Starting phenix.real_space_refine on Sat Nov 16 16:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/11_2024/8qa5_18299_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/11_2024/8qa5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/11_2024/8qa5_18299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/11_2024/8qa5_18299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/11_2024/8qa5_18299_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qa5_18299/11_2024/8qa5_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 4809 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10376 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'FAD': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Classifications: {'peptide': 1} Time building chain proxies: 6.11, per 1000 atoms: 0.59 Number of scatterers: 10376 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 4809 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: 3.17 Conformation dependent library (CDL) restraints added in 889.3 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 46.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 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: 3.77 Time building geometry restraints manager: 3.63 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: 1436 1.05 - 1.24: 4216 1.24 - 1.43: 1785 1.43 - 1.62: 3056 1.62 - 1.82: 16 Bond restraints: 10509 Sorted by residual: bond pdb=" C2 SAH A 702 " pdb=" H2 SAH A 702 " ideal model delta sigma weight residual 0.930 1.084 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C2 SAH B 701 " pdb=" H2 SAH B 701 " ideal model delta sigma weight residual 0.930 1.083 -0.153 2.00e-02 2.50e+03 5.85e+01 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=" C8 SAH A 702 " pdb=" H8 SAH A 702 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" C8 SAH B 701 " pdb=" H8 SAH B 701 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.79e+01 ... (remaining 10504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 16747 3.44 - 6.87: 1506 6.87 - 10.31: 211 10.31 - 13.75: 9 13.75 - 17.19: 3 Bond angle restraints: 18476 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 SAH A 702 " pdb=" N SAH A 702 " pdb=" HN1 SAH A 702 " ideal model delta sigma weight residual 107.56 124.75 -17.19 3.00e+00 1.11e-01 3.28e+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 ... (remaining 18471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.50: 4448 29.50 - 59.00: 223 59.00 - 88.51: 43 88.51 - 118.01: 3 118.01 - 147.51: 3 Dihedral angle restraints: 4720 sinusoidal: 2541 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 4717 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: 1834 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 1831 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.93: 164 1.93 - 2.60: 9373 2.60 - 3.26: 30855 3.26 - 3.93: 38984 3.93 - 4.60: 58016 Nonbonded interactions: 137392 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 137387 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: 3.020 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: 0.210 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.930 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 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= 1.051 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 *********************** 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 : 0.799 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: 0.5027 time to fit residues: 90.0321 Evaluate side-chains 117 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5700 Z= 0.249 Angle : 0.674 6.031 7653 Z= 0.357 Chirality : 0.044 0.151 662 Planarity : 0.005 0.046 1074 Dihedral : 9.518 137.149 914 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.90 % Allowed : 15.22 % 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: 0.28 (0.29), residues: 335 sheet: -0.34 (0.43), residues: 133 loop : -0.86 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 561 HIS 0.005 0.001 HIS A 613 PHE 0.015 0.002 PHE A 384 TYR 0.015 0.002 TYR A 512 ARG 0.003 0.001 ARG A 445 *********************** 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 135 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.867 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: symmetry clash REVERT: A 514 GLU cc_start: 0.7378 (tt0) cc_final: 0.6614 (tt0) REVERT: A 586 GLU cc_start: 0.7535 (tt0) cc_final: 0.7125 (tt0) REVERT: B 555 GLN cc_start: 0.7524 (mt0) cc_final: 0.7323 (mt0) outliers start: 9 outliers final: 6 residues processed: 132 average time/residue: 0.4774 time to fit residues: 77.2663 Evaluate side-chains 122 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 512 TYR 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 40 optimal weight: 0.5980 chunk 22 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 20 optimal weight: 20.0000 chunk 73 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5700 Z= 0.173 Angle : 0.580 7.066 7653 Z= 0.301 Chirality : 0.042 0.142 662 Planarity : 0.004 0.038 1074 Dihedral : 8.643 137.629 910 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.69 % Allowed : 16.70 % Favored : 81.61 % 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: 0.13 (0.31), residues: 802 helix: 0.93 (0.30), residues: 334 sheet: -0.22 (0.43), residues: 141 loop : -0.56 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.005 0.002 HIS A 613 PHE 0.011 0.002 PHE A 406 TYR 0.015 0.002 TYR A 512 ARG 0.004 0.001 ARG B 606 *********************** 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 130 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.791 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 512 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.5915 (t80) REVERT: A 514 GLU cc_start: 0.7498 (tt0) cc_final: 0.6678 (tt0) REVERT: A 557 ASN cc_start: 0.7167 (t0) cc_final: 0.6692 (m-40) REVERT: B 555 GLN cc_start: 0.7606 (mt0) cc_final: 0.7338 (mt0) outliers start: 8 outliers final: 3 residues processed: 127 average time/residue: 0.4559 time to fit residues: 71.3651 Evaluate side-chains 121 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 50.0000 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5700 Z= 0.219 Angle : 0.579 5.282 7653 Z= 0.300 Chirality : 0.042 0.143 662 Planarity : 0.005 0.041 1074 Dihedral : 8.277 139.675 906 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.69 % Allowed : 16.28 % Favored : 82.03 % 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: 0.32 (0.32), residues: 802 helix: 1.15 (0.31), residues: 334 sheet: -0.07 (0.44), residues: 140 loop : -0.54 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 561 HIS 0.003 0.001 HIS A 613 PHE 0.012 0.002 PHE A 435 TYR 0.013 0.002 TYR B 512 ARG 0.003 0.000 ARG B 606 *********************** 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 124 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.913 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: A 405 LEU cc_start: 0.6914 (mm) cc_final: 0.6712 (pp) REVERT: A 512 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5960 (t80) REVERT: A 557 ASN cc_start: 0.7217 (t0) cc_final: 0.6704 (m-40) REVERT: B 555 GLN cc_start: 0.7676 (mt0) cc_final: 0.7424 (mt0) outliers start: 8 outliers final: 4 residues processed: 122 average time/residue: 0.4591 time to fit residues: 69.1440 Evaluate side-chains 115 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 B residue 537 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 20.0000 chunk 58 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 50.0000 chunk 26 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4114 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= 0.279 Angle : 0.609 6.516 7653 Z= 0.318 Chirality : 0.043 0.151 662 Planarity : 0.005 0.041 1074 Dihedral : 7.998 138.478 903 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.75 % Allowed : 16.07 % 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: 0.24 (0.32), residues: 802 helix: 1.22 (0.31), residues: 335 sheet: -0.17 (0.44), residues: 139 loop : -0.74 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 561 HIS 0.003 0.001 HIS A 613 PHE 0.016 0.002 PHE A 626 TYR 0.016 0.002 TYR B 512 ARG 0.007 0.001 ARG A 445 *********************** 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 123 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.945 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: A 512 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.5863 (t80) REVERT: A 557 ASN cc_start: 0.7175 (t0) cc_final: 0.6685 (m-40) REVERT: B 555 GLN cc_start: 0.7708 (mt0) cc_final: 0.7476 (mt0) outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 0.4650 time to fit residues: 68.5309 Evaluate side-chains 116 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 563 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5700 Z= 0.209 Angle : 0.567 5.345 7653 Z= 0.294 Chirality : 0.042 0.142 662 Planarity : 0.005 0.037 1074 Dihedral : 7.684 138.998 903 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.69 % Allowed : 17.55 % 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: 0.44 (0.32), residues: 802 helix: 1.43 (0.31), residues: 338 sheet: -0.06 (0.45), residues: 138 loop : -0.71 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 561 HIS 0.004 0.001 HIS B 613 PHE 0.011 0.002 PHE B 508 TYR 0.013 0.002 TYR A 512 ARG 0.004 0.000 ARG B 606 *********************** 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 115 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.842 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: A 345 ARG cc_start: 0.6766 (mmm-85) cc_final: 0.6459 (mmm-85) REVERT: A 357 ARG cc_start: 0.5726 (mtp85) cc_final: 0.5201 (mtp85) REVERT: A 512 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5859 (t80) REVERT: A 550 ASN cc_start: 0.5787 (m110) cc_final: 0.5534 (m110) REVERT: A 557 ASN cc_start: 0.7213 (t0) cc_final: 0.6745 (m-40) outliers start: 8 outliers final: 6 residues processed: 112 average time/residue: 0.4899 time to fit residues: 67.5313 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 : 0.815 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 43 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 20.0000 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5700 Z= 0.165 Angle : 0.545 7.665 7653 Z= 0.279 Chirality : 0.041 0.137 662 Planarity : 0.004 0.034 1074 Dihedral : 7.394 138.252 903 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.48 % Allowed : 17.76 % 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: 0.72 (0.32), residues: 802 helix: 1.68 (0.32), residues: 337 sheet: 0.08 (0.46), residues: 140 loop : -0.57 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 561 HIS 0.002 0.001 HIS A 539 PHE 0.010 0.001 PHE B 515 TYR 0.012 0.001 TYR A 512 ARG 0.005 0.001 ARG B 606 *********************** 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: 7 poor density : 109 time to evaluate : 0.882 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 345 ARG cc_start: 0.6695 (mmm-85) cc_final: 0.6396 (mmm-85) REVERT: A 550 ASN cc_start: 0.5843 (m110) cc_final: 0.5564 (m110) REVERT: A 557 ASN cc_start: 0.7234 (t0) cc_final: 0.6748 (m-40) REVERT: B 555 GLN cc_start: 0.7663 (mt0) cc_final: 0.7456 (mt0) outliers start: 7 outliers final: 5 residues processed: 114 average time/residue: 0.4678 time to fit residues: 65.2138 Evaluate side-chains 106 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 644 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 571 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 50.0000 chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.4527 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= 0.205 Angle : 0.562 6.821 7653 Z= 0.290 Chirality : 0.042 0.140 662 Planarity : 0.004 0.042 1074 Dihedral : 7.398 137.069 903 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.48 % Allowed : 17.97 % Favored : 80.55 % 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: 0.72 (0.32), residues: 802 helix: 1.70 (0.31), residues: 337 sheet: 0.14 (0.46), residues: 139 loop : -0.63 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 561 HIS 0.003 0.001 HIS A 613 PHE 0.011 0.002 PHE A 626 TYR 0.012 0.001 TYR A 512 ARG 0.004 0.000 ARG B 606 *********************** 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 110 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.873 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: A 345 ARG cc_start: 0.6716 (mmm-85) cc_final: 0.6408 (mmm-85) REVERT: A 512 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5775 (t80) REVERT: A 550 ASN cc_start: 0.5807 (m110) cc_final: 0.5535 (m110) REVERT: A 557 ASN cc_start: 0.7211 (t0) cc_final: 0.6730 (m-40) REVERT: B 570 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6359 (mt) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.5040 time to fit residues: 67.0167 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 : 0.929 ------------------------------------------------------------------------------- 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 570 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 615 ASN ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5700 Z= 0.189 Angle : 0.559 6.758 7653 Z= 0.288 Chirality : 0.042 0.144 662 Planarity : 0.004 0.034 1074 Dihedral : 7.319 136.063 903 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.48 % Allowed : 18.39 % Favored : 80.13 % 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: 0.85 (0.32), residues: 802 helix: 1.81 (0.32), residues: 336 sheet: 0.19 (0.46), residues: 139 loop : -0.55 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.002 0.000 HIS B 539 PHE 0.010 0.002 PHE A 435 TYR 0.012 0.001 TYR A 538 ARG 0.006 0.000 ARG B 606 *********************** 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 109 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.950 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 345 ARG cc_start: 0.6713 (mmm-85) cc_final: 0.6406 (mmm-85) REVERT: A 512 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5797 (t80) REVERT: A 550 ASN cc_start: 0.5826 (m110) cc_final: 0.5549 (m110) REVERT: A 557 ASN cc_start: 0.7235 (t0) cc_final: 0.6741 (m-40) REVERT: B 570 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6441 (mt) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.5009 time to fit residues: 66.8059 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 : 0.799 ------------------------------------------------------------------------------- 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 570 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 0.0970 chunk 64 optimal weight: 0.0870 chunk 6 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 19 optimal weight: 50.0000 chunk 59 optimal weight: 0.0470 chunk 9 optimal weight: 6.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN A 571 GLN B 547 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5700 Z= 0.156 Angle : 0.536 6.851 7653 Z= 0.275 Chirality : 0.041 0.162 662 Planarity : 0.004 0.036 1074 Dihedral : 7.178 135.593 903 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.06 % Allowed : 19.24 % Favored : 79.70 % 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: 1.09 (0.33), residues: 802 helix: 2.00 (0.32), residues: 337 sheet: 0.28 (0.47), residues: 140 loop : -0.40 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 561 HIS 0.002 0.001 HIS B 539 PHE 0.007 0.001 PHE B 508 TYR 0.011 0.001 TYR A 538 ARG 0.004 0.000 ARG B 606 ********************** 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 111 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.896 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 512 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5735 (t80) REVERT: A 550 ASN cc_start: 0.5872 (m110) cc_final: 0.5591 (m110) REVERT: A 557 ASN cc_start: 0.7265 (t0) cc_final: 0.6757 (m-40) REVERT: B 526 LEU cc_start: 0.7756 (mt) cc_final: 0.7418 (mt) outliers start: 5 outliers final: 4 residues processed: 110 average time/residue: 0.5060 time to fit residues: 68.1816 Evaluate side-chains 110 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 B residue 517 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 50.0000 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 547 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 = 0.4728 r_free = 0.4728 target = 0.227756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.184555 restraints weight = 16562.725| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.26 r_work: 0.4146 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5700 Z= 0.339 Angle : 0.619 5.884 7653 Z= 0.327 Chirality : 0.044 0.154 662 Planarity : 0.005 0.042 1074 Dihedral : 7.501 132.832 903 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.27 % Allowed : 19.45 % Favored : 79.28 % 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: 0.70 (0.32), residues: 802 helix: 1.70 (0.31), residues: 337 sheet: 0.08 (0.46), residues: 138 loop : -0.64 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 583 HIS 0.004 0.001 HIS A 613 PHE 0.022 0.003 PHE A 626 TYR 0.018 0.002 TYR B 616 ARG 0.006 0.001 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3782.90 seconds wall clock time: 67 minutes 57.59 seconds (4077.59 seconds total)