Starting phenix.real_space_refine on Mon Aug 25 23:52:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mhx_9121/08_2025/6mhx_9121.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mhx_9121/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mhx_9121/08_2025/6mhx_9121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mhx_9121/08_2025/6mhx_9121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mhx_9121/08_2025/6mhx_9121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mhx_9121/08_2025/6mhx_9121.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 15, 'GLU:plan': 39, 'GLN:plan1': 9, 'ASP:plan': 21, 'ASN:plan1': 7, 'PHE:plan': 6, 'TYR:plan': 1, 'HIS:plan': 2, 'TRP:plan': 1} 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: {'ARG:plan': 15, 'GLU:plan': 41, 'GLN:plan1': 9, 'ASP:plan': 19, 'PHE:plan': 8, 'ASN:plan1': 12, 'TYR:plan': 2, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 444 Restraints were copied for chains: D, C Time building chain proxies: 15.48, per 1000 atoms: 0.49 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: 2.23 Conformation dependent library (CDL) restraints added in 918.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.83 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: 5.99 Time building geometry restraints manager: 3.03 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: 0.04 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: 1.840 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 35.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- 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 : 6.90 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG D 716 TYR 0.011 0.001 TYR B 650 PHE 0.032 0.002 PHE B 597 TRP 0.016 0.002 TRP B 559 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00436 (17338) covalent geometry : angle 0.67028 (23822) hydrogen bonds : bond 0.14764 ( 1208) hydrogen bonds : angle 6.60648 ( 3588) *********************** 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 : 0.539 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: symmetry clash revert: symmetry clash REVERT: B 572 MET cc_start: 0.7750 (mmm) cc_final: 0.7499 (mmm) REVERT: A 169 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8722 (ttmm) REVERT: A 557 LEU cc_start: 0.9412 (tp) cc_final: 0.9141 (mm) REVERT: A 561 ASN cc_start: 0.8984 (m-40) cc_final: 0.8768 (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: 0.8715 (ttmm) REVERT: C 557 LEU cc_start: 0.9414 (tp) cc_final: 0.9144 (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: 0.7925 (p) outliers start: 4 outliers final: 0 residues processed: 462 average time/residue: 0.2232 time to fit residues: 157.2221 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 : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN A 330 ASN A 645 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 ASN C 439 HIS C 645 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087812 restraints weight = 176015.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089951 restraints weight = 98563.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091457 restraints weight = 67618.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.092486 restraints weight = 52439.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093123 restraints weight = 43944.550| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17338 Z= 0.167 Angle : 0.535 5.030 23822 Z= 0.298 Chirality : 0.036 0.147 2968 Planarity : 0.004 0.039 2976 Dihedral : 4.277 21.949 2570 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 1.77 % Allowed : 7.68 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2404 helix: 0.83 (0.12), residues: 1584 sheet: -0.97 (0.50), residues: 100 loop : -1.80 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 416 TYR 0.011 0.001 TYR A 661 PHE 0.018 0.001 PHE A 449 TRP 0.012 0.001 TRP D 692 HIS 0.005 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00347 (17338) covalent geometry : angle 0.53455 (23822) hydrogen bonds : bond 0.03962 ( 1208) hydrogen bonds : angle 4.95650 ( 3588) *********************** 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 300 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.636 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: B 351 MET cc_start: 0.8671 (mmm) cc_final: 0.8430 (mmm) REVERT: B 453 ILE cc_start: 0.9527 (mt) cc_final: 0.9297 (tp) REVERT: B 572 MET cc_start: 0.7706 (mmm) cc_final: 0.7208 (tpp) REVERT: A 169 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8779 (ttmm) REVERT: A 221 ILE cc_start: 0.9070 (mt) cc_final: 0.8834 (tt) REVERT: A 561 ASN cc_start: 0.9065 (m-40) cc_final: 0.8725 (m-40) REVERT: C 169 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8777 (ttmm) REVERT: C 221 ILE cc_start: 0.9062 (mt) cc_final: 0.8828 (tt) REVERT: C 553 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8988 (mm) REVERT: C 561 ASN cc_start: 0.9070 (m-40) cc_final: 0.8731 (m-40) REVERT: D 351 MET cc_start: 0.8675 (mmm) cc_final: 0.8433 (mmm) REVERT: D 453 ILE cc_start: 0.9528 (mt) cc_final: 0.9302 (tp) outliers start: 24 outliers final: 10 residues processed: 293 average time/residue: 0.1836 time to fit residues: 89.3962 Evaluate side-chains 249 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 238 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 198 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 178 ASN A 313 GLN A 645 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN C 313 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075486 restraints weight = 192566.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077758 restraints weight = 97388.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.079237 restraints weight = 61514.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080201 restraints weight = 45273.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.080825 restraints weight = 36855.020| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17338 Z= 0.277 Angle : 0.629 6.616 23822 Z= 0.357 Chirality : 0.038 0.159 2968 Planarity : 0.005 0.053 2976 Dihedral : 4.611 23.530 2570 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.62 % Allowed : 9.31 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.16), residues: 2404 helix: 1.07 (0.12), residues: 1592 sheet: -1.13 (0.49), residues: 100 loop : -2.01 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 693 TYR 0.015 0.002 TYR A 575 PHE 0.017 0.002 PHE C 449 TRP 0.018 0.002 TRP D 692 HIS 0.006 0.002 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00582 (17338) covalent geometry : angle 0.62861 (23822) hydrogen bonds : bond 0.04354 ( 1208) hydrogen bonds : angle 5.01756 ( 3588) *********************** 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 255 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.576 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 451 TYR cc_start: 0.9507 (OUTLIER) cc_final: 0.9028 (t80) REVERT: B 572 MET cc_start: 0.7828 (mmm) cc_final: 0.7391 (tpp) REVERT: A 561 ASN cc_start: 0.9030 (m-40) cc_final: 0.8792 (m-40) REVERT: A 672 MET cc_start: 0.9326 (ppp) cc_final: 0.9106 (tmm) REVERT: C 561 ASN cc_start: 0.9017 (m-40) cc_final: 0.8779 (m-40) REVERT: C 672 MET cc_start: 0.9338 (ppp) cc_final: 0.9098 (tmm) REVERT: D 451 TYR cc_start: 0.9504 (OUTLIER) cc_final: 0.9022 (t80) REVERT: D 670 LEU cc_start: 0.9483 (tp) cc_final: 0.9219 (tp) outliers start: 22 outliers final: 16 residues processed: 250 average time/residue: 0.1947 time to fit residues: 79.9955 Evaluate side-chains 228 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 451 TYR 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 496 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 639 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 446 CYS Chi-restraints excluded: chain D residue 451 TYR 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 61 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 671 ASN A 178 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089945 restraints weight = 186129.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.092204 restraints weight = 94577.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093722 restraints weight = 60627.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094703 restraints weight = 45024.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.095395 restraints weight = 36899.314| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17338 Z= 0.154 Angle : 0.496 5.096 23822 Z= 0.278 Chirality : 0.035 0.135 2968 Planarity : 0.003 0.040 2976 Dihedral : 4.127 23.416 2570 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.85 % Allowed : 10.34 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.17), residues: 2404 helix: 1.77 (0.13), residues: 1596 sheet: -1.05 (0.46), residues: 100 loop : -1.92 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 693 TYR 0.010 0.001 TYR D 451 PHE 0.012 0.001 PHE C 449 TRP 0.013 0.001 TRP D 692 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00312 (17338) covalent geometry : angle 0.49564 (23822) hydrogen bonds : bond 0.03578 ( 1208) hydrogen bonds : angle 4.44321 ( 3588) *********************** 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 252 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.874 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: B 572 MET cc_start: 0.7715 (mmm) cc_final: 0.7170 (tpp) REVERT: A 169 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8802 (ttmm) REVERT: A 561 ASN cc_start: 0.8963 (m-40) cc_final: 0.8740 (m-40) REVERT: C 169 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8736 (ttmm) REVERT: C 561 ASN cc_start: 0.8954 (m-40) cc_final: 0.8740 (m-40) outliers start: 25 outliers final: 23 residues processed: 247 average time/residue: 0.1850 time to fit residues: 74.8195 Evaluate side-chains 233 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 B residue 734 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 ASN 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 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 446 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3536 r_free = 0.3536 target = 0.103603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088914 restraints weight = 190529.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091164 restraints weight = 98987.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.092630 restraints weight = 64481.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.093595 restraints weight = 48913.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.094161 restraints weight = 40785.188| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17338 Z= 0.195 Angle : 0.521 5.081 23822 Z= 0.292 Chirality : 0.035 0.166 2968 Planarity : 0.003 0.049 2976 Dihedral : 4.093 21.190 2570 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.14 % Allowed : 11.23 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2404 helix: 1.92 (0.13), residues: 1596 sheet: -0.89 (0.47), residues: 100 loop : -1.96 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 693 TYR 0.011 0.001 TYR B 451 PHE 0.012 0.001 PHE A 259 TRP 0.012 0.001 TRP D 692 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00402 (17338) covalent geometry : angle 0.52117 (23822) hydrogen bonds : bond 0.03539 ( 1208) hydrogen bonds : angle 4.44997 ( 3588) *********************** 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 246 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.149 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: B 351 MET cc_start: 0.8654 (mmm) cc_final: 0.8276 (mmm) REVERT: B 451 TYR cc_start: 0.9486 (OUTLIER) cc_final: 0.8948 (t80) REVERT: B 661 TYR cc_start: 0.9430 (t80) cc_final: 0.9153 (t80) REVERT: A 169 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8732 (ttmm) REVERT: A 529 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 169 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8726 (ttmm) REVERT: D 351 MET cc_start: 0.8624 (mmm) cc_final: 0.8257 (mmm) REVERT: D 451 TYR cc_start: 0.9485 (OUTLIER) cc_final: 0.8849 (t80) REVERT: D 572 MET cc_start: 0.7341 (mmm) cc_final: 0.6872 (tpp) REVERT: D 661 TYR cc_start: 0.9429 (t80) cc_final: 0.9157 (t80) outliers start: 29 outliers final: 20 residues processed: 241 average time/residue: 0.1928 time to fit residues: 78.4365 Evaluate side-chains 229 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 451 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL 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 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 266 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 446 CYS Chi-restraints excluded: chain D residue 451 TYR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3553 r_free = 0.3553 target = 0.104419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089477 restraints weight = 187321.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.091743 restraints weight = 97578.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093209 restraints weight = 63974.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094210 restraints weight = 48688.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.094850 restraints weight = 40591.015| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17338 Z= 0.129 Angle : 0.471 5.039 23822 Z= 0.260 Chirality : 0.034 0.159 2968 Planarity : 0.003 0.030 2976 Dihedral : 3.817 19.474 2570 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.99 % Allowed : 12.33 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.18), residues: 2404 helix: 2.33 (0.13), residues: 1592 sheet: -0.58 (0.48), residues: 100 loop : -1.87 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 693 TYR 0.012 0.001 TYR D 661 PHE 0.010 0.001 PHE A 449 TRP 0.010 0.001 TRP B 692 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00259 (17338) covalent geometry : angle 0.47121 (23822) hydrogen bonds : bond 0.03232 ( 1208) hydrogen bonds : angle 4.16962 ( 3588) *********************** 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 261 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.828 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: B 351 MET cc_start: 0.8666 (mmm) cc_final: 0.8298 (mmm) REVERT: B 561 ASN cc_start: 0.9047 (m-40) cc_final: 0.8772 (t0) REVERT: B 661 TYR cc_start: 0.9364 (t80) cc_final: 0.9053 (t80) REVERT: B 677 MET cc_start: 0.8346 (mmm) cc_final: 0.8124 (mmp) REVERT: A 169 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8707 (ttmm) REVERT: A 529 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8456 (tm-30) REVERT: C 169 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8702 (ttmm) REVERT: C 529 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8474 (tm-30) REVERT: D 351 MET cc_start: 0.8651 (mmm) cc_final: 0.8294 (mmm) REVERT: D 561 ASN cc_start: 0.9048 (m-40) cc_final: 0.8776 (t0) REVERT: D 572 MET cc_start: 0.7404 (mmm) cc_final: 0.6863 (tpp) REVERT: D 661 TYR cc_start: 0.9367 (t80) cc_final: 0.9060 (t80) outliers start: 27 outliers final: 22 residues processed: 252 average time/residue: 0.1965 time to fit residues: 83.4324 Evaluate side-chains 237 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 B residue 734 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 216 GLN 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 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 446 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 523 HIS C 523 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.088302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074381 restraints weight = 194479.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076665 restraints weight = 97653.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078144 restraints weight = 62194.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079122 restraints weight = 46178.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079571 restraints weight = 37826.461| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17338 Z= 0.192 Angle : 0.524 8.047 23822 Z= 0.292 Chirality : 0.035 0.179 2968 Planarity : 0.003 0.031 2976 Dihedral : 3.969 19.225 2570 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.14 % Allowed : 13.00 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.17), residues: 2404 helix: 2.14 (0.13), residues: 1604 sheet: -0.56 (0.46), residues: 100 loop : -1.94 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 363 TYR 0.009 0.001 TYR B 451 PHE 0.014 0.001 PHE D 633 TRP 0.010 0.001 TRP B 692 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00395 (17338) covalent geometry : angle 0.52428 (23822) hydrogen bonds : bond 0.03368 ( 1208) hydrogen bonds : angle 4.32818 ( 3588) *********************** 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 235 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.916 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 351 MET cc_start: 0.8723 (mmm) cc_final: 0.8390 (mmm) REVERT: B 561 ASN cc_start: 0.9162 (m-40) cc_final: 0.8807 (t0) REVERT: B 677 MET cc_start: 0.8359 (mmm) cc_final: 0.8097 (mmp) REVERT: A 169 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8773 (ttmm) REVERT: A 529 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8507 (tm-30) REVERT: C 169 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8780 (ttmm) REVERT: C 529 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8522 (tm-30) REVERT: D 351 MET cc_start: 0.8716 (mmm) cc_final: 0.8395 (mmm) REVERT: D 561 ASN cc_start: 0.9165 (m-40) cc_final: 0.8806 (t0) REVERT: D 572 MET cc_start: 0.7473 (mmm) cc_final: 0.6947 (tpp) REVERT: D 661 TYR cc_start: 0.9341 (t80) cc_final: 0.9030 (t80) outliers start: 29 outliers final: 22 residues processed: 226 average time/residue: 0.2068 time to fit residues: 79.3612 Evaluate side-chains 219 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 577 VAL 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 591 LEU Chi-restraints excluded: chain D residue 637 ILE 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 107 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 127 optimal weight: 0.0870 chunk 146 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3494 r_free = 0.3494 target = 0.088624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.074723 restraints weight = 194235.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.077009 restraints weight = 97136.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078507 restraints weight = 61642.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079245 restraints weight = 45626.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.079900 restraints weight = 38542.070| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17338 Z= 0.167 Angle : 0.506 5.476 23822 Z= 0.279 Chirality : 0.035 0.179 2968 Planarity : 0.003 0.029 2976 Dihedral : 3.882 19.510 2570 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.36 % Allowed : 12.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.17), residues: 2404 helix: 2.30 (0.13), residues: 1600 sheet: -0.44 (0.47), residues: 100 loop : -1.88 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 693 TYR 0.009 0.001 TYR B 661 PHE 0.012 0.001 PHE A 259 TRP 0.010 0.001 TRP B 692 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00338 (17338) covalent geometry : angle 0.50633 (23822) hydrogen bonds : bond 0.03266 ( 1208) hydrogen bonds : angle 4.26555 ( 3588) *********************** 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 232 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.907 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 351 MET cc_start: 0.8783 (mmm) cc_final: 0.8404 (mmm) REVERT: B 451 TYR cc_start: 0.9484 (OUTLIER) cc_final: 0.8745 (t80) REVERT: B 561 ASN cc_start: 0.9127 (m-40) cc_final: 0.8805 (t0) REVERT: B 661 TYR cc_start: 0.9392 (t80) cc_final: 0.9138 (t80) REVERT: B 677 MET cc_start: 0.8305 (mmm) cc_final: 0.8041 (mmp) REVERT: A 169 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8787 (ttmm) REVERT: A 529 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8526 (tm-30) REVERT: C 169 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8779 (ttmm) REVERT: C 529 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 351 MET cc_start: 0.8772 (mmm) cc_final: 0.8400 (mmm) REVERT: D 451 TYR cc_start: 0.9485 (OUTLIER) cc_final: 0.8741 (t80) REVERT: D 561 ASN cc_start: 0.9121 (m-40) cc_final: 0.8803 (t0) outliers start: 32 outliers final: 25 residues processed: 225 average time/residue: 0.2077 time to fit residues: 79.4600 Evaluate side-chains 226 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 451 TYR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 571 SER 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 216 GLN 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 216 GLN 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 173 MET 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 451 TYR Chi-restraints excluded: chain D residue 541 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.073712 restraints weight = 194711.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075963 restraints weight = 97540.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077406 restraints weight = 62063.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078388 restraints weight = 46261.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078821 restraints weight = 37929.628| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.6601 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= 0.210 Angle : 0.542 5.113 23822 Z= 0.302 Chirality : 0.036 0.189 2968 Planarity : 0.003 0.031 2976 Dihedral : 4.049 19.221 2570 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.14 % Allowed : 12.85 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.17), residues: 2404 helix: 2.06 (0.13), residues: 1604 sheet: -0.48 (0.47), residues: 100 loop : -1.93 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 363 TYR 0.010 0.001 TYR B 451 PHE 0.014 0.001 PHE C 259 TRP 0.010 0.001 TRP C 692 HIS 0.004 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00428 (17338) covalent geometry : angle 0.54248 (23822) hydrogen bonds : bond 0.03429 ( 1208) hydrogen bonds : angle 4.42230 ( 3588) *********************** 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 235 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.865 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 351 MET cc_start: 0.8798 (mmm) cc_final: 0.8461 (mmm) REVERT: B 451 TYR cc_start: 0.9521 (OUTLIER) cc_final: 0.8775 (t80) REVERT: B 561 ASN cc_start: 0.9201 (m-40) cc_final: 0.8853 (t0) REVERT: B 661 TYR cc_start: 0.9327 (t80) cc_final: 0.9039 (t80) REVERT: A 169 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8812 (ttmm) REVERT: A 529 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8554 (tm-30) REVERT: C 169 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8756 (ttmm) REVERT: C 529 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 351 MET cc_start: 0.8794 (mmm) cc_final: 0.8459 (mmm) REVERT: D 451 TYR cc_start: 0.9522 (OUTLIER) cc_final: 0.8781 (t80) REVERT: D 561 ASN cc_start: 0.9205 (m-40) cc_final: 0.8850 (t0) outliers start: 29 outliers final: 20 residues processed: 228 average time/residue: 0.2042 time to fit residues: 79.2661 Evaluate side-chains 223 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 451 TYR Chi-restraints excluded: chain B residue 571 SER 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 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 636 THR Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 173 MET 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 451 TYR 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 148 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 221 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074846 restraints weight = 184206.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077095 restraints weight = 91905.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078625 restraints weight = 58026.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079617 restraints weight = 42440.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080265 restraints weight = 34500.094| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17338 Z= 0.114 Angle : 0.479 5.716 23822 Z= 0.259 Chirality : 0.035 0.187 2968 Planarity : 0.003 0.029 2976 Dihedral : 3.714 18.941 2570 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.92 % Allowed : 13.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2404 helix: 2.51 (0.13), residues: 1596 sheet: -0.27 (0.47), residues: 100 loop : -1.78 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 693 TYR 0.009 0.001 TYR C 565 PHE 0.010 0.001 PHE D 193 TRP 0.010 0.001 TRP B 692 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00235 (17338) covalent geometry : angle 0.47943 (23822) hydrogen bonds : bond 0.03120 ( 1208) hydrogen bonds : angle 4.07609 ( 3588) ********************** 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 241 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.752 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: B 351 MET cc_start: 0.8872 (mmm) cc_final: 0.8467 (mmm) REVERT: B 451 TYR cc_start: 0.9515 (OUTLIER) cc_final: 0.8761 (t80) REVERT: B 561 ASN cc_start: 0.9147 (m-40) cc_final: 0.8818 (t0) REVERT: A 169 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8814 (ttmm) REVERT: A 529 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 169 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8802 (ttmm) REVERT: C 529 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8513 (tm-30) REVERT: D 351 MET cc_start: 0.8871 (mmm) cc_final: 0.8474 (mmm) REVERT: D 451 TYR cc_start: 0.9514 (OUTLIER) cc_final: 0.8751 (t80) REVERT: D 561 ASN cc_start: 0.9158 (m-40) cc_final: 0.8824 (t0) outliers start: 26 outliers final: 20 residues processed: 234 average time/residue: 0.2016 time to fit residues: 79.6210 Evaluate side-chains 226 residues out of total 2152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 451 TYR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain C residue 216 GLN 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 451 TYR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 756 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 63 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.087550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.073688 restraints weight = 186273.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.075914 restraints weight = 93041.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077382 restraints weight = 58802.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078352 restraints weight = 43254.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078990 restraints weight = 35312.776| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17338 Z= 0.190 Angle : 0.523 6.083 23822 Z= 0.291 Chirality : 0.036 0.204 2968 Planarity : 0.003 0.031 2976 Dihedral : 3.847 18.917 2570 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.77 % Allowed : 14.03 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.17), residues: 2404 helix: 2.34 (0.13), residues: 1600 sheet: -0.33 (0.47), residues: 100 loop : -1.84 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 363 TYR 0.009 0.001 TYR D 451 PHE 0.013 0.001 PHE B 633 TRP 0.008 0.001 TRP B 493 HIS 0.003 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00388 (17338) covalent geometry : angle 0.52253 (23822) hydrogen bonds : bond 0.03258 ( 1208) hydrogen bonds : angle 4.29507 ( 3588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3979.85 seconds wall clock time: 68 minutes 44.83 seconds (4124.83 seconds total)