Starting phenix.real_space_refine on Fri Jun 27 11:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mhx_9121/06_2025/6mhx_9121.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mhx_9121/06_2025/6mhx_9121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mhx_9121/06_2025/6mhx_9121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mhx_9121/06_2025/6mhx_9121.map" model { file = "/net/cci-nas-00/data/ceres_data/6mhx_9121/06_2025/6mhx_9121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mhx_9121/06_2025/6mhx_9121.cif" } resolution = 4.0 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 11132 2.51 5 N 2874 2.21 5 O 2902 1.98 5 H 14648 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31612 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 8019 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 13, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 563 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 410 Chain: "A" Number of atoms: 7787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 7787 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 13, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 766 Unresolved non-hydrogen angles: 936 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 19, 'PHE:plan': 8, 'GLU:plan': 41, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 444 Restraints were copied for chains: D, C Time building chain proxies: 38.25, per 1000 atoms: 1.21 Number of scatterers: 31612 At special positions: 0 Unit cell: (129.95, 132.25, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 2902 8.00 N 2874 7.00 C 11132 6.00 H 14648 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: 8.68 Conformation dependent library (CDL) restraints added in 2.9 seconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4648 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 4 sheets defined 67.8% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.647A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.978A pdb=" N VAL B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.656A pdb=" N ASN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.715A pdb=" N ALA B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.553A pdb=" N GLN B 313 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 436 through 462 Processing helix chain 'B' and resid 481 through 508 Processing helix chain 'B' and resid 520 through 542 removed outlier: 4.141A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 567 removed outlier: 3.599A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 610 removed outlier: 4.755A pdb=" N VAL B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 650 through 707 removed outlier: 4.519A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 707 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 147 removed outlier: 4.057A pdb=" N VAL A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.608A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.779A pdb=" N ALA A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.768A pdb=" N GLN A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 422 through 436 Processing helix chain 'A' and resid 436 through 462 Processing helix chain 'A' and resid 481 through 508 Processing helix chain 'A' and resid 520 through 542 removed outlier: 4.208A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 567 removed outlier: 3.578A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 610 removed outlier: 4.717A pdb=" N VAL A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 Processing helix chain 'A' and resid 650 through 707 removed outlier: 5.006A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 132 through 147 removed outlier: 4.057A pdb=" N VAL C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.608A pdb=" N ASN C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.778A pdb=" N ALA C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.769A pdb=" N GLN C 313 " --> pdb=" O ASP C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 436 through 462 Processing helix chain 'C' and resid 481 through 508 Processing helix chain 'C' and resid 520 through 542 removed outlier: 4.208A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 567 removed outlier: 3.579A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 610 removed outlier: 4.717A pdb=" N VAL C 587 " --> pdb=" O ILE C 583 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 Processing helix chain 'C' and resid 650 through 707 removed outlier: 5.005A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.979A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 170 through 178 Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.656A pdb=" N ASN D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.715A pdb=" N ALA D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.553A pdb=" N GLN D 313 " --> pdb=" O ASP D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 421 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 436 through 462 Processing helix chain 'D' and resid 481 through 508 Processing helix chain 'D' and resid 520 through 542 removed outlier: 4.142A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 567 removed outlier: 3.598A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 610 removed outlier: 4.755A pdb=" N VAL D 587 " --> pdb=" O ILE D 583 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS D 589 " --> pdb=" O HIS D 585 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 Processing helix chain 'D' and resid 650 through 707 removed outlier: 4.519A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 716 Processing sheet with id=AA1, first strand: chain 'B' and resid 377 through 378 Processing sheet with id=AA2, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 378 Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 378 1208 hydrogen bonds defined for protein. 3588 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: 12.33 Time building geometry restraints manager: 10.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14626 1.02 - 1.22: 22 1.22 - 1.41: 7297 1.41 - 1.61: 9951 1.61 - 1.81: 90 Bond restraints: 31986 Sorted by residual: bond pdb=" C LEU C 707 " pdb=" N PRO C 708 " ideal model delta sigma weight residual 1.326 1.356 -0.029 1.44e-02 4.82e+03 4.16e+00 bond pdb=" C LEU A 707 " pdb=" N PRO A 708 " ideal model delta sigma weight residual 1.326 1.355 -0.028 1.44e-02 4.82e+03 3.91e+00 bond pdb=" C GLY D 383 " pdb=" N PRO D 384 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.19e-02 7.06e+03 2.60e+00 bond pdb=" C GLY B 383 " pdb=" N PRO B 384 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.19e-02 7.06e+03 2.25e+00 bond pdb=" C GLY C 383 " pdb=" N PRO C 384 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.19e-02 7.06e+03 2.07e+00 ... (remaining 31981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 56219 1.94 - 3.87: 785 3.87 - 5.81: 78 5.81 - 7.74: 8 7.74 - 9.68: 2 Bond angle restraints: 57092 Sorted by residual: angle pdb=" N VAL A 306 " pdb=" CA VAL A 306 " pdb=" C VAL A 306 " ideal model delta sigma weight residual 110.72 120.40 -9.68 1.01e+00 9.80e-01 9.18e+01 angle pdb=" N VAL C 306 " pdb=" CA VAL C 306 " pdb=" C VAL C 306 " ideal model delta sigma weight residual 110.72 120.31 -9.59 1.01e+00 9.80e-01 9.02e+01 angle pdb=" N THR B 680 " pdb=" CA THR B 680 " pdb=" C THR B 680 " ideal model delta sigma weight residual 111.28 117.70 -6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N THR D 680 " pdb=" CA THR D 680 " pdb=" C THR D 680 " ideal model delta sigma weight residual 111.28 117.70 -6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N THR C 312 " pdb=" CA THR C 312 " pdb=" C THR C 312 " ideal model delta sigma weight residual 111.28 115.85 -4.57 1.09e+00 8.42e-01 1.76e+01 ... (remaining 57087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.13: 14193 12.13 - 24.26: 1072 24.26 - 36.39: 209 36.39 - 48.52: 68 48.52 - 60.65: 106 Dihedral angle restraints: 15648 sinusoidal: 7138 harmonic: 8510 Sorted by residual: dihedral pdb=" CA PHE C 436 " pdb=" C PHE C 436 " pdb=" N ALA C 437 " pdb=" CA ALA C 437 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE A 436 " pdb=" C PHE A 436 " pdb=" N ALA A 437 " pdb=" CA ALA A 437 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA PHE B 436 " pdb=" C PHE B 436 " pdb=" N ALA B 437 " pdb=" CA ALA B 437 " ideal model delta harmonic sigma weight residual 180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 15645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2088 0.035 - 0.071: 640 0.071 - 0.106: 193 0.106 - 0.141: 41 0.141 - 0.176: 6 Chirality restraints: 2968 Sorted by residual: chirality pdb=" CA VAL A 306 " pdb=" N VAL A 306 " pdb=" C VAL A 306 " pdb=" CB VAL A 306 " both_signs ideal model delta sigma weight residual False 2.44 2.26 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE C 734 " pdb=" N ILE C 734 " pdb=" C ILE C 734 " pdb=" CB ILE C 734 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2965 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 313 " 0.212 2.00e-02 2.50e+03 2.53e-01 9.57e+02 pdb=" CD GLN A 313 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN A 313 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN A 313 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 313 " -0.382 2.00e-02 2.50e+03 pdb="HE22 GLN A 313 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 313 " 0.211 2.00e-02 2.50e+03 2.52e-01 9.55e+02 pdb=" CD GLN C 313 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN C 313 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN C 313 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 313 " -0.381 2.00e-02 2.50e+03 pdb="HE22 GLN C 313 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 313 " 0.080 2.00e-02 2.50e+03 8.57e-02 1.10e+02 pdb=" CD GLN B 313 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN B 313 " -0.075 2.00e-02 2.50e+03 pdb=" NE2 GLN B 313 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 313 " -0.125 2.00e-02 2.50e+03 pdb="HE22 GLN B 313 " 0.128 2.00e-02 2.50e+03 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 195 2.09 - 2.71: 48503 2.71 - 3.34: 87662 3.34 - 3.97: 103139 3.97 - 4.60: 162792 Nonbonded interactions: 402291 Sorted by model distance: nonbonded pdb=" HB3 PHE D 542 " pdb=" HE2 TYR D 544 " model vdw 1.457 2.270 nonbonded pdb=" HB3 PHE B 542 " pdb=" HE2 TYR B 544 " model vdw 1.457 2.270 nonbonded pdb=" HB2 PHE D 542 " pdb=" HD2 TYR D 544 " model vdw 1.557 2.270 nonbonded pdb=" HB2 PHE B 542 " pdb=" HD2 TYR B 544 " model vdw 1.557 2.270 nonbonded pdb="HD11 LEU A 455 " pdb="HD11 LEU A 551 " model vdw 1.634 2.440 ... (remaining 402286 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: 0.10 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.650 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 90.830 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.004 0.045 17338 Z= 0.208 Angle : 0.670 9.677 23822 Z= 0.421 Chirality : 0.039 0.176 2968 Planarity : 0.004 0.037 2976 Dihedral : 7.565 41.426 5246 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.30 % Allowed : 0.59 % Favored : 99.11 % 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: -2.52 (0.14), residues: 2404 helix: -1.43 (0.10), residues: 1592 sheet: -1.33 (0.54), residues: 76 loop : -1.87 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 559 HIS 0.006 0.001 HIS A 426 PHE 0.032 0.002 PHE B 597 TYR 0.011 0.001 TYR B 650 ARG 0.006 0.001 ARG D 716 Details of bonding type rmsd hydrogen bonds : bond 0.14764 ( 1208) hydrogen bonds : angle 6.60648 ( 3588) covalent geometry : bond 0.00436 (17338) covalent geometry : angle 0.67028 (23822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 462 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 458 time to evaluate : 2.687 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 MET cc_start: 0.7750 (mmm) cc_final: 0.7500 (mmm) REVERT: A 169 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8721 (ttmm) REVERT: A 557 LEU cc_start: 0.9412 (tp) cc_final: 0.9143 (mm) REVERT: A 561 ASN cc_start: 0.8984 (m-40) cc_final: 0.8770 (m-40) REVERT: A 636 THR cc_start: 0.8468 (p) cc_final: 0.7929 (p) REVERT: C 169 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8714 (ttmm) REVERT: C 557 LEU cc_start: 0.9414 (tp) cc_final: 0.9147 (mm) REVERT: C 561 ASN cc_start: 0.8990 (m-40) cc_final: 0.8766 (m-40) REVERT: C 636 THR cc_start: 0.8471 (p) cc_final: 0.7926 (p) outliers start: 4 outliers final: 0 residues processed: 462 average time/residue: 0.5683 time to fit residues: 401.5311 Evaluate side-chains 252 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.106802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.091761 restraints weight = 182664.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094245 restraints weight = 94427.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095886 restraints weight = 60475.880| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17338 Z= 0.193 Angle : 0.555 5.153 23822 Z= 0.311 Chirality : 0.036 0.144 2968 Planarity : 0.004 0.038 2976 Dihedral : 4.346 23.043 2570 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 1.48 % Allowed : 8.12 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2404 helix: 0.70 (0.12), residues: 1588 sheet: -1.02 (0.50), residues: 100 loop : -1.86 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 692 HIS 0.005 0.001 HIS A 439 PHE 0.016 0.001 PHE A 449 TYR 0.016 0.002 TYR A 661 ARG 0.004 0.001 ARG D 416 Details of bonding type rmsd hydrogen bonds : bond 0.04046 ( 1208) hydrogen bonds : angle 5.01919 ( 3588) covalent geometry : bond 0.00406 (17338) covalent geometry : angle 0.55519 (23822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 273 time to evaluate : 2.570 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: 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: B 446 CYS cc_start: 0.8656 (t) cc_final: 0.8440 (p) REVERT: B 572 MET cc_start: 0.7689 (mmm) cc_final: 0.7260 (tpp) REVERT: B 595 ILE cc_start: 0.9619 (mt) cc_final: 0.9371 (tp) REVERT: A 169 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8854 (ttmm) REVERT: A 221 ILE cc_start: 0.9092 (mt) cc_final: 0.8863 (tt) REVERT: A 561 ASN cc_start: 0.9054 (m-40) cc_final: 0.8753 (m-40) REVERT: C 169 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8848 (ttmm) REVERT: C 221 ILE cc_start: 0.9091 (mt) cc_final: 0.8861 (tt) REVERT: C 553 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9030 (mm) REVERT: C 561 ASN cc_start: 0.9051 (m-40) cc_final: 0.8757 (m-40) REVERT: D 446 CYS cc_start: 0.8654 (t) cc_final: 0.8449 (p) REVERT: D 453 ILE cc_start: 0.9536 (mt) cc_final: 0.9311 (tp) REVERT: D 595 ILE cc_start: 0.9619 (mt) cc_final: 0.9368 (tp) outliers start: 20 outliers final: 10 residues processed: 287 average time/residue: 0.4631 time to fit residues: 218.4382 Evaluate side-chains 240 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 229 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 166 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.101323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085730 restraints weight = 173577.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087930 restraints weight = 97940.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089342 restraints weight = 67503.688| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17338 Z= 0.169 Angle : 0.506 5.101 23822 Z= 0.284 Chirality : 0.035 0.146 2968 Planarity : 0.004 0.038 2976 Dihedral : 4.071 21.096 2570 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.26 % Allowed : 9.08 % Favored : 89.66 % 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: 0.86 (0.17), residues: 2404 helix: 1.71 (0.13), residues: 1568 sheet: -0.92 (0.49), residues: 100 loop : -1.79 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 380 HIS 0.003 0.001 HIS B 284 PHE 0.017 0.001 PHE C 449 TYR 0.013 0.001 TYR C 661 ARG 0.006 0.001 ARG A 693 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1208) hydrogen bonds : angle 4.56263 ( 3588) covalent geometry : bond 0.00356 (17338) covalent geometry : angle 0.50644 (23822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 2.636 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: 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: B 446 CYS cc_start: 0.8946 (t) cc_final: 0.8671 (p) REVERT: B 572 MET cc_start: 0.7705 (mmm) cc_final: 0.7160 (tpp) REVERT: B 593 VAL cc_start: 0.9501 (m) cc_final: 0.9209 (p) REVERT: B 595 ILE cc_start: 0.9647 (mt) cc_final: 0.9409 (tp) REVERT: A 169 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8801 (ttmm) REVERT: A 561 ASN cc_start: 0.9084 (m-40) cc_final: 0.8768 (m-40) REVERT: A 727 ASP cc_start: 0.7839 (m-30) cc_final: 0.7620 (m-30) REVERT: C 169 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8801 (ttmm) REVERT: C 561 ASN cc_start: 0.9090 (m-40) cc_final: 0.8778 (m-40) REVERT: C 727 ASP cc_start: 0.7810 (m-30) cc_final: 0.7606 (m-30) REVERT: D 446 CYS cc_start: 0.8947 (t) cc_final: 0.8676 (p) REVERT: D 593 VAL cc_start: 0.9495 (m) cc_final: 0.9214 (p) REVERT: D 595 ILE cc_start: 0.9651 (mt) cc_final: 0.9414 (tp) outliers start: 17 outliers final: 16 residues processed: 260 average time/residue: 0.4648 time to fit residues: 196.8499 Evaluate side-chains 237 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.104576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089712 restraints weight = 186481.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.092033 restraints weight = 94840.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093482 restraints weight = 60674.068| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17338 Z= 0.168 Angle : 0.499 5.514 23822 Z= 0.277 Chirality : 0.035 0.139 2968 Planarity : 0.003 0.047 2976 Dihedral : 3.952 19.620 2570 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.22 % Allowed : 10.19 % Favored : 87.59 % 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: 1.28 (0.17), residues: 2404 helix: 2.06 (0.13), residues: 1592 sheet: -0.86 (0.48), residues: 100 loop : -1.81 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 692 HIS 0.003 0.001 HIS B 160 PHE 0.013 0.001 PHE C 449 TYR 0.009 0.001 TYR B 451 ARG 0.009 0.001 ARG C 693 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 1208) hydrogen bonds : angle 4.32487 ( 3588) covalent geometry : bond 0.00348 (17338) covalent geometry : angle 0.49877 (23822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 2.703 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: 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: B 446 CYS cc_start: 0.8865 (t) cc_final: 0.8617 (p) REVERT: B 595 ILE cc_start: 0.9681 (mt) cc_final: 0.9426 (tp) REVERT: B 661 TYR cc_start: 0.9399 (t80) cc_final: 0.9123 (t80) REVERT: A 169 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8805 (ttmm) REVERT: A 561 ASN cc_start: 0.8996 (m-40) cc_final: 0.8743 (m-40) REVERT: C 169 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8799 (ttmm) REVERT: C 561 ASN cc_start: 0.8992 (m-40) cc_final: 0.8741 (m-40) REVERT: D 446 CYS cc_start: 0.8864 (t) cc_final: 0.8622 (p) REVERT: D 595 ILE cc_start: 0.9685 (mt) cc_final: 0.9423 (tp) REVERT: D 661 TYR cc_start: 0.9406 (t80) cc_final: 0.9127 (t80) outliers start: 30 outliers final: 18 residues processed: 250 average time/residue: 0.4663 time to fit residues: 191.7285 Evaluate side-chains 230 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.091658 restraints weight = 184927.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093961 restraints weight = 94399.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095519 restraints weight = 60890.441| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17338 Z= 0.108 Angle : 0.452 5.009 23822 Z= 0.247 Chirality : 0.034 0.156 2968 Planarity : 0.003 0.029 2976 Dihedral : 3.688 20.986 2570 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.85 % Allowed : 11.00 % Favored : 87.15 % 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: 1.78 (0.18), residues: 2404 helix: 2.43 (0.13), residues: 1596 sheet: -0.60 (0.50), residues: 100 loop : -1.61 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 692 HIS 0.002 0.001 HIS A 301 PHE 0.012 0.001 PHE C 449 TYR 0.011 0.001 TYR B 661 ARG 0.005 0.000 ARG B 327 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 1208) hydrogen bonds : angle 4.05097 ( 3588) covalent geometry : bond 0.00220 (17338) covalent geometry : angle 0.45229 (23822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 2.612 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: 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: B 595 ILE cc_start: 0.9706 (mt) cc_final: 0.9493 (tp) REVERT: B 661 TYR cc_start: 0.9370 (t80) cc_final: 0.9081 (t80) REVERT: B 677 MET cc_start: 0.8498 (mmm) cc_final: 0.8196 (mmp) REVERT: A 169 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8729 (ttmm) REVERT: A 529 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8455 (tm-30) REVERT: A 561 ASN cc_start: 0.8968 (m-40) cc_final: 0.8737 (m-40) REVERT: C 169 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8719 (ttmm) REVERT: C 529 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8452 (tm-30) REVERT: C 561 ASN cc_start: 0.8968 (m-40) cc_final: 0.8735 (m-40) REVERT: D 572 MET cc_start: 0.7528 (mmm) cc_final: 0.7122 (tpp) REVERT: D 595 ILE cc_start: 0.9705 (mt) cc_final: 0.9490 (tp) REVERT: D 661 TYR cc_start: 0.9371 (t80) cc_final: 0.9080 (t80) REVERT: D 677 MET cc_start: 0.8491 (mmm) cc_final: 0.8251 (mmp) outliers start: 25 outliers final: 23 residues processed: 270 average time/residue: 0.4624 time to fit residues: 204.6241 Evaluate side-chains 244 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 195 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 199 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089923 restraints weight = 186466.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092136 restraints weight = 95358.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093611 restraints weight = 61852.314| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17338 Z= 0.161 Angle : 0.492 7.976 23822 Z= 0.271 Chirality : 0.035 0.157 2968 Planarity : 0.003 0.035 2976 Dihedral : 3.731 19.320 2570 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.70 % Allowed : 12.78 % Favored : 85.52 % 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: 1.76 (0.18), residues: 2404 helix: 2.45 (0.13), residues: 1592 sheet: -0.38 (0.50), residues: 100 loop : -1.72 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.003 0.001 HIS B 160 PHE 0.011 0.001 PHE D 633 TYR 0.009 0.001 TYR B 451 ARG 0.003 0.000 ARG C 693 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 1208) hydrogen bonds : angle 4.13838 ( 3588) covalent geometry : bond 0.00331 (17338) covalent geometry : angle 0.49231 (23822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 2.400 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 ASN cc_start: 0.9050 (m-40) cc_final: 0.8812 (t0) REVERT: B 595 ILE cc_start: 0.9699 (mt) cc_final: 0.9477 (tp) REVERT: B 661 TYR cc_start: 0.9345 (t80) cc_final: 0.9056 (t80) REVERT: B 670 LEU cc_start: 0.9444 (tp) cc_final: 0.9177 (tp) REVERT: A 169 LYS cc_start: 0.9041 (ttmt) cc_final: 0.8736 (ttmm) REVERT: A 529 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 561 ASN cc_start: 0.8968 (m-40) cc_final: 0.8760 (m-40) REVERT: C 169 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8731 (ttmm) REVERT: C 529 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 561 ASN cc_start: 0.8968 (m-40) cc_final: 0.8766 (m-40) REVERT: D 561 ASN cc_start: 0.9058 (m-40) cc_final: 0.8817 (t0) REVERT: D 595 ILE cc_start: 0.9692 (mt) cc_final: 0.9464 (tp) REVERT: D 661 TYR cc_start: 0.9342 (t80) cc_final: 0.9052 (t80) outliers start: 23 outliers final: 22 residues processed: 247 average time/residue: 0.4655 time to fit residues: 194.8202 Evaluate side-chains 238 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 158 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 0.0870 chunk 195 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN C 671 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.099450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083954 restraints weight = 176636.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086245 restraints weight = 94963.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087701 restraints weight = 63788.990| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17338 Z= 0.096 Angle : 0.449 6.974 23822 Z= 0.242 Chirality : 0.034 0.153 2968 Planarity : 0.003 0.028 2976 Dihedral : 3.508 20.777 2570 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.55 % Allowed : 13.66 % Favored : 84.79 % 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: 2.09 (0.18), residues: 2404 helix: 2.70 (0.13), residues: 1592 sheet: -0.34 (0.49), residues: 100 loop : -1.60 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.002 0.000 HIS A 160 PHE 0.011 0.001 PHE D 193 TYR 0.007 0.001 TYR C 565 ARG 0.003 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 1208) hydrogen bonds : angle 3.91378 ( 3588) covalent geometry : bond 0.00196 (17338) covalent geometry : angle 0.44926 (23822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 2.668 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: 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: B 561 ASN cc_start: 0.9010 (m-40) cc_final: 0.8734 (t0) REVERT: B 595 ILE cc_start: 0.9705 (mt) cc_final: 0.9489 (tp) REVERT: B 661 TYR cc_start: 0.9338 (t80) cc_final: 0.9073 (t80) REVERT: A 169 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8746 (ttmm) REVERT: A 529 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 561 ASN cc_start: 0.8926 (m-40) cc_final: 0.8706 (m-40) REVERT: C 169 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8739 (ttmm) REVERT: C 529 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8491 (tm-30) REVERT: C 561 ASN cc_start: 0.8968 (m-40) cc_final: 0.8737 (m-40) REVERT: D 561 ASN cc_start: 0.9011 (m-40) cc_final: 0.8737 (t0) REVERT: D 595 ILE cc_start: 0.9706 (mt) cc_final: 0.9484 (tp) REVERT: D 661 TYR cc_start: 0.9367 (t80) cc_final: 0.9099 (t80) outliers start: 21 outliers final: 21 residues processed: 240 average time/residue: 0.4491 time to fit residues: 182.2799 Evaluate side-chains 233 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 192 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 78 optimal weight: 0.0020 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN C 645 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.099707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.084206 restraints weight = 175058.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.086405 restraints weight = 96292.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.087787 restraints weight = 65657.658| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17338 Z= 0.115 Angle : 0.458 6.954 23822 Z= 0.248 Chirality : 0.034 0.168 2968 Planarity : 0.003 0.028 2976 Dihedral : 3.454 20.003 2570 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.07 % Allowed : 13.59 % Favored : 84.34 % 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: 2.18 (0.18), residues: 2404 helix: 2.77 (0.13), residues: 1600 sheet: -0.23 (0.49), residues: 100 loop : -1.62 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 692 HIS 0.002 0.001 HIS D 160 PHE 0.010 0.001 PHE A 449 TYR 0.008 0.001 TYR B 451 ARG 0.003 0.000 ARG D 363 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 1208) hydrogen bonds : angle 3.88398 ( 3588) covalent geometry : bond 0.00236 (17338) covalent geometry : angle 0.45754 (23822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 2.354 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 561 ASN cc_start: 0.9022 (m-40) cc_final: 0.8743 (t0) REVERT: B 595 ILE cc_start: 0.9708 (mt) cc_final: 0.9503 (tp) REVERT: B 661 TYR cc_start: 0.9338 (t80) cc_final: 0.9059 (t80) REVERT: A 169 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8728 (ttmm) REVERT: A 529 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8500 (tm-30) REVERT: A 561 ASN cc_start: 0.8942 (m-40) cc_final: 0.8727 (m-40) REVERT: C 169 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8729 (ttmm) REVERT: C 529 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8497 (tm-30) REVERT: C 561 ASN cc_start: 0.8942 (m-40) cc_final: 0.8720 (m-40) REVERT: D 561 ASN cc_start: 0.9022 (m-40) cc_final: 0.8748 (t0) REVERT: D 595 ILE cc_start: 0.9706 (mt) cc_final: 0.9491 (tp) REVERT: D 661 TYR cc_start: 0.9366 (t80) cc_final: 0.9079 (t80) outliers start: 28 outliers final: 28 residues processed: 234 average time/residue: 0.4810 time to fit residues: 190.2951 Evaluate side-chains 231 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS A 645 GLN C 523 HIS C 645 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075548 restraints weight = 191615.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077851 restraints weight = 94718.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079340 restraints weight = 59156.505| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17338 Z= 0.166 Angle : 0.499 6.454 23822 Z= 0.275 Chirality : 0.035 0.151 2968 Planarity : 0.003 0.027 2976 Dihedral : 3.636 18.609 2570 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.07 % Allowed : 13.59 % Favored : 84.34 % 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: 2.05 (0.18), residues: 2404 helix: 2.66 (0.13), residues: 1600 sheet: -0.07 (0.49), residues: 100 loop : -1.68 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 521 HIS 0.003 0.001 HIS D 160 PHE 0.012 0.001 PHE D 633 TYR 0.009 0.001 TYR C 565 ARG 0.003 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 1208) hydrogen bonds : angle 4.09407 ( 3588) covalent geometry : bond 0.00342 (17338) covalent geometry : angle 0.49857 (23822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 2.548 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: B 561 ASN cc_start: 0.9053 (m-40) cc_final: 0.8774 (t0) REVERT: A 169 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8746 (ttmm) REVERT: A 529 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 169 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8747 (ttmm) REVERT: C 529 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8473 (tm-30) REVERT: D 561 ASN cc_start: 0.9061 (m-40) cc_final: 0.8800 (t0) REVERT: D 595 ILE cc_start: 0.9683 (mt) cc_final: 0.9478 (tp) outliers start: 28 outliers final: 26 residues processed: 225 average time/residue: 0.6418 time to fit residues: 249.1704 Evaluate side-chains 224 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 204 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076575 restraints weight = 191113.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.078971 restraints weight = 93963.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.080515 restraints weight = 58824.219| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17338 Z= 0.105 Angle : 0.469 7.971 23822 Z= 0.252 Chirality : 0.034 0.197 2968 Planarity : 0.003 0.028 2976 Dihedral : 3.459 18.711 2570 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.99 % Allowed : 13.66 % Favored : 84.34 % 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: 2.24 (0.18), residues: 2404 helix: 2.79 (0.13), residues: 1600 sheet: -0.03 (0.48), residues: 100 loop : -1.55 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 692 HIS 0.002 0.001 HIS C 160 PHE 0.011 0.001 PHE B 193 TYR 0.008 0.001 TYR C 565 ARG 0.003 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 1208) hydrogen bonds : angle 3.91993 ( 3588) covalent geometry : bond 0.00216 (17338) covalent geometry : angle 0.46927 (23822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue MET 173 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue LYS 318 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue LEU 392 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue SER 402 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue THR 421 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 443 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue ILE 505 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 605 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue ILE 644 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue TYR 650 is missing expected H atoms. Skipping. Residue ILE 652 is missing expected H atoms. Skipping. Residue LEU 653 is missing expected H atoms. Skipping. Residue LEU 655 is missing expected H atoms. Skipping. Residue LEU 657 is missing expected H atoms. Skipping. Residue LEU 670 is missing expected H atoms. Skipping. Residue THR 680 is missing expected H atoms. Skipping. Residue VAL 681 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue SER 685 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 722 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Residue SER 747 is missing expected H atoms. Skipping. Residue LEU 749 is missing expected H atoms. Skipping. Residue LEU 119 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 138 is missing expected H atoms. Skipping. Residue VAL 140 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue LEU 145 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue MET 159 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue SER 165 is missing expected H atoms. Skipping. Residue LYS 174 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue THR 217 is missing expected H atoms. Skipping. Residue LYS 246 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue TYR 254 is missing expected H atoms. Skipping. Residue LYS 311 is missing expected H atoms. Skipping. Residue MET 323 is missing expected H atoms. Skipping. Residue THR 335 is missing expected H atoms. Skipping. Residue LYS 350 is missing expected H atoms. Skipping. Residue MET 351 is missing expected H atoms. Skipping. Residue LYS 353 is missing expected H atoms. Skipping. Residue LYS 358 is missing expected H atoms. Skipping. Residue ILE 360 is missing expected H atoms. Skipping. Residue LYS 366 is missing expected H atoms. Skipping. Residue LYS 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue SER 372 is missing expected H atoms. Skipping. Residue LEU 373 is missing expected H atoms. Skipping. Residue SER 374 is missing expected H atoms. Skipping. Residue LYS 376 is missing expected H atoms. Skipping. Residue THR 399 is missing expected H atoms. Skipping. Residue THR 411 is missing expected H atoms. Skipping. Residue ILE 413 is missing expected H atoms. Skipping. Residue MET 419 is missing expected H atoms. Skipping. Residue MET 431 is missing expected H atoms. Skipping. Residue LYS 434 is missing expected H atoms. Skipping. Residue LYS 435 is missing expected H atoms. Skipping. Residue LYS 438 is missing expected H atoms. Skipping. Residue MET 440 is missing expected H atoms. Skipping. Residue LEU 457 is missing expected H atoms. Skipping. Residue LEU 482 is missing expected H atoms. Skipping. Residue LEU 484 is missing expected H atoms. Skipping. Residue LEU 485 is missing expected H atoms. Skipping. Residue MET 488 is missing expected H atoms. Skipping. Residue LEU 491 is missing expected H atoms. Skipping. Residue MET 495 is missing expected H atoms. Skipping. Residue LYS 500 is missing expected H atoms. Skipping. Residue ILE 503 is missing expected H atoms. Skipping. Residue LEU 507 is missing expected H atoms. Skipping. Residue LEU 508 is missing expected H atoms. Skipping. Residue SER 518 is missing expected H atoms. Skipping. Residue ILE 528 is missing expected H atoms. Skipping. Residue ILE 534 is missing expected H atoms. Skipping. Residue LEU 535 is missing expected H atoms. Skipping. Residue LEU 539 is missing expected H atoms. Skipping. Residue LYS 545 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue LEU 553 is missing expected H atoms. Skipping. Residue MET 562 is missing expected H atoms. Skipping. Residue LEU 563 is missing expected H atoms. Skipping. Residue MET 574 is missing expected H atoms. Skipping. Residue MET 578 is missing expected H atoms. Skipping. Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 583 is missing expected H atoms. Skipping. Residue LEU 584 is missing expected H atoms. Skipping. Residue LYS 589 is missing expected H atoms. Skipping. Residue LEU 599 is missing expected H atoms. Skipping. Residue ILE 609 is missing expected H atoms. Skipping. Residue LYS 611 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue LYS 617 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Residue LEU 639 is missing expected H atoms. Skipping. Residue LEU 642 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue VAL 684 is missing expected H atoms. Skipping. Residue LYS 686 is missing expected H atoms. Skipping. Residue ILE 700 is missing expected H atoms. Skipping. Residue LYS 705 is missing expected H atoms. Skipping. Residue MET 717 is missing expected H atoms. Skipping. Residue LYS 738 is missing expected H atoms. Skipping. Residue LYS 743 is missing expected H atoms. Skipping. Residue VAL 746 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 2.534 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: B 561 ASN cc_start: 0.8963 (m-40) cc_final: 0.8741 (t0) REVERT: A 169 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8730 (ttmm) REVERT: A 529 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8490 (tm-30) REVERT: C 169 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8730 (ttmm) REVERT: C 529 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8484 (tm-30) REVERT: D 561 ASN cc_start: 0.8971 (m-40) cc_final: 0.8758 (t0) outliers start: 27 outliers final: 24 residues processed: 224 average time/residue: 0.4406 time to fit residues: 165.5267 Evaluate side-chains 224 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 533 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 67 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 224 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080343 restraints weight = 180152.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082501 restraints weight = 93949.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083994 restraints weight = 61238.005| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17338 Z= 0.094 Angle : 0.465 8.073 23822 Z= 0.246 Chirality : 0.034 0.168 2968 Planarity : 0.002 0.027 2976 Dihedral : 3.339 18.101 2570 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.40 % Allowed : 14.33 % Favored : 84.27 % 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: 2.42 (0.18), residues: 2404 helix: 2.94 (0.13), residues: 1596 sheet: -0.02 (0.48), residues: 100 loop : -1.50 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 380 HIS 0.002 0.000 HIS A 426 PHE 0.011 0.001 PHE B 193 TYR 0.009 0.001 TYR C 565 ARG 0.003 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 1208) hydrogen bonds : angle 3.79660 ( 3588) covalent geometry : bond 0.00195 (17338) covalent geometry : angle 0.46457 (23822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8647.06 seconds wall clock time: 151 minutes 26.96 seconds (9086.96 seconds total)