" N LEU A 554 " --> pdb=" O ALA A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 593 removed outlier: 3.929A pdb=" N PHE A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 635 through 644 removed outlier: 4.064A pdb=" N LEU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 427 through 440 removed outlier: 3.698A pdb=" N VAL B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 467 through 477 Processing helix chain 'B' and resid 519 through 533 removed outlier: 4.064A pdb=" N GLU B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 4.399A pdb=" N ASP B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 603 through 614 Processing helix chain 'B' and resid 631 through 644 Processing sheet with id=AA1, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.474A pdb=" N ILE A 225 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 224 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 193 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 195 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 124 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N MET A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 126 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU A 156 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N MET A 128 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 125 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE A 91 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N HIS A 127 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 93 " --> pdb=" O HIS A 127 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR A 129 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE A 60 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE A 91 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 62 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 93 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A 64 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 256 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.651A pdb=" N VAL A 574 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 571 " --> pdb=" O TRP A 561 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TRP A 561 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR A 573 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 559 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 480 through 485 removed outlier: 4.967A pdb=" N THR A 481 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 516 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A 483 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 511 " --> pdb=" O ASP A 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 479 through 485 removed outlier: 6.589A pdb=" N GLU B 514 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER B 484 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR B 512 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 511 " --> pdb=" O ASP B 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 491 through 492 removed outlier: 6.654A pdb=" N THR B 573 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N TRP B 561 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 571 " --> pdb=" O TRP B 561 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 780 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: 4.08 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 1424 1.05 - 1.24: 4190 1.24 - 1.43: 1785 1.43 - 1.62: 3056 1.62 - 1.82: 16 Bond restraints: 10471 Sorted by residual: bond pdb=" CZ ARG B 473 " pdb=" NH2 ARG B 473 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.81e+01 bond pdb=" N SER B 503 " pdb=" H SER B 503 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N LEU B 418 " pdb=" H LEU B 418 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ALA A 353 " pdb=" H ALA A 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 PHE A 366 " pdb=" HE1 PHE A 366 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 10466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 16299 3.12 - 6.25: 1730 6.25 - 9.37: 342 9.37 - 12.49: 18 12.49 - 15.62: 3 Bond angle restraints: 18392 Sorted by residual: angle pdb=" CA ASP B 495 " pdb=" CB ASP B 495 " pdb=" CG ASP B 495 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" CA ASN B 644 " pdb=" CB ASN B 644 " pdb=" CG ASN B 644 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" CA PHE B 432 " pdb=" CB PHE B 432 " pdb=" CG PHE B 432 " ideal model delta sigma weight residual 113.80 119.42 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" N SER A 603 " pdb=" CA SER A 603 " pdb=" CB SER A 603 " ideal model delta sigma weight residual 111.27 106.05 5.22 9.40e-01 1.13e+00 3.08e+01 angle pdb=" C PRO A 413 " pdb=" N LYS A 414 " pdb=" CA LYS A 414 " ideal model delta sigma weight residual 120.38 128.36 -7.98 1.46e+00 4.69e-01 2.99e+01 ... (remaining 18387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 4386 25.20 - 50.40: 215 50.40 - 75.60: 86 75.60 - 100.81: 6 100.81 - 126.01: 1 Dihedral angle restraints: 4694 sinusoidal: 2515 harmonic: 2179 Sorted by residual: dihedral pdb=" CA GLU A 458 " pdb=" C GLU A 458 " pdb=" N PRO A 459 " pdb=" CA PRO A 459 " ideal model delta harmonic sigma weight residual 180.00 151.02 28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LEU A 405 " pdb=" C LEU A 405 " pdb=" N PHE A 406 " pdb=" CA PHE A 406 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ILE B 482 " pdb=" C ILE B 482 " pdb=" N ASN B 483 " pdb=" CA ASN B 483 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 4691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 526 0.142 - 0.283: 93 0.283 - 0.425: 5 0.425 - 0.567: 25 0.567 - 0.708: 13 Chirality restraints: 662 Sorted by residual: chirality pdb=" CG LEU A 642 " pdb=" CB LEU A 642 " pdb=" CD1 LEU A 642 " pdb=" CD2 LEU A 642 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CG LEU B 418 " pdb=" CB LEU B 418 " pdb=" CD1 LEU B 418 " pdb=" CD2 LEU B 418 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CG LEU B 554 " pdb=" CB LEU B 554 " pdb=" CD1 LEU B 554 " pdb=" CD2 LEU B 554 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 659 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 455 " -0.289 2.00e-02 2.50e+03 1.03e-01 4.27e+02 pdb=" CG TRP A 455 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 455 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TRP A 455 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP A 455 " 0.109 2.00e-02 2.50e+03 pdb=" CE2 TRP A 455 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 455 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 455 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 455 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 455 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 TRP A 455 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP A 455 " 0.109 2.00e-02 2.50e+03 pdb=" HE3 TRP A 455 " 0.113 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 455 " -0.114 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 455 " 0.087 2.00e-02 2.50e+03 pdb=" HH2 TRP A 455 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 583 " 0.218 2.00e-02 2.50e+03 7.18e-02 2.06e+02 pdb=" CG TRP A 583 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP A 583 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP A 583 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 583 " -0.072 2.00e-02 2.50e+03 pdb=" CE2 TRP A 583 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP A 583 " -0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 583 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 583 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 583 " 0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP A 583 " -0.038 2.00e-02 2.50e+03 pdb=" HE1 TRP A 583 " 0.030 2.00e-02 2.50e+03 pdb=" HE3 TRP A 583 " -0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 583 " 0.051 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 583 " -0.016 2.00e-02 2.50e+03 pdb=" HH2 TRP A 583 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 500 " -0.171 2.00e-02 2.50e+03 6.86e-02 1.88e+02 pdb=" CG TRP B 500 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 500 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 500 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP B 500 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP B 500 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 500 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 500 " -0.052 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 500 " 0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP B 500 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP B 500 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 500 " 0.111 2.00e-02 2.50e+03 pdb=" HE3 TRP B 500 " 0.086 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 500 " -0.079 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 500 " 0.047 2.00e-02 2.50e+03 pdb=" HH2 TRP B 500 " -0.065 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.93: 158 1.93 - 2.60: 9270 2.60 - 3.26: 30627 3.26 - 3.93: 38665 3.93 - 4.60: 57492 Nonbonded interactions: 136212 Sorted by model distance: nonbonded pdb=" O GLY A 121 " pdb=" HD2 HIS A 354 " model vdw 1.261 2.450 nonbonded pdb=" OE1 GLU B 600 " pdb=" H GLU B 600 " model vdw 1.548 2.450 nonbonded pdb=" OE1 GLU B 553 " pdb=" H GLU B 553 " model vdw 1.563 2.450 nonbonded pdb=" O ILE A 192 " pdb=" H ASP A 223 " model vdw 1.567 2.450 nonbonded pdb=" H ARG A 344 " pdb=" H ARG A 345 " model vdw 1.583 2.100 ... (remaining 136207 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.220 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.720 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 : 0.016 0.123 5700 Z= 0.904 Angle : 1.941 15.617 7653 Z= 1.231 Chirality : 0.169 0.708 662 Planarity : 0.014 0.167 1074 Dihedral : 15.491 126.008 1961 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.14 % Rotamer: Outliers : 1.48 % Allowed : 8.46 % Favored : 90.06 % Cbeta Deviations : 3.41 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.29), residues: 802 helix: -0.46 (0.28), residues: 324 sheet: 0.24 (0.47), residues: 114 loop : -0.86 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.191 0.027 TRP A 455 HIS 0.011 0.003 HIS A 539 PHE 0.115 0.016 PHE B 515 TYR 0.137 0.028 TYR A 512 ARG 0.012 0.002 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.17342 ( 278) hydrogen bonds : angle 7.44614 ( 780) covalent geometry : bond 0.01633 ( 5700) covalent geometry : angle 1.94077 ( 7653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ARG cc_start: 0.6601 (mmm-85) cc_final: 0.6272 (mmm-85) REVERT: A 349 TRP cc_start: 0.6969 (OUTLIER) cc_final: 0.6674 (p-90) outliers start: 7 outliers final: 4 residues processed: 148 average time/residue: 0.5034 time to fit residues: 89.9075 Evaluate side-chains 116 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 600 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.233888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.192631 restraints weight = 16477.527| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 2.34 r_work: 0.4225 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4066 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5700 Z= 0.173 Angle : 0.677 6.099 7653 Z= 0.359 Chirality : 0.044 0.152 662 Planarity : 0.005 0.045 1074 Dihedral : 9.464 136.999 914 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.48 % Allowed : 15.64 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.30), residues: 802 helix: 0.27 (0.29), residues: 335 sheet: -0.33 (0.43), residues: 133 loop : -0.84 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 561 HIS 0.006 0.001 HIS A 613 PHE 0.015 0.002 PHE B 564 TYR 0.015 0.002 TYR A 512 ARG 0.003 0.001 ARG A 377 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 278) hydrogen bonds : angle 5.09003 ( 780) covalent geometry : bond 0.00394 ( 5700) covalent geometry : angle 0.67653 ( 7653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ARG cc_start: 0.7289 (mmm-85) cc_final: 0.7077 (mmm-85) REVERT: A 514 GLU cc_start: 0.7589 (tt0) cc_final: 0.6774 (tt0) REVERT: A 586 GLU cc_start: 0.7665 (tt0) cc_final: 0.7208 (tt0) REVERT: B 555 GLN cc_start: 0.7945 (mt0) cc_final: 0.7731 (mt0) outliers start: 7 outliers final: 5 residues processed: 127 average time/residue: 0.4722 time to fit residues: 72.8840 Evaluate side-chains 120 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 491 LYS Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 644 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.231461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.187215 restraints weight = 16490.040| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 2.38 r_work: 0.4169 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5700 Z= 0.162 Angle : 0.617 6.572 7653 Z= 0.324 Chirality : 0.043 0.146 662 Planarity : 0.005 0.039 1074 Dihedral : 8.909 136.140 910 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.33 % Allowed : 16.91 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.31), residues: 802 helix: 0.78 (0.30), residues: 334 sheet: -0.34 (0.43), residues: 139 loop : -0.75 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 561 HIS 0.005 0.001 HIS A 613 PHE 0.014 0.002 PHE A 435 TYR 0.016 0.002 TYR A 512 ARG 0.003 0.001 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 278) hydrogen bonds : angle 4.64408 ( 780) covalent geometry : bond 0.00374 ( 5700) covalent geometry : angle 0.61726 ( 7653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.7229 (ptt) cc_final: 0.6848 (ptt) REVERT: A 512 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6260 (t80) REVERT: A 557 ASN cc_start: 0.7590 (t0) cc_final: 0.6949 (m-40) REVERT: A 586 GLU cc_start: 0.7615 (tt0) cc_final: 0.7183 (tt0) REVERT: B 555 GLN cc_start: 0.8047 (mt0) cc_final: 0.7783 (mt0) REVERT: B 637 GLU cc_start: 0.7889 (tt0) cc_final: 0.7619 (tp30) outliers start: 11 outliers final: 5 residues processed: 126 average time/residue: 0.4474 time to fit residues: 69.5195 Evaluate side-chains 116 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain B residue 537 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 21 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.233112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.190310 restraints weight = 16291.923| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.30 r_work: 0.4214 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5700 Z= 0.121 Angle : 0.572 5.609 7653 Z= 0.297 Chirality : 0.042 0.143 662 Planarity : 0.005 0.046 1074 Dihedral : 8.398 138.640 906 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.48 % Allowed : 17.12 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.31), residues: 802 helix: 1.18 (0.31), residues: 333 sheet: -0.15 (0.44), residues: 141 loop : -0.64 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.002 0.001 HIS A 539 PHE 0.010 0.002 PHE A 406 TYR 0.013 0.002 TYR A 512 ARG 0.004 0.001 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 278) hydrogen bonds : angle 4.34365 ( 780) covalent geometry : bond 0.00285 ( 5700) covalent geometry : angle 0.57172 ( 7653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6237 (t80) REVERT: A 557 ASN cc_start: 0.7629 (t0) cc_final: 0.7004 (m-40) REVERT: A 586 GLU cc_start: 0.7499 (tt0) cc_final: 0.7167 (tt0) REVERT: B 555 GLN cc_start: 0.8067 (mt0) cc_final: 0.7800 (mt0) outliers start: 7 outliers final: 5 residues processed: 116 average time/residue: 0.4480 time to fit residues: 63.8364 Evaluate side-chains 113 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 644 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 50.0000 chunk 17 optimal weight: 0.0370 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.0040 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.232078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.189349 restraints weight = 16291.297| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 2.28 r_work: 0.4193 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4036 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5700 Z= 0.142 Angle : 0.588 5.845 7653 Z= 0.305 Chirality : 0.042 0.143 662 Planarity : 0.005 0.039 1074 Dihedral : 8.242 138.632 906 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.48 % Allowed : 17.34 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.32), residues: 802 helix: 1.36 (0.31), residues: 333 sheet: 0.00 (0.45), residues: 140 loop : -0.72 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.003 0.001 HIS A 613 PHE 0.012 0.002 PHE A 626 TYR 0.013 0.002 TYR A 512 ARG 0.006 0.001 ARG A 445 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 278) hydrogen bonds : angle 4.32637 ( 780) covalent geometry : bond 0.00334 ( 5700) covalent geometry : angle 0.58789 ( 7653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 LEU cc_start: 0.7009 (mm) cc_final: 0.6764 (pp) REVERT: A 512 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6183 (t80) REVERT: A 557 ASN cc_start: 0.7623 (t0) cc_final: 0.7032 (m-40) REVERT: A 586 GLU cc_start: 0.7426 (tt0) cc_final: 0.7028 (tt0) REVERT: B 555 GLN cc_start: 0.8090 (mt0) cc_final: 0.7852 (mt0) outliers start: 7 outliers final: 5 residues processed: 111 average time/residue: 0.4676 time to fit residues: 64.6764 Evaluate side-chains 110 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain B residue 537 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 72 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.226224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.182313 restraints weight = 16617.489| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.32 r_work: 0.4117 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5700 Z= 0.220 Angle : 0.650 6.582 7653 Z= 0.341 Chirality : 0.045 0.156 662 Planarity : 0.005 0.042 1074 Dihedral : 8.118 136.362 903 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.54 % Allowed : 18.39 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.32), residues: 802 helix: 1.20 (0.31), residues: 337 sheet: -0.30 (0.44), residues: 139 loop : -0.83 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 583 HIS 0.005 0.001 HIS A 613 PHE 0.019 0.003 PHE A 626 TYR 0.018 0.002 TYR B 512 ARG 0.006 0.001 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 278) hydrogen bonds : angle 4.60758 ( 780) covalent geometry : bond 0.00513 ( 5700) covalent geometry : angle 0.64953 ( 7653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 MET cc_start: 0.7313 (ptt) cc_final: 0.6914 (ptt) REVERT: A 512 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6233 (t80) REVERT: A 550 ASN cc_start: 0.6122 (m110) cc_final: 0.5881 (m110) REVERT: A 586 GLU cc_start: 0.7605 (tt0) cc_final: 0.7160 (tt0) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.4353 time to fit residues: 61.4085 Evaluate side-chains 111 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN B 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.228514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.185846 restraints weight = 16872.352| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 2.38 r_work: 0.4167 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5700 Z= 0.140 Angle : 0.582 5.810 7653 Z= 0.304 Chirality : 0.042 0.140 662 Planarity : 0.005 0.037 1074 Dihedral : 7.917 136.971 903 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.54 % Allowed : 18.60 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.32), residues: 802 helix: 1.42 (0.31), residues: 337 sheet: -0.08 (0.45), residues: 139 loop : -0.80 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 561 HIS 0.004 0.001 HIS B 613 PHE 0.016 0.002 PHE A 384 TYR 0.014 0.001 TYR A 538 ARG 0.004 0.000 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03074 ( 278) hydrogen bonds : angle 4.29610 ( 780) covalent geometry : bond 0.00328 ( 5700) covalent geometry : angle 0.58151 ( 7653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ARG cc_start: 0.7213 (mmm-85) cc_final: 0.6880 (mmm-85) REVERT: A 512 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.6110 (t80) REVERT: A 586 GLU cc_start: 0.7495 (tt0) cc_final: 0.7277 (tt0) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.4614 time to fit residues: 62.6665 Evaluate side-chains 111 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 24 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 44 optimal weight: 1.9990 overall best weight: 1.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.226261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.183349 restraints weight = 16663.996| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.33 r_work: 0.4142 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5700 Z= 0.190 Angle : 0.613 5.854 7653 Z= 0.322 Chirality : 0.044 0.145 662 Planarity : 0.005 0.040 1074 Dihedral : 7.923 135.256 903 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.54 % Allowed : 19.66 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.32), residues: 802 helix: 1.38 (0.31), residues: 336 sheet: -0.15 (0.45), residues: 137 loop : -0.88 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 561 HIS 0.003 0.001 HIS A 613 PHE 0.015 0.003 PHE A 626 TYR 0.015 0.002 TYR B 512 ARG 0.004 0.000 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 278) hydrogen bonds : angle 4.45180 ( 780) covalent geometry : bond 0.00443 ( 5700) covalent geometry : angle 0.61336 ( 7653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ARG cc_start: 0.7217 (mmm-85) cc_final: 0.6891 (mmm-85) REVERT: A 512 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6176 (t80) REVERT: A 586 GLU cc_start: 0.7558 (tt0) cc_final: 0.7051 (tt0) outliers start: 12 outliers final: 10 residues processed: 110 average time/residue: 0.4634 time to fit residues: 62.3818 Evaluate side-chains 111 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.0980 chunk 14 optimal weight: 30.0000 chunk 9 optimal weight: 40.0000 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 22 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN A 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.222683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.179782 restraints weight = 16962.565| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.32 r_work: 0.4092 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5700 Z= 0.258 Angle : 0.679 8.303 7653 Z= 0.359 Chirality : 0.047 0.156 662 Planarity : 0.005 0.049 1074 Dihedral : 8.085 131.441 903 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.54 % Allowed : 19.45 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.32), residues: 802 helix: 1.18 (0.31), residues: 334 sheet: -0.30 (0.44), residues: 137 loop : -1.14 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 583 HIS 0.004 0.002 HIS B 613 PHE 0.020 0.003 PHE A 626 TYR 0.020 0.002 TYR B 512 ARG 0.004 0.001 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 278) hydrogen bonds : angle 4.71947 ( 780) covalent geometry : bond 0.00597 ( 5700) covalent geometry : angle 0.67894 ( 7653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ARG cc_start: 0.7170 (mmm-85) cc_final: 0.6954 (mmm-85) REVERT: A 512 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6213 (t80) REVERT: A 550 ASN cc_start: 0.6194 (m110) cc_final: 0.5970 (m110) outliers start: 12 outliers final: 11 residues processed: 111 average time/residue: 0.4624 time to fit residues: 63.0396 Evaluate side-chains 112 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 643 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 50.0000 chunk 74 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** B 537 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 = 0.4737 r_free = 0.4737 target = 0.229736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.188465 restraints weight = 16644.822| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.31 r_work: 0.4185 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5700 Z= 0.112 Angle : 0.573 5.286 7653 Z= 0.298 Chirality : 0.043 0.157 662 Planarity : 0.004 0.042 1074 Dihedral : 7.666 133.164 903 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.48 % Allowed : 21.14 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.32), residues: 802 helix: 1.52 (0.32), residues: 336 sheet: 0.03 (0.45), residues: 138 loop : -0.81 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 561 HIS 0.003 0.001 HIS A 539 PHE 0.011 0.002 PHE B 515 TYR 0.015 0.001 TYR A 538 ARG 0.004 0.001 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 278) hydrogen bonds : angle 4.21305 ( 780) covalent geometry : bond 0.00262 ( 5700) covalent geometry : angle 0.57315 ( 7653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue ALA 70 is missing expected H atoms. Skipping. Residue ALA 73 is missing expected H atoms. Skipping. Residue VAL 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue SER 78 is missing expected H atoms. Skipping. Residue MET 83 is missing expected H atoms. Skipping. Residue ALA 84 is missing expected H atoms. Skipping. Residue ALA 85 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue TYR 90 is missing expected H atoms. Skipping. Residue ILE 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue THR 94 is missing expected H atoms. Skipping. Residue ALA 98 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue THR 107 is missing expected H atoms. Skipping. Residue SER 108 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue MET 111 is missing expected H atoms. Skipping. Residue ILE 112 is missing expected H atoms. Skipping. Residue ALA 113 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue VAL 117 is missing expected H atoms. Skipping. Residue TYR 119 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue ILE 125 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue ILE 138 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue ALA 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue LYS 151 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue MET 154 is missing expected H atoms. Skipping. Residue ALA 155 is missing expected H atoms. Skipping. Residue LEU 156 is missing expected H atoms. Skipping. Residue TYR 174 is missing expected H atoms. Skipping. Residue ALA 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue ILE 182 is missing expected H atoms. Skipping. Residue SER 184 is missing expected H atoms. Skipping. Residue TYR 189 is missing expected H atoms. Skipping. Residue ILE 192 is missing expected H atoms. Skipping. Residue VAL 194 is missing expected H atoms. Skipping. Residue ALA 195 is missing expected H atoms. Skipping. Residue TYR 197 is missing expected H atoms. Skipping. Residue LYS 199 is missing expected H atoms. Skipping. Residue ALA 204 is missing expected H atoms. Skipping. Residue SER 206 is missing expected H atoms. Skipping. Residue ALA 209 is missing expected H atoms. Skipping. Residue LEU 211 is missing expected H atoms. Skipping. Residue LYS 212 is missing expected H atoms. Skipping. Residue LEU 214 is missing expected H atoms. Skipping. Residue LYS 215 is missing expected H atoms. Skipping. Residue LYS 217 is missing expected H atoms. Skipping. Residue VAL 218 is missing expected H atoms. Skipping. Residue SER 219 is missing expected H atoms. Skipping. Residue ALA 220 is missing expected H atoms. Skipping. Residue ALA 222 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue ILE 226 is missing expected H atoms. Skipping. Residue THR 227 is missing expected H atoms. Skipping. Residue LEU 229 is missing expected H atoms. Skipping. Residue ALA 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue VAL 240 is missing expected H atoms. Skipping. Residue LYS 241 is missing expected H atoms. Skipping. Residue ALA 242 is missing expected H atoms. Skipping. Residue THR 244 is missing expected H atoms. Skipping. Residue MET 246 is missing expected H atoms. Skipping. Residue ILE 248 is missing expected H atoms. Skipping. Residue THR 249 is missing expected H atoms. Skipping. Residue ILE 252 is missing expected H atoms. Skipping. Residue VAL 253 is missing expected H atoms. Skipping. Residue ILE 256 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue TYR 262 is missing expected H atoms. Skipping. Residue SER 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 269 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 272 is missing expected H atoms. Skipping. Residue LYS 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue VAL 276 is missing expected H atoms. Skipping. Residue ILE 280 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 283 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue ILE 287 is missing expected H atoms. Skipping. Residue LYS 288 is missing expected H atoms. Skipping. Residue ALA 292 is missing expected H atoms. Skipping. Residue ALA 293 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue TYR 297 is missing expected H atoms. Skipping. Residue ILE 299 is missing expected H atoms. Skipping. Residue LEU 301 is missing expected H atoms. Skipping. Residue ALA 302 is missing expected H atoms. Skipping. Residue VAL 303 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LEU 309 is missing expected H atoms. Skipping. Residue LEU 310 is missing expected H atoms. Skipping. Residue ALA 311 is missing expected H atoms. Skipping. Residue SER 312 is missing expected H atoms. Skipping. Residue LEU 314 is missing expected H atoms. Skipping. Residue VAL 315 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue MET 327 is missing expected H atoms. Skipping. Residue ALA 328 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue THR 330 is missing expected H atoms. Skipping. Residue VAL 332 is missing expected H atoms. Skipping. Residue LEU 333 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.6076 (t80) REVERT: A 550 ASN cc_start: 0.6059 (m110) cc_final: 0.5778 (m110) REVERT: B 526 LEU cc_start: 0.7807 (mt) cc_final: 0.7479 (mt) outliers start: 7 outliers final: 6 residues processed: 108 average time/residue: 0.4770 time to fit residues: 62.8086 Evaluate side-chains 110 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 549 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 50.0000 chunk 55 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 15 optimal weight: 50.0000 chunk 2 optimal weight: 20.0000 chunk 62 optimal weight: 0.0040 chunk 23 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.228141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.186061 restraints weight = 16688.357| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 2.31 r_work: 0.4159 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3997 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5700 Z= 0.145 Angle : 0.583 5.347 7653 Z= 0.304 Chirality : 0.043 0.152 662 Planarity : 0.005 0.043 1074 Dihedral : 7.606 131.944 903 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.90 % Allowed : 20.93 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.32), residues: 802 helix: 1.56 (0.32), residues: 336 sheet: 0.08 (0.46), residues: 137 loop : -0.77 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 561 HIS 0.003 0.001 HIS A 613 PHE 0.012 0.002 PHE A 626 TYR 0.013 0.001 TYR A 512 ARG 0.004 0.001 ARG B 606 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 278) hydrogen bonds : angle 4.23056 ( 780) covalent geometry : bond 0.00343 ( 5700) covalent geometry : angle 0.58309 ( 7653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6930.84 seconds wall clock time: 119 minutes 10.40 seconds (7150.40 seconds total)