Starting phenix.real_space_refine on Sat Mar 7 10:01:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k5c_22680/03_2026/7k5c_22680.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k5c_22680/03_2026/7k5c_22680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k5c_22680/03_2026/7k5c_22680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k5c_22680/03_2026/7k5c_22680.map" model { file = "/net/cci-nas-00/data/ceres_data/7k5c_22680/03_2026/7k5c_22680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k5c_22680/03_2026/7k5c_22680.cif" } resolution = 2.7 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= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 204 5.16 5 C 25632 2.51 5 N 7242 2.21 5 O 8469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 312 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41547 Number of models: 1 Model: "" Number of chains: 14 Chain: "H" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5160 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 628} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1728 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: A, C, E, I, K, B, D, F, J, L Time building chain proxies: 6.52, per 1000 atoms: 0.16 Number of scatterers: 41547 At special positions: 0 Unit cell: (146.88, 163.08, 236.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 204 16.00 O 8469 8.00 N 7242 7.00 C 25632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9840 Finding SS restraints... Secondary structure from input PDB file: 276 helices and 18 sheets defined 72.5% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'H' and resid 57 through 77 removed outlier: 3.547A pdb=" N LYS H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASN H 88 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP H 119 " --> pdb=" O LEU H 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL H 120 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA H 147 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 169 Processing helix chain 'H' and resid 170 through 203 removed outlier: 3.618A pdb=" N PHE H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 214 through 232 removed outlier: 3.974A pdb=" N ALA H 218 " --> pdb=" O ARG H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 252 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 278 through 282 Processing helix chain 'H' and resid 283 through 297 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 302 through 317 removed outlier: 3.604A pdb=" N ASN H 306 " --> pdb=" O ASP H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 337 Processing helix chain 'H' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP H 351 " --> pdb=" O PRO H 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 352 " --> pdb=" O GLN H 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA H 369 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER H 380 " --> pdb=" O ASP H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 407 removed outlier: 3.668A pdb=" N MET H 407 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET H 421 " --> pdb=" O LYS H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 453 Processing helix chain 'H' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR H 465 " --> pdb=" O THR H 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET H 466 " --> pdb=" O ALA H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 500 Processing helix chain 'H' and resid 500 through 508 removed outlier: 3.563A pdb=" N ILE H 504 " --> pdb=" O ASP H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 525 Processing helix chain 'H' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE H 531 " --> pdb=" O ASP H 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS H 540 " --> pdb=" O ARG H 536 " (cutoff:3.500A) Processing helix chain 'H' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE H 547 " --> pdb=" O LYS H 543 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU H 548 " --> pdb=" O GLU H 544 " (cutoff:3.500A) Processing helix chain 'H' and resid 562 through 567 Processing helix chain 'H' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER H 575 " --> pdb=" O SER H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 589 through 603 Processing helix chain 'H' and resid 624 through 626 No H-bonds generated for 'chain 'H' and resid 624 through 626' Processing helix chain 'H' and resid 631 through 633 No H-bonds generated for 'chain 'H' and resid 631 through 633' Processing helix chain 'H' and resid 634 through 653 removed outlier: 3.545A pdb=" N LYS H 647 " --> pdb=" O GLU H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 685 through 705 Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP G 5 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G 6 " --> pdb=" O LYS G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 15 through 24 Processing helix chain 'G' and resid 26 through 39 Processing helix chain 'G' and resid 57 through 64 Processing helix chain 'G' and resid 78 through 96 removed outlier: 3.737A pdb=" N ALA G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 106 through 111 removed outlier: 3.745A pdb=" N GLN G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 126 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'G' and resid 132 through 141 Processing helix chain 'G' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 205 through 214 Processing helix chain 'G' and resid 217 through 226 Processing helix chain 'A' and resid 58 through 77 removed outlier: 3.547A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASN A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 148 " --> pdb=" O GLN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 170 through 203 removed outlier: 3.620A pdb=" N PHE A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 252 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.602A pdb=" N ASN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 Processing helix chain 'A' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.668A pdb=" N MET A 407 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 453 Processing helix chain 'A' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.562A pdb=" N ILE A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 548 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 603 Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 653 removed outlier: 3.546A pdb=" N LYS A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 705 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP B 5 " --> pdb=" O ASP B 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 6 " --> pdb=" O LYS B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.697A pdb=" N GLU B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'C' and resid 58 through 77 removed outlier: 3.547A pdb=" N LYS C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.770A pdb=" N ASN C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 152 removed outlier: 3.784A pdb=" N ALA C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA C 218 " --> pdb=" O ARG C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 252 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 302 through 317 removed outlier: 3.603A pdb=" N ASN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 Processing helix chain 'C' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP C 351 " --> pdb=" O PRO C 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C 380 " --> pdb=" O ASP C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.669A pdb=" N MET C 407 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 434 removed outlier: 3.639A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 453 Processing helix chain 'C' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 500 Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.561A pdb=" N ILE C 504 " --> pdb=" O ASP C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE C 531 " --> pdb=" O ASP C 527 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 540 " --> pdb=" O ARG C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 603 Processing helix chain 'C' and resid 624 through 626 No H-bonds generated for 'chain 'C' and resid 624 through 626' Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 634 through 653 removed outlier: 3.545A pdb=" N LYS C 647 " --> pdb=" O GLU C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 705 Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP D 5 " --> pdb=" O ASP D 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS D 6 " --> pdb=" O LYS D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 6' Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 126 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.697A pdb=" N GLU D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 217 through 226 Processing helix chain 'E' and resid 58 through 77 removed outlier: 3.546A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 removed outlier: 3.771A pdb=" N ASN E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 120 " --> pdb=" O VAL E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS E 148 " --> pdb=" O GLN E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'E' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA E 218 " --> pdb=" O ARG E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 252 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 283 through 297 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 302 through 317 removed outlier: 3.603A pdb=" N ASN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 Processing helix chain 'E' and resid 346 through 396 removed outlier: 3.680A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 369 " --> pdb=" O ALA E 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.668A pdb=" N MET E 407 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 453 Processing helix chain 'E' and resid 457 through 481 removed outlier: 3.763A pdb=" N THR E 465 " --> pdb=" O THR E 461 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 500 Processing helix chain 'E' and resid 500 through 508 removed outlier: 3.562A pdb=" N ILE E 504 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 527 through 540 removed outlier: 4.280A pdb=" N ILE E 531 " --> pdb=" O ASP E 527 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS E 540 " --> pdb=" O ARG E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU E 548 " --> pdb=" O GLU E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 603 Processing helix chain 'E' and resid 624 through 626 No H-bonds generated for 'chain 'E' and resid 624 through 626' Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 634 through 653 removed outlier: 3.545A pdb=" N LYS E 647 " --> pdb=" O GLU E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 705 Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.558A pdb=" N ASP F 5 " --> pdb=" O ASP F 2 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS F 6 " --> pdb=" O LYS F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 15 through 24 Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 105 No H-bonds generated for 'chain 'F' and resid 103 through 105' Processing helix chain 'F' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 132 through 141 Processing helix chain 'F' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 205 through 214 Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'I' and resid 58 through 77 removed outlier: 3.547A pdb=" N LYS I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 removed outlier: 3.769A pdb=" N ASN I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 127 removed outlier: 3.722A pdb=" N ASP I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL I 120 " --> pdb=" O VAL I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 152 removed outlier: 3.783A pdb=" N ALA I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS I 148 " --> pdb=" O GLN I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 213 Processing helix chain 'I' and resid 214 through 232 removed outlier: 3.976A pdb=" N ALA I 218 " --> pdb=" O ARG I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 252 Processing helix chain 'I' and resid 256 through 265 Processing helix chain 'I' and resid 278 through 282 Processing helix chain 'I' and resid 283 through 297 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 302 through 317 removed outlier: 3.602A pdb=" N ASN I 306 " --> pdb=" O ASP I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 337 Processing helix chain 'I' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP I 351 " --> pdb=" O PRO I 347 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA I 369 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER I 380 " --> pdb=" O ASP I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 407 removed outlier: 3.669A pdb=" N MET I 407 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET I 421 " --> pdb=" O LYS I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 453 Processing helix chain 'I' and resid 457 through 481 removed outlier: 3.762A pdb=" N THR I 465 " --> pdb=" O THR I 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET I 466 " --> pdb=" O ALA I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 500 Processing helix chain 'I' and resid 500 through 508 removed outlier: 3.562A pdb=" N ILE I 504 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 525 Processing helix chain 'I' and resid 527 through 540 removed outlier: 4.279A pdb=" N ILE I 531 " --> pdb=" O ASP I 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS I 540 " --> pdb=" O ARG I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 542 through 559 removed outlier: 3.600A pdb=" N PHE I 547 " --> pdb=" O LYS I 543 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU I 548 " --> pdb=" O GLU I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 567 Processing helix chain 'I' and resid 569 through 587 removed outlier: 3.797A pdb=" N SER I 575 " --> pdb=" O SER I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 603 Processing helix chain 'I' and resid 624 through 626 No H-bonds generated for 'chain 'I' and resid 624 through 626' Processing helix chain 'I' and resid 631 through 633 No H-bonds generated for 'chain 'I' and resid 631 through 633' Processing helix chain 'I' and resid 634 through 653 removed outlier: 3.546A pdb=" N LYS I 647 " --> pdb=" O GLU I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 685 through 705 Processing helix chain 'J' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP J 5 " --> pdb=" O ASP J 2 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS J 6 " --> pdb=" O LYS J 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 2 through 6' Processing helix chain 'J' and resid 15 through 24 Processing helix chain 'J' and resid 26 through 39 Processing helix chain 'J' and resid 57 through 64 Processing helix chain 'J' and resid 78 through 96 removed outlier: 3.738A pdb=" N ALA J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 105 No H-bonds generated for 'chain 'J' and resid 103 through 105' Processing helix chain 'J' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN J 110 " --> pdb=" O LEU J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 126 Processing helix chain 'J' and resid 127 through 131 Processing helix chain 'J' and resid 132 through 141 Processing helix chain 'J' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU J 155 " --> pdb=" O ALA J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 205 through 214 Processing helix chain 'J' and resid 217 through 226 Processing helix chain 'K' and resid 58 through 77 removed outlier: 3.546A pdb=" N LYS K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.771A pdb=" N ASN K 88 " --> pdb=" O ARG K 84 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 127 removed outlier: 3.721A pdb=" N ASP K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 152 removed outlier: 3.782A pdb=" N ALA K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS K 148 " --> pdb=" O GLN K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 170 through 203 removed outlier: 3.619A pdb=" N PHE K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'K' and resid 214 through 232 removed outlier: 3.975A pdb=" N ALA K 218 " --> pdb=" O ARG K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 252 Processing helix chain 'K' and resid 256 through 265 Processing helix chain 'K' and resid 278 through 282 Processing helix chain 'K' and resid 283 through 297 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 302 through 317 removed outlier: 3.602A pdb=" N ASN K 306 " --> pdb=" O ASP K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 337 Processing helix chain 'K' and resid 346 through 396 removed outlier: 3.681A pdb=" N TRP K 351 " --> pdb=" O PRO K 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 352 " --> pdb=" O GLN K 348 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER K 380 " --> pdb=" O ASP K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 removed outlier: 3.669A pdb=" N MET K 407 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 434 removed outlier: 3.638A pdb=" N MET K 421 " --> pdb=" O LYS K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 453 Processing helix chain 'K' and resid 457 through 481 removed outlier: 3.762A pdb=" N THR K 465 " --> pdb=" O THR K 461 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET K 466 " --> pdb=" O ALA K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 500 Processing helix chain 'K' and resid 500 through 508 removed outlier: 3.561A pdb=" N ILE K 504 " --> pdb=" O ASP K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 525 Processing helix chain 'K' and resid 527 through 540 removed outlier: 4.279A pdb=" N ILE K 531 " --> pdb=" O ASP K 527 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS K 540 " --> pdb=" O ARG K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 542 through 559 removed outlier: 3.601A pdb=" N PHE K 547 " --> pdb=" O LYS K 543 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU K 548 " --> pdb=" O GLU K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 567 Processing helix chain 'K' and resid 569 through 587 removed outlier: 3.798A pdb=" N SER K 575 " --> pdb=" O SER K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 589 through 603 Processing helix chain 'K' and resid 624 through 626 No H-bonds generated for 'chain 'K' and resid 624 through 626' Processing helix chain 'K' and resid 631 through 633 No H-bonds generated for 'chain 'K' and resid 631 through 633' Processing helix chain 'K' and resid 634 through 653 removed outlier: 3.546A pdb=" N LYS K 647 " --> pdb=" O GLU K 643 " (cutoff:3.500A) Processing helix chain 'K' and resid 685 through 705 Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.557A pdb=" N ASP L 5 " --> pdb=" O ASP L 2 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS L 6 " --> pdb=" O LYS L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'L' and resid 15 through 24 Processing helix chain 'L' and resid 26 through 39 Processing helix chain 'L' and resid 57 through 64 Processing helix chain 'L' and resid 78 through 96 removed outlier: 3.737A pdb=" N ALA L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 105 No H-bonds generated for 'chain 'L' and resid 103 through 105' Processing helix chain 'L' and resid 106 through 111 removed outlier: 3.744A pdb=" N GLN L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 126 Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'L' and resid 132 through 141 Processing helix chain 'L' and resid 150 through 156 removed outlier: 3.696A pdb=" N GLU L 155 " --> pdb=" O ALA L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 205 through 214 Processing helix chain 'L' and resid 217 through 226 Processing sheet with id=AA1, first strand: chain 'H' and resid 268 through 271 Processing sheet with id=AA2, first strand: chain 'H' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY H 619 " --> pdb=" O PHE H 608 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 662 through 666 Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 271 Processing sheet with id=AA5, first strand: chain 'A' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY A 619 " --> pdb=" O PHE A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 662 through 666 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY C 619 " --> pdb=" O PHE C 608 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 662 through 666 Processing sheet with id=AB1, first strand: chain 'E' and resid 268 through 271 Processing sheet with id=AB2, first strand: chain 'E' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY E 619 " --> pdb=" O PHE E 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 662 through 666 Processing sheet with id=AB4, first strand: chain 'I' and resid 268 through 271 Processing sheet with id=AB5, first strand: chain 'I' and resid 605 through 609 removed outlier: 3.811A pdb=" N GLY I 619 " --> pdb=" O PHE I 608 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 662 through 666 Processing sheet with id=AB7, first strand: chain 'K' and resid 268 through 271 Processing sheet with id=AB8, first strand: chain 'K' and resid 605 through 609 removed outlier: 3.812A pdb=" N GLY K 619 " --> pdb=" O PHE K 608 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 662 through 666 2677 hydrogen bonds defined for protein. 7923 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: 7.90 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14256 1.34 - 1.46: 4728 1.46 - 1.57: 22596 1.57 - 1.69: 0 1.69 - 1.81: 408 Bond restraints: 41988 Sorted by residual: bond pdb=" CA ARG G 76 " pdb=" CB ARG G 76 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.31e-02 5.83e+03 1.97e+00 bond pdb=" CA ARG J 76 " pdb=" CB ARG J 76 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.31e-02 5.83e+03 1.90e+00 bond pdb=" CA ARG F 76 " pdb=" CB ARG F 76 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.31e-02 5.83e+03 1.89e+00 bond pdb=" CA ARG B 76 " pdb=" CB ARG B 76 " ideal model delta sigma weight residual 1.524 1.541 -0.018 1.31e-02 5.83e+03 1.83e+00 bond pdb=" CA ARG D 76 " pdb=" CB ARG D 76 " ideal model delta sigma weight residual 1.524 1.541 -0.018 1.31e-02 5.83e+03 1.83e+00 ... (remaining 41983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 54212 1.15 - 2.30: 1859 2.30 - 3.45: 395 3.45 - 4.60: 66 4.60 - 5.75: 42 Bond angle restraints: 56574 Sorted by residual: angle pdb=" CA ARG B 76 " pdb=" CB ARG B 76 " pdb=" CG ARG B 76 " ideal model delta sigma weight residual 114.10 118.81 -4.71 2.00e+00 2.50e-01 5.55e+00 angle pdb=" CA ARG L 76 " pdb=" CB ARG L 76 " pdb=" CG ARG L 76 " ideal model delta sigma weight residual 114.10 118.81 -4.71 2.00e+00 2.50e-01 5.54e+00 angle pdb=" CA ARG F 76 " pdb=" CB ARG F 76 " pdb=" CG ARG F 76 " ideal model delta sigma weight residual 114.10 118.79 -4.69 2.00e+00 2.50e-01 5.51e+00 angle pdb=" CA ARG J 76 " pdb=" CB ARG J 76 " pdb=" CG ARG J 76 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 angle pdb=" CA ARG D 76 " pdb=" CB ARG D 76 " pdb=" CG ARG D 76 " ideal model delta sigma weight residual 114.10 118.76 -4.66 2.00e+00 2.50e-01 5.44e+00 ... (remaining 56569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 23372 17.51 - 35.03: 2122 35.03 - 52.54: 288 52.54 - 70.06: 102 70.06 - 87.57: 60 Dihedral angle restraints: 25944 sinusoidal: 10692 harmonic: 15252 Sorted by residual: dihedral pdb=" CA LEU J 106 " pdb=" C LEU J 106 " pdb=" N ALA J 107 " pdb=" CA ALA J 107 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU L 106 " pdb=" C LEU L 106 " pdb=" N ALA L 107 " pdb=" CA ALA L 107 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU D 106 " pdb=" C LEU D 106 " pdb=" N ALA D 107 " pdb=" CA ALA D 107 " ideal model delta harmonic sigma weight residual 180.00 154.88 25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 25941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 4213 0.037 - 0.074: 1425 0.074 - 0.111: 314 0.111 - 0.148: 114 0.148 - 0.186: 12 Chirality restraints: 6078 Sorted by residual: chirality pdb=" CA VAL J 8 " pdb=" N VAL J 8 " pdb=" C VAL J 8 " pdb=" CB VAL J 8 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA VAL F 8 " pdb=" N VAL F 8 " pdb=" C VAL F 8 " pdb=" CB VAL F 8 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA VAL L 8 " pdb=" N VAL L 8 " pdb=" C VAL L 8 " pdb=" CB VAL L 8 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 6075 not shown) Planarity restraints: 7560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 527 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO I 528 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO I 528 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 528 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 527 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO E 528 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 528 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 528 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 527 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO C 528 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 528 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 528 " -0.020 5.00e-02 4.00e+02 ... (remaining 7557 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3636 2.74 - 3.28: 41249 3.28 - 3.82: 70875 3.82 - 4.36: 84928 4.36 - 4.90: 146277 Nonbonded interactions: 346965 Sorted by model distance: nonbonded pdb=" O HOH I 811 " pdb=" O HOH I 835 " model vdw 2.201 3.040 nonbonded pdb=" OE2 GLU F 101 " pdb=" OG SER F 148 " model vdw 2.209 3.040 nonbonded pdb=" OE2 GLU J 101 " pdb=" OG SER J 148 " model vdw 2.209 3.040 nonbonded pdb=" OE2 GLU L 101 " pdb=" OG SER L 148 " model vdw 2.209 3.040 nonbonded pdb=" OE2 GLU G 101 " pdb=" OG SER G 148 " model vdw 2.210 3.040 ... (remaining 346960 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: 0.06 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'J' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 33.290 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 0.038 41988 Z= 0.160 Angle : 0.528 5.750 56574 Z= 0.304 Chirality : 0.041 0.186 6078 Planarity : 0.004 0.036 7560 Dihedral : 14.166 87.572 16104 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 1.14 (0.11), residues: 5244 helix: 1.52 (0.09), residues: 3678 sheet: 0.64 (0.38), residues: 150 loop : -1.27 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 486 TYR 0.013 0.001 TYR C 424 PHE 0.011 0.001 PHE A 391 TRP 0.014 0.001 TRP K 366 HIS 0.007 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00355 (41988) covalent geometry : angle 0.52791 (56574) hydrogen bonds : bond 0.14574 ( 2677) hydrogen bonds : angle 4.74686 ( 7923) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 874 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7428 (tt0) cc_final: 0.7175 (tt0) REVERT: H 266 ASP cc_start: 0.8066 (m-30) cc_final: 0.7824 (m-30) REVERT: H 328 MET cc_start: 0.8799 (mtp) cc_final: 0.8498 (mtp) REVERT: H 407 MET cc_start: 0.8979 (mmt) cc_final: 0.8778 (mmt) REVERT: H 690 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7826 (mtpp) REVERT: H 694 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6790 (mt-10) REVERT: G 88 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7792 (tttm) REVERT: G 139 MET cc_start: 0.8742 (mtp) cc_final: 0.8294 (mtm) REVERT: G 156 THR cc_start: 0.8668 (t) cc_final: 0.8318 (p) REVERT: G 219 ASP cc_start: 0.7746 (m-30) cc_final: 0.7382 (m-30) REVERT: A 102 GLU cc_start: 0.7824 (tt0) cc_final: 0.7205 (tt0) REVERT: A 119 ASP cc_start: 0.8286 (t0) cc_final: 0.8074 (t0) REVERT: A 162 ASP cc_start: 0.8301 (m-30) cc_final: 0.7814 (m-30) REVERT: A 207 GLN cc_start: 0.8641 (tt0) cc_final: 0.8316 (tt0) REVERT: A 239 GLN cc_start: 0.8693 (tt0) cc_final: 0.8487 (tt0) REVERT: A 328 MET cc_start: 0.8787 (mtp) cc_final: 0.8361 (mtp) REVERT: A 358 GLN cc_start: 0.8498 (mt0) cc_final: 0.8252 (mt0) REVERT: A 456 ASP cc_start: 0.7586 (m-30) cc_final: 0.7338 (m-30) REVERT: A 522 ASP cc_start: 0.7960 (m-30) cc_final: 0.7395 (m-30) REVERT: A 543 LYS cc_start: 0.8432 (ttpp) cc_final: 0.8177 (ttpp) REVERT: A 572 LEU cc_start: 0.8932 (mp) cc_final: 0.8688 (mt) REVERT: A 594 MET cc_start: 0.8680 (tpt) cc_final: 0.8395 (tpp) REVERT: A 683 TYR cc_start: 0.8809 (m-80) cc_final: 0.8605 (m-80) REVERT: A 690 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7721 (ttmm) REVERT: C 102 GLU cc_start: 0.7882 (tt0) cc_final: 0.7395 (tt0) REVERT: C 162 ASP cc_start: 0.7798 (m-30) cc_final: 0.7591 (m-30) REVERT: C 219 ASP cc_start: 0.7827 (m-30) cc_final: 0.7533 (m-30) REVERT: C 226 ASP cc_start: 0.7549 (m-30) cc_final: 0.7136 (m-30) REVERT: C 227 ASN cc_start: 0.8108 (t0) cc_final: 0.7530 (m-40) REVERT: C 323 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7894 (mtt90) REVERT: C 421 MET cc_start: 0.8637 (mmm) cc_final: 0.8397 (mmt) REVERT: C 466 MET cc_start: 0.9030 (ttm) cc_final: 0.8797 (ttp) REVERT: C 510 ASP cc_start: 0.7045 (m-30) cc_final: 0.6813 (m-30) REVERT: C 518 MET cc_start: 0.8598 (mtp) cc_final: 0.8264 (mtp) REVERT: C 522 ASP cc_start: 0.7808 (m-30) cc_final: 0.7520 (m-30) REVERT: C 690 LYS cc_start: 0.8276 (ttpp) cc_final: 0.8015 (ttpp) REVERT: D 37 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5986 (mm-30) REVERT: D 130 SER cc_start: 0.8885 (m) cc_final: 0.8630 (m) REVERT: D 156 THR cc_start: 0.8663 (t) cc_final: 0.8441 (p) REVERT: E 70 ARG cc_start: 0.8748 (mtt180) cc_final: 0.8520 (mtt180) REVERT: E 102 GLU cc_start: 0.7864 (tt0) cc_final: 0.7616 (tt0) REVERT: E 121 MET cc_start: 0.9055 (tpp) cc_final: 0.8623 (tpt) REVERT: E 135 MET cc_start: 0.9104 (tmm) cc_final: 0.8629 (tmt) REVERT: E 161 VAL cc_start: 0.8606 (m) cc_final: 0.8299 (p) REVERT: E 227 ASN cc_start: 0.7816 (t0) cc_final: 0.7404 (m110) REVERT: E 363 MET cc_start: 0.8501 (tpt) cc_final: 0.8178 (tpt) REVERT: E 433 ASP cc_start: 0.8133 (m-30) cc_final: 0.7931 (m-30) REVERT: E 445 MET cc_start: 0.8189 (mtp) cc_final: 0.7980 (mtm) REVERT: E 546 ARG cc_start: 0.8452 (mtt180) cc_final: 0.7875 (mtt180) REVERT: E 550 ASP cc_start: 0.8401 (m-30) cc_final: 0.8007 (m-30) REVERT: E 572 LEU cc_start: 0.8898 (mp) cc_final: 0.8511 (mt) REVERT: E 594 MET cc_start: 0.8577 (tpt) cc_final: 0.8152 (tpt) REVERT: E 673 MET cc_start: 0.8970 (ttt) cc_final: 0.8449 (ttt) REVERT: E 690 LYS cc_start: 0.8226 (ttpp) cc_final: 0.8022 (ttpp) REVERT: I 69 GLU cc_start: 0.7417 (tt0) cc_final: 0.7134 (tt0) REVERT: I 101 MET cc_start: 0.8532 (mmp) cc_final: 0.8230 (mmp) REVERT: I 219 ASP cc_start: 0.7693 (m-30) cc_final: 0.7492 (m-30) REVERT: I 227 ASN cc_start: 0.7989 (t0) cc_final: 0.7593 (m-40) REVERT: I 338 LYS cc_start: 0.8521 (mttp) cc_final: 0.8254 (mtmt) REVERT: I 372 LYS cc_start: 0.8249 (tttm) cc_final: 0.8033 (ttpt) REVERT: I 396 ASN cc_start: 0.7977 (m-40) cc_final: 0.7741 (m-40) REVERT: I 435 MET cc_start: 0.8662 (mtt) cc_final: 0.8442 (mtt) REVERT: I 466 MET cc_start: 0.9034 (ttm) cc_final: 0.8752 (ttp) REVERT: I 518 MET cc_start: 0.8672 (mtp) cc_final: 0.8361 (mtp) REVERT: I 546 ARG cc_start: 0.8477 (mtt180) cc_final: 0.8247 (mtt180) REVERT: I 607 THR cc_start: 0.9290 (t) cc_final: 0.8982 (m) REVERT: I 690 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8115 (ttmm) REVERT: J 36 THR cc_start: 0.7964 (m) cc_final: 0.7606 (p) REVERT: J 88 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8116 (tmmt) REVERT: J 156 THR cc_start: 0.8760 (t) cc_final: 0.8492 (p) REVERT: J 219 ASP cc_start: 0.7736 (m-30) cc_final: 0.7425 (m-30) REVERT: K 119 ASP cc_start: 0.7998 (t0) cc_final: 0.7660 (t70) REVERT: K 121 MET cc_start: 0.9034 (tpp) cc_final: 0.8792 (tpt) REVERT: K 219 ASP cc_start: 0.7725 (m-30) cc_final: 0.7347 (m-30) REVERT: K 227 ASN cc_start: 0.7942 (t0) cc_final: 0.7441 (m-40) REVERT: K 239 GLN cc_start: 0.8553 (tt0) cc_final: 0.8304 (tt0) REVERT: K 323 ARG cc_start: 0.8156 (mpp80) cc_final: 0.7928 (mtt90) REVERT: K 372 LYS cc_start: 0.8394 (tttm) cc_final: 0.8176 (tttp) REVERT: K 421 MET cc_start: 0.8536 (mmm) cc_final: 0.8123 (mmm) REVERT: K 445 MET cc_start: 0.8161 (mtp) cc_final: 0.7870 (mtp) REVERT: K 543 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7934 (ttpp) REVERT: K 550 ASP cc_start: 0.8322 (m-30) cc_final: 0.8103 (m-30) REVERT: K 572 LEU cc_start: 0.8813 (mp) cc_final: 0.8606 (mt) REVERT: K 625 MET cc_start: 0.8357 (mtp) cc_final: 0.8106 (mtp) REVERT: K 690 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8129 (tttp) REVERT: L 30 LEU cc_start: 0.8084 (tp) cc_final: 0.7759 (tt) REVERT: L 54 MET cc_start: 0.6727 (mmt) cc_final: 0.6513 (mpt) outliers start: 0 outliers final: 2 residues processed: 874 average time/residue: 0.8300 time to fit residues: 863.0027 Evaluate side-chains 698 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 696 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain I residue 668 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 394 optimal weight: 0.5980 chunk 430 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 516 optimal weight: 0.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 188 GLN H 308 GLN H 451 GLN H 695 ASN G 178 HIS A 95 GLN A 164 GLN A 308 GLN A 410 ASN A 629 ASN A 695 ASN B 23 ASN B 153 GLN B 184 GLN C 191 GLN C 308 GLN C 695 ASN D 141 ASN E 95 GLN E 191 GLN E 298 GLN E 308 GLN E 629 ASN F 178 HIS F 184 GLN I 95 GLN I 203 ASN I 246 GLN I 308 GLN I 629 ASN J 180 GLN J 184 GLN K 95 GLN K 308 GLN K 629 ASN K 695 ASN L 141 ASN L 178 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109755 restraints weight = 44300.309| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.79 r_work: 0.3045 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 41988 Z= 0.118 Angle : 0.469 9.561 56574 Z= 0.250 Chirality : 0.038 0.151 6078 Planarity : 0.004 0.036 7560 Dihedral : 4.419 160.461 5717 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.77 % Allowed : 8.08 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.12), residues: 5244 helix: 2.01 (0.08), residues: 3726 sheet: 1.22 (0.49), residues: 90 loop : -0.84 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 349 TYR 0.013 0.001 TYR C 508 PHE 0.010 0.001 PHE H 391 TRP 0.012 0.001 TRP E 366 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00235 (41988) covalent geometry : angle 0.46895 (56574) hydrogen bonds : bond 0.05228 ( 2677) hydrogen bonds : angle 3.63132 ( 7923) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 761 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7522 (tt0) cc_final: 0.7261 (tt0) REVERT: H 211 MET cc_start: 0.8675 (mtp) cc_final: 0.8473 (mtp) REVERT: H 266 ASP cc_start: 0.8664 (m-30) cc_final: 0.8380 (m-30) REVERT: H 328 MET cc_start: 0.9105 (mtp) cc_final: 0.8818 (mtp) REVERT: H 407 MET cc_start: 0.9238 (mmt) cc_final: 0.8985 (mmt) REVERT: H 520 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8303 (tpp) REVERT: H 543 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8221 (tttm) REVERT: H 690 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7800 (mtpp) REVERT: H 694 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6796 (mt-10) REVERT: G 54 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6903 (mpt) REVERT: G 88 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7703 (ttpt) REVERT: G 219 ASP cc_start: 0.7777 (m-30) cc_final: 0.7361 (m-30) REVERT: A 102 GLU cc_start: 0.8057 (tt0) cc_final: 0.7611 (tt0) REVERT: A 110 ARG cc_start: 0.8541 (mtp180) cc_final: 0.8269 (mtm180) REVERT: A 152 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7648 (mm-30) REVERT: A 207 GLN cc_start: 0.8851 (tt0) cc_final: 0.8572 (tt0) REVERT: A 239 GLN cc_start: 0.8768 (tt0) cc_final: 0.8557 (tt0) REVERT: A 307 GLU cc_start: 0.8742 (tt0) cc_final: 0.8529 (tt0) REVERT: A 328 MET cc_start: 0.9150 (mtp) cc_final: 0.8721 (mtp) REVERT: A 543 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8158 (ttpp) REVERT: A 548 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8406 (mm-30) REVERT: A 554 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: A 572 LEU cc_start: 0.8812 (mp) cc_final: 0.8570 (mt) REVERT: A 594 MET cc_start: 0.8891 (tpt) cc_final: 0.8689 (tpp) REVERT: A 683 TYR cc_start: 0.8925 (m-80) cc_final: 0.8709 (m-80) REVERT: A 690 LYS cc_start: 0.8023 (ttpp) cc_final: 0.7548 (ttmm) REVERT: B 193 ASP cc_start: 0.8130 (t70) cc_final: 0.7726 (t0) REVERT: C 102 GLU cc_start: 0.8060 (tt0) cc_final: 0.7556 (tt0) REVERT: C 162 ASP cc_start: 0.8046 (m-30) cc_final: 0.7800 (m-30) REVERT: C 219 ASP cc_start: 0.8143 (m-30) cc_final: 0.7740 (m-30) REVERT: C 226 ASP cc_start: 0.8051 (m-30) cc_final: 0.7575 (m-30) REVERT: C 227 ASN cc_start: 0.8007 (t0) cc_final: 0.7222 (m-40) REVERT: C 239 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: C 266 ASP cc_start: 0.8619 (m-30) cc_final: 0.8375 (m-30) REVERT: C 421 MET cc_start: 0.8811 (mmm) cc_final: 0.8570 (mmt) REVERT: C 466 MET cc_start: 0.9189 (ttm) cc_final: 0.8756 (ttp) REVERT: C 510 ASP cc_start: 0.7742 (m-30) cc_final: 0.7463 (m-30) REVERT: C 518 MET cc_start: 0.8722 (mtp) cc_final: 0.8460 (mtp) REVERT: C 554 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: C 690 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7918 (tttp) REVERT: D 13 ASP cc_start: 0.6607 (p0) cc_final: 0.5233 (m-30) REVERT: D 37 GLU cc_start: 0.6289 (mm-30) cc_final: 0.5572 (mm-30) REVERT: D 188 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: E 70 ARG cc_start: 0.8745 (mtt180) cc_final: 0.8531 (mtt180) REVERT: E 102 GLU cc_start: 0.8213 (tt0) cc_final: 0.7674 (tt0) REVERT: E 121 MET cc_start: 0.9272 (tpp) cc_final: 0.8901 (tpt) REVERT: E 135 MET cc_start: 0.9196 (tmm) cc_final: 0.8640 (tmt) REVERT: E 161 VAL cc_start: 0.8339 (m) cc_final: 0.7977 (p) REVERT: E 162 ASP cc_start: 0.8376 (m-30) cc_final: 0.7684 (m-30) REVERT: E 211 MET cc_start: 0.8504 (mtp) cc_final: 0.8171 (mtp) REVERT: E 286 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: E 546 ARG cc_start: 0.8449 (mtt180) cc_final: 0.8128 (mtm180) REVERT: E 572 LEU cc_start: 0.8841 (mp) cc_final: 0.8516 (mt) REVERT: E 592 MET cc_start: 0.9104 (ttt) cc_final: 0.8779 (ttt) REVERT: E 616 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7487 (t0) REVERT: E 673 MET cc_start: 0.9164 (ttt) cc_final: 0.8705 (ttt) REVERT: E 690 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7715 (ttmm) REVERT: F 28 ASP cc_start: 0.6928 (m-30) cc_final: 0.6492 (OUTLIER) REVERT: F 130 SER cc_start: 0.8523 (m) cc_final: 0.8260 (m) REVERT: F 153 GLN cc_start: 0.8238 (mt0) cc_final: 0.8023 (mt0) REVERT: F 188 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: I 69 GLU cc_start: 0.7653 (tt0) cc_final: 0.7252 (tt0) REVERT: I 82 GLN cc_start: 0.8136 (mt0) cc_final: 0.7932 (mt0) REVERT: I 101 MET cc_start: 0.8294 (mmp) cc_final: 0.7976 (mmp) REVERT: I 160 ASP cc_start: 0.8164 (t70) cc_final: 0.7944 (t70) REVERT: I 188 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8071 (pt0) REVERT: I 201 GLU cc_start: 0.8043 (tt0) cc_final: 0.7765 (tt0) REVERT: I 219 ASP cc_start: 0.8066 (m-30) cc_final: 0.7675 (m-30) REVERT: I 223 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8223 (mttp) REVERT: I 227 ASN cc_start: 0.8005 (t0) cc_final: 0.7321 (m-40) REVERT: I 286 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: I 338 LYS cc_start: 0.8769 (mttp) cc_final: 0.8462 (mtmt) REVERT: I 374 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8289 (mt) REVERT: I 378 MET cc_start: 0.9063 (ttm) cc_final: 0.8690 (ttp) REVERT: I 466 MET cc_start: 0.9208 (ttm) cc_final: 0.8945 (ttm) REVERT: I 518 MET cc_start: 0.8782 (mtp) cc_final: 0.8495 (mtp) REVERT: I 546 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8312 (mtt180) REVERT: I 607 THR cc_start: 0.9268 (t) cc_final: 0.8855 (m) REVERT: I 636 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: I 690 LYS cc_start: 0.8287 (ttpp) cc_final: 0.8011 (ttmm) REVERT: J 36 THR cc_start: 0.7333 (m) cc_final: 0.6978 (p) REVERT: J 88 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7988 (tttt) REVERT: J 102 LEU cc_start: 0.8073 (tp) cc_final: 0.7810 (mt) REVERT: J 127 ASP cc_start: 0.7132 (t70) cc_final: 0.6549 (t0) REVERT: J 155 GLU cc_start: 0.7853 (pt0) cc_final: 0.7641 (tt0) REVERT: J 156 THR cc_start: 0.8584 (t) cc_final: 0.8379 (m) REVERT: J 219 ASP cc_start: 0.7805 (m-30) cc_final: 0.7431 (m-30) REVERT: K 119 ASP cc_start: 0.8219 (t0) cc_final: 0.7952 (t70) REVERT: K 121 MET cc_start: 0.9204 (tpp) cc_final: 0.8936 (tpt) REVERT: K 152 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7666 (mm-30) REVERT: K 188 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: K 211 MET cc_start: 0.8725 (mtp) cc_final: 0.8294 (mtm) REVERT: K 219 ASP cc_start: 0.7994 (m-30) cc_final: 0.7568 (m-30) REVERT: K 227 ASN cc_start: 0.7814 (t0) cc_final: 0.7154 (m-40) REVERT: K 239 GLN cc_start: 0.8645 (tt0) cc_final: 0.8395 (tt0) REVERT: K 372 LYS cc_start: 0.8685 (tttm) cc_final: 0.8367 (tttp) REVERT: K 445 MET cc_start: 0.8645 (mtp) cc_final: 0.8417 (mtp) REVERT: K 543 LYS cc_start: 0.8353 (ttpp) cc_final: 0.7946 (ttpp) REVERT: K 550 ASP cc_start: 0.8385 (m-30) cc_final: 0.8106 (m-30) REVERT: K 572 LEU cc_start: 0.8768 (mp) cc_final: 0.8548 (mt) REVERT: K 690 LYS cc_start: 0.8260 (ttpp) cc_final: 0.8023 (tttp) REVERT: L 1 MET cc_start: 0.4808 (mtm) cc_final: 0.3866 (ppp) REVERT: L 30 LEU cc_start: 0.7378 (tp) cc_final: 0.7149 (tp) REVERT: L 54 MET cc_start: 0.6954 (mmt) cc_final: 0.6273 (mpt) REVERT: L 102 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7710 (mp) REVERT: L 188 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7510 (mp0) outliers start: 77 outliers final: 17 residues processed: 785 average time/residue: 0.8476 time to fit residues: 794.5616 Evaluate side-chains 720 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 687 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 368 LYS Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 616 ASP Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 188 GLN Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 239 GLN Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 285 GLU Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 308 optimal weight: 2.9990 chunk 488 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 391 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 390 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 392 GLN H 524 GLN H 695 ASN G 109 ASN G 141 ASN A 695 ASN B 153 GLN B 178 HIS B 184 GLN C 191 GLN C 203 ASN C 629 ASN D 178 HIS E 191 GLN E 203 ASN E 298 GLN E 629 ASN I 191 GLN I 410 ASN ** J 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109551 restraints weight = 44311.386| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.78 r_work: 0.3048 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 41988 Z= 0.118 Angle : 0.456 7.118 56574 Z= 0.241 Chirality : 0.038 0.164 6078 Planarity : 0.004 0.037 7560 Dihedral : 4.335 159.712 5715 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.04 % Allowed : 10.26 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.12), residues: 5244 helix: 2.24 (0.09), residues: 3726 sheet: 1.26 (0.48), residues: 90 loop : -0.75 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 349 TYR 0.012 0.001 TYR E 424 PHE 0.009 0.001 PHE A 404 TRP 0.011 0.001 TRP E 366 HIS 0.004 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00249 (41988) covalent geometry : angle 0.45555 (56574) hydrogen bonds : bond 0.05080 ( 2677) hydrogen bonds : angle 3.47246 ( 7923) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 714 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 69 GLU cc_start: 0.7506 (tt0) cc_final: 0.7240 (tt0) REVERT: H 161 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8169 (m) REVERT: H 201 GLU cc_start: 0.8048 (tt0) cc_final: 0.7813 (tm-30) REVERT: H 266 ASP cc_start: 0.8739 (m-30) cc_final: 0.8429 (m-30) REVERT: H 286 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: H 328 MET cc_start: 0.9093 (mtp) cc_final: 0.8803 (mtp) REVERT: H 407 MET cc_start: 0.9299 (mmt) cc_final: 0.8949 (mmt) REVERT: H 520 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8320 (tpp) REVERT: H 554 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: H 690 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7830 (ttmm) REVERT: H 694 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6848 (mt-10) REVERT: G 88 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7689 (ttpt) REVERT: G 141 ASN cc_start: 0.8473 (m-40) cc_final: 0.8185 (m-40) REVERT: G 219 ASP cc_start: 0.7930 (m-30) cc_final: 0.7527 (m-30) REVERT: A 102 GLU cc_start: 0.7974 (tt0) cc_final: 0.7553 (tt0) REVERT: A 110 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8187 (mtm180) REVERT: A 152 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7683 (mm-30) REVERT: A 207 GLN cc_start: 0.8836 (tt0) cc_final: 0.8560 (tt0) REVERT: A 239 GLN cc_start: 0.8764 (tt0) cc_final: 0.8522 (tt0) REVERT: A 298 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: A 307 GLU cc_start: 0.8770 (tt0) cc_final: 0.8537 (tt0) REVERT: A 328 MET cc_start: 0.9122 (mtp) cc_final: 0.8739 (mtp) REVERT: A 543 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8109 (ttpp) REVERT: A 554 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: A 572 LEU cc_start: 0.8781 (mp) cc_final: 0.8521 (mt) REVERT: A 594 MET cc_start: 0.8893 (tpt) cc_final: 0.8691 (tpp) REVERT: A 636 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: A 683 TYR cc_start: 0.8901 (m-80) cc_final: 0.8683 (m-80) REVERT: A 690 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7544 (ttmm) REVERT: B 188 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8048 (pm20) REVERT: C 102 GLU cc_start: 0.8047 (tt0) cc_final: 0.7499 (tt0) REVERT: C 162 ASP cc_start: 0.8066 (m-30) cc_final: 0.7774 (m-30) REVERT: C 219 ASP cc_start: 0.8141 (m-30) cc_final: 0.7678 (m-30) REVERT: C 223 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8102 (mtpt) REVERT: C 226 ASP cc_start: 0.7982 (m-30) cc_final: 0.7531 (m-30) REVERT: C 227 ASN cc_start: 0.8086 (t0) cc_final: 0.7273 (m-40) REVERT: C 239 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: C 262 MET cc_start: 0.8706 (ttp) cc_final: 0.8498 (ttp) REVERT: C 266 ASP cc_start: 0.8603 (m-30) cc_final: 0.8383 (m-30) REVERT: C 421 MET cc_start: 0.8832 (mmm) cc_final: 0.8522 (mmt) REVERT: C 466 MET cc_start: 0.9166 (ttm) cc_final: 0.8667 (ttp) REVERT: C 510 ASP cc_start: 0.7940 (m-30) cc_final: 0.7668 (m-30) REVERT: C 554 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: C 690 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7936 (tttp) REVERT: D 13 ASP cc_start: 0.6725 (p0) cc_final: 0.5859 (m-30) REVERT: D 37 GLU cc_start: 0.6297 (mm-30) cc_final: 0.5600 (mm-30) REVERT: D 53 MET cc_start: 0.3689 (tpp) cc_final: 0.3253 (tpp) REVERT: D 156 THR cc_start: 0.8626 (t) cc_final: 0.8299 (m) REVERT: D 188 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: E 70 ARG cc_start: 0.8728 (mtt180) cc_final: 0.8505 (mtt180) REVERT: E 121 MET cc_start: 0.9263 (tpp) cc_final: 0.8877 (tpt) REVERT: E 211 MET cc_start: 0.8591 (mtp) cc_final: 0.8271 (mtp) REVERT: E 227 ASN cc_start: 0.7963 (t0) cc_final: 0.7229 (m110) REVERT: E 286 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7807 (mp10) REVERT: E 345 MET cc_start: 0.9356 (mmm) cc_final: 0.9049 (mmm) REVERT: E 572 LEU cc_start: 0.8875 (mp) cc_final: 0.8555 (mt) REVERT: E 592 MET cc_start: 0.9114 (ttt) cc_final: 0.8807 (ttt) REVERT: E 673 MET cc_start: 0.9135 (ttt) cc_final: 0.8664 (ttt) REVERT: F 153 GLN cc_start: 0.8162 (mt0) cc_final: 0.7949 (mt0) REVERT: F 188 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: F 200 GLU cc_start: 0.7862 (tt0) cc_final: 0.7474 (mt-10) REVERT: I 69 GLU cc_start: 0.7637 (tt0) cc_final: 0.7291 (tt0) REVERT: I 160 ASP cc_start: 0.8145 (t70) cc_final: 0.7909 (t70) REVERT: I 219 ASP cc_start: 0.7999 (m-30) cc_final: 0.7591 (m-30) REVERT: I 227 ASN cc_start: 0.8043 (t0) cc_final: 0.7341 (m-40) REVERT: I 286 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: I 338 LYS cc_start: 0.8777 (mttp) cc_final: 0.8464 (mtmt) REVERT: I 374 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8291 (mt) REVERT: I 378 MET cc_start: 0.8998 (ttm) cc_final: 0.8666 (ttp) REVERT: I 518 MET cc_start: 0.8758 (mtp) cc_final: 0.8497 (mtp) REVERT: I 546 ARG cc_start: 0.8637 (mtt180) cc_final: 0.8391 (mtt180) REVERT: I 607 THR cc_start: 0.9267 (t) cc_final: 0.8909 (m) REVERT: I 690 LYS cc_start: 0.8250 (ttpp) cc_final: 0.7971 (ttmm) REVERT: J 1 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.2583 (tmm) REVERT: J 36 THR cc_start: 0.7351 (m) cc_final: 0.6936 (p) REVERT: J 155 GLU cc_start: 0.7889 (pt0) cc_final: 0.7659 (tt0) REVERT: J 156 THR cc_start: 0.8618 (t) cc_final: 0.8403 (m) REVERT: J 219 ASP cc_start: 0.7812 (m-30) cc_final: 0.7437 (m-30) REVERT: K 85 GLU cc_start: 0.7717 (pt0) cc_final: 0.7395 (pt0) REVERT: K 119 ASP cc_start: 0.8275 (t0) cc_final: 0.8001 (t70) REVERT: K 188 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: K 211 MET cc_start: 0.8700 (mtp) cc_final: 0.8294 (mtm) REVERT: K 219 ASP cc_start: 0.7975 (m-30) cc_final: 0.7559 (m-30) REVERT: K 227 ASN cc_start: 0.7794 (t0) cc_final: 0.7133 (m-40) REVERT: K 239 GLN cc_start: 0.8664 (tt0) cc_final: 0.8398 (tt0) REVERT: K 291 MET cc_start: 0.9343 (mmm) cc_final: 0.9117 (mmm) REVERT: K 372 LYS cc_start: 0.8722 (tttm) cc_final: 0.8389 (tttp) REVERT: K 374 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8345 (tp) REVERT: K 445 MET cc_start: 0.8662 (mtp) cc_final: 0.8413 (mtp) REVERT: K 543 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7921 (ttpp) REVERT: K 550 ASP cc_start: 0.8383 (m-30) cc_final: 0.7826 (m-30) REVERT: K 554 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: K 572 LEU cc_start: 0.8766 (mp) cc_final: 0.8556 (mt) REVERT: K 690 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7997 (tttp) REVERT: L 1 MET cc_start: 0.4830 (mtm) cc_final: 0.4112 (pp-130) REVERT: L 13 ASP cc_start: 0.7069 (p0) cc_final: 0.6413 (m-30) REVERT: L 30 LEU cc_start: 0.7377 (tp) cc_final: 0.7145 (tp) REVERT: L 54 MET cc_start: 0.7180 (mmt) cc_final: 0.6292 (mpt) REVERT: L 188 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7470 (mp0) outliers start: 89 outliers final: 33 residues processed: 747 average time/residue: 0.8476 time to fit residues: 756.2786 Evaluate side-chains 747 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 694 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 368 LYS Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 554 GLU Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 188 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 263 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 416 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 389 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 434 optimal weight: 0.0570 chunk 304 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 164 GLN H 695 ASN A 695 ASN B 153 GLN C 191 GLN C 629 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 95 GLN E 191 GLN E 298 GLN E 308 GLN F 23 ASN F 184 GLN I 191 GLN I 410 ASN J 199 GLN K 246 GLN K 629 ASN L 184 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.105516 restraints weight = 44167.997| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.79 r_work: 0.2983 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 41988 Z= 0.202 Angle : 0.533 7.423 56574 Z= 0.281 Chirality : 0.042 0.170 6078 Planarity : 0.005 0.068 7560 Dihedral : 4.092 24.829 5712 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.57 % Allowed : 10.93 % Favored : 86.50 % 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 are not related in a simple way. whole: 1.90 (0.12), residues: 5244 helix: 2.04 (0.08), residues: 3738 sheet: 1.30 (0.49), residues: 90 loop : -0.90 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 349 TYR 0.017 0.002 TYR E 424 PHE 0.016 0.001 PHE L 128 TRP 0.012 0.002 TRP K 399 HIS 0.004 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.00485 (41988) covalent geometry : angle 0.53326 (56574) hydrogen bonds : bond 0.06482 ( 2677) hydrogen bonds : angle 3.64677 ( 7923) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 699 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 201 GLU cc_start: 0.8078 (tt0) cc_final: 0.7873 (tm-30) REVERT: H 262 MET cc_start: 0.8941 (ttp) cc_final: 0.8711 (ttp) REVERT: H 266 ASP cc_start: 0.8782 (m-30) cc_final: 0.8458 (m-30) REVERT: H 286 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: H 328 MET cc_start: 0.9102 (mtp) cc_final: 0.8830 (mtp) REVERT: H 407 MET cc_start: 0.9306 (mmt) cc_final: 0.8887 (mmt) REVERT: H 520 MET cc_start: 0.8714 (ttp) cc_final: 0.8408 (tpp) REVERT: H 554 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: H 644 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: H 690 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7869 (ttmm) REVERT: H 694 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6867 (mt-10) REVERT: G 88 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7651 (ttpt) REVERT: G 150 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7391 (mtm) REVERT: G 219 ASP cc_start: 0.7939 (m-30) cc_final: 0.7540 (m-30) REVERT: A 85 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 102 GLU cc_start: 0.8111 (tt0) cc_final: 0.7728 (tt0) REVERT: A 110 ARG cc_start: 0.8570 (mtp180) cc_final: 0.8353 (mtm180) REVERT: A 152 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7702 (mm-30) REVERT: A 207 GLN cc_start: 0.8824 (tt0) cc_final: 0.8568 (tt0) REVERT: A 239 GLN cc_start: 0.8824 (tt0) cc_final: 0.8590 (tt0) REVERT: A 298 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: A 307 GLU cc_start: 0.8833 (tt0) cc_final: 0.8576 (tt0) REVERT: A 523 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8323 (mttp) REVERT: A 543 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8243 (ttpp) REVERT: A 572 LEU cc_start: 0.8896 (mp) cc_final: 0.8629 (mt) REVERT: A 636 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: A 683 TYR cc_start: 0.8950 (m-80) cc_final: 0.8712 (m-80) REVERT: A 690 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7568 (ttmm) REVERT: B 13 ASP cc_start: 0.7747 (p0) cc_final: 0.7067 (m-30) REVERT: B 193 ASP cc_start: 0.8153 (t70) cc_final: 0.7755 (t0) REVERT: C 102 GLU cc_start: 0.8113 (tt0) cc_final: 0.7654 (tt0) REVERT: C 152 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 162 ASP cc_start: 0.8111 (m-30) cc_final: 0.7831 (m-30) REVERT: C 219 ASP cc_start: 0.8150 (m-30) cc_final: 0.7666 (m-30) REVERT: C 223 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: C 226 ASP cc_start: 0.7950 (m-30) cc_final: 0.7498 (m-30) REVERT: C 227 ASN cc_start: 0.8203 (t0) cc_final: 0.7336 (m-40) REVERT: C 239 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8584 (tt0) REVERT: C 421 MET cc_start: 0.8962 (mmm) cc_final: 0.8544 (mmt) REVERT: C 510 ASP cc_start: 0.8003 (m-30) cc_final: 0.7763 (m-30) REVERT: C 554 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: C 690 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7932 (tttp) REVERT: D 13 ASP cc_start: 0.6629 (p0) cc_final: 0.5997 (m-30) REVERT: D 37 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5577 (mm-30) REVERT: D 53 MET cc_start: 0.3914 (tpp) cc_final: 0.2626 (mtp) REVERT: D 88 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7397 (ttmt) REVERT: D 179 LYS cc_start: 0.8533 (mtpt) cc_final: 0.7905 (mptp) REVERT: D 188 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: E 70 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8540 (mtt180) REVERT: E 121 MET cc_start: 0.9266 (tpp) cc_final: 0.8868 (tpp) REVERT: E 211 MET cc_start: 0.8622 (mtp) cc_final: 0.8273 (mtp) REVERT: E 227 ASN cc_start: 0.8006 (t0) cc_final: 0.7188 (m110) REVERT: E 286 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: E 345 MET cc_start: 0.9359 (mmm) cc_final: 0.9114 (mmm) REVERT: E 374 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8375 (mp) REVERT: E 451 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7741 (tp40) REVERT: E 572 LEU cc_start: 0.8934 (mp) cc_final: 0.8537 (mt) REVERT: E 673 MET cc_start: 0.9197 (ttt) cc_final: 0.8886 (ttp) REVERT: F 153 GLN cc_start: 0.8040 (mt0) cc_final: 0.7801 (mt0) REVERT: F 180 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7673 (mm-40) REVERT: F 188 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: F 198 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6950 (tp30) REVERT: I 69 GLU cc_start: 0.7731 (tt0) cc_final: 0.7338 (tt0) REVERT: I 148 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7880 (mtmp) REVERT: I 173 GLU cc_start: 0.8498 (mp0) cc_final: 0.8269 (mp0) REVERT: I 191 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: I 219 ASP cc_start: 0.8108 (m-30) cc_final: 0.7686 (m-30) REVERT: I 227 ASN cc_start: 0.8113 (t0) cc_final: 0.7317 (m-40) REVERT: I 286 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: I 338 LYS cc_start: 0.8889 (mttp) cc_final: 0.8584 (mtmt) REVERT: I 374 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8264 (mt) REVERT: I 378 MET cc_start: 0.9013 (ttm) cc_final: 0.8648 (ttp) REVERT: I 510 ASP cc_start: 0.8082 (m-30) cc_final: 0.7722 (m-30) REVERT: I 518 MET cc_start: 0.8823 (mtp) cc_final: 0.8565 (mtp) REVERT: I 546 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8389 (mtt180) REVERT: I 607 THR cc_start: 0.9337 (t) cc_final: 0.8993 (m) REVERT: I 636 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: I 690 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7902 (ttmm) REVERT: I 694 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: J 1 MET cc_start: 0.4356 (pp-130) cc_final: 0.2854 (tmm) REVERT: J 36 THR cc_start: 0.7298 (m) cc_final: 0.6917 (p) REVERT: J 88 LYS cc_start: 0.8232 (ttpp) cc_final: 0.8020 (tttt) REVERT: J 219 ASP cc_start: 0.7816 (m-30) cc_final: 0.7442 (m-30) REVERT: K 85 GLU cc_start: 0.7745 (pt0) cc_final: 0.7415 (pt0) REVERT: K 119 ASP cc_start: 0.8247 (t70) cc_final: 0.7964 (t70) REVERT: K 188 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: K 211 MET cc_start: 0.8715 (mtp) cc_final: 0.8278 (mtm) REVERT: K 219 ASP cc_start: 0.8039 (m-30) cc_final: 0.7614 (m-30) REVERT: K 227 ASN cc_start: 0.7822 (t0) cc_final: 0.7186 (m-40) REVERT: K 239 GLN cc_start: 0.8751 (tt0) cc_final: 0.8481 (tt0) REVERT: K 262 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8914 (ttm) REVERT: K 291 MET cc_start: 0.9362 (mmm) cc_final: 0.9078 (mmm) REVERT: K 372 LYS cc_start: 0.8764 (tttm) cc_final: 0.8436 (tttp) REVERT: K 445 MET cc_start: 0.8669 (mtp) cc_final: 0.8429 (mtp) REVERT: K 543 LYS cc_start: 0.8409 (ttpp) cc_final: 0.8056 (ttpp) REVERT: K 550 ASP cc_start: 0.8423 (m-30) cc_final: 0.7864 (m-30) REVERT: K 554 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: K 572 LEU cc_start: 0.8732 (mp) cc_final: 0.8468 (mt) REVERT: K 690 LYS cc_start: 0.8307 (ttpp) cc_final: 0.8044 (tttp) REVERT: L 1 MET cc_start: 0.4744 (mtm) cc_final: 0.4000 (pp-130) REVERT: L 13 ASP cc_start: 0.7016 (p0) cc_final: 0.6413 (m-30) REVERT: L 30 LEU cc_start: 0.7346 (tp) cc_final: 0.7074 (tt) REVERT: L 54 MET cc_start: 0.7233 (mmt) cc_final: 0.6280 (mpt) REVERT: L 155 GLU cc_start: 0.7830 (pt0) cc_final: 0.7479 (tt0) REVERT: L 216 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8029 (pp20) outliers start: 112 outliers final: 45 residues processed: 750 average time/residue: 0.7966 time to fit residues: 714.8692 Evaluate side-chains 752 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 681 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 298 GLN Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain H residue 644 GLU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 451 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 191 GLN Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 262 MET Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain I residue 694 GLU Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 262 MET Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 554 GLU Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 378 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 479 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 319 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 282 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 695 ASN G 109 ASN G 141 ASN A 95 GLN A 188 GLN A 695 ASN B 153 GLN C 88 ASN C 191 GLN D 141 ASN E 191 GLN E 298 GLN E 629 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 629 ASN K 695 ASN L 184 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109007 restraints weight = 43939.041| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.74 r_work: 0.3042 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41988 Z= 0.119 Angle : 0.457 8.194 56574 Z= 0.241 Chirality : 0.038 0.189 6078 Planarity : 0.004 0.038 7560 Dihedral : 3.786 21.011 5712 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.50 % Allowed : 11.82 % 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 are not related in a simple way. whole: 2.20 (0.12), residues: 5244 helix: 2.28 (0.09), residues: 3720 sheet: 1.40 (0.49), residues: 90 loop : -0.80 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 349 TYR 0.012 0.001 TYR C 508 PHE 0.007 0.001 PHE A 404 TRP 0.012 0.001 TRP C 366 HIS 0.002 0.001 HIS G 178 Details of bonding type rmsd covalent geometry : bond 0.00252 (41988) covalent geometry : angle 0.45682 (56574) hydrogen bonds : bond 0.05077 ( 2677) hydrogen bonds : angle 3.47147 ( 7923) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 708 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 152 GLU cc_start: 0.8264 (pt0) cc_final: 0.8004 (mm-30) REVERT: H 211 MET cc_start: 0.8689 (mtp) cc_final: 0.8483 (mtp) REVERT: H 266 ASP cc_start: 0.8774 (m-30) cc_final: 0.8501 (m-30) REVERT: H 286 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: H 298 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: H 328 MET cc_start: 0.9119 (mtp) cc_final: 0.8838 (mtp) REVERT: H 407 MET cc_start: 0.9310 (mmt) cc_final: 0.8923 (mmt) REVERT: H 520 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8412 (tpp) REVERT: H 554 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: H 636 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8298 (mt-10) REVERT: H 690 LYS cc_start: 0.8400 (ttpp) cc_final: 0.7958 (ttmm) REVERT: H 694 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6748 (mt-10) REVERT: G 54 MET cc_start: 0.6751 (mpt) cc_final: 0.6316 (mpm) REVERT: G 88 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7705 (ttpt) REVERT: G 141 ASN cc_start: 0.8333 (m-40) cc_final: 0.8032 (m-40) REVERT: G 219 ASP cc_start: 0.7842 (m-30) cc_final: 0.7474 (m-30) REVERT: A 85 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 102 GLU cc_start: 0.8055 (tt0) cc_final: 0.7698 (tt0) REVERT: A 110 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8257 (mtm180) REVERT: A 152 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7735 (mm-30) REVERT: A 207 GLN cc_start: 0.8854 (tt0) cc_final: 0.8586 (tt0) REVERT: A 298 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: A 307 GLU cc_start: 0.8791 (tt0) cc_final: 0.8558 (tt0) REVERT: A 451 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: A 543 LYS cc_start: 0.8509 (ttpp) cc_final: 0.8221 (ttpp) REVERT: A 554 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7590 (tp30) REVERT: A 572 LEU cc_start: 0.8855 (mp) cc_final: 0.8588 (mt) REVERT: A 683 TYR cc_start: 0.8925 (m-80) cc_final: 0.8721 (m-80) REVERT: A 690 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7671 (ttmm) REVERT: B 1 MET cc_start: 0.5180 (ppp) cc_final: 0.4118 (mpp) REVERT: C 102 GLU cc_start: 0.8076 (tt0) cc_final: 0.7497 (tt0) REVERT: C 162 ASP cc_start: 0.8076 (m-30) cc_final: 0.7733 (m-30) REVERT: C 219 ASP cc_start: 0.8158 (m-30) cc_final: 0.7686 (m-30) REVERT: C 223 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8124 (mtpt) REVERT: C 226 ASP cc_start: 0.7942 (m-30) cc_final: 0.7500 (m-30) REVERT: C 227 ASN cc_start: 0.8164 (t0) cc_final: 0.7367 (m-40) REVERT: C 239 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 266 ASP cc_start: 0.8575 (m-30) cc_final: 0.8359 (m-30) REVERT: C 421 MET cc_start: 0.8970 (mmm) cc_final: 0.8622 (mmt) REVERT: C 510 ASP cc_start: 0.8049 (m-30) cc_final: 0.7790 (m-30) REVERT: C 554 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: C 690 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7991 (tttp) REVERT: D 13 ASP cc_start: 0.6469 (p0) cc_final: 0.6168 (m-30) REVERT: D 37 GLU cc_start: 0.6380 (mm-30) cc_final: 0.5590 (mm-30) REVERT: D 53 MET cc_start: 0.3967 (tpp) cc_final: 0.2804 (mtp) REVERT: D 156 THR cc_start: 0.8631 (t) cc_final: 0.8307 (m) REVERT: D 179 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7959 (mptp) REVERT: E 70 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8571 (mtt180) REVERT: E 121 MET cc_start: 0.9300 (tpp) cc_final: 0.8935 (tpp) REVERT: E 211 MET cc_start: 0.8596 (mtp) cc_final: 0.8259 (mtp) REVERT: E 227 ASN cc_start: 0.8047 (t0) cc_final: 0.7265 (m110) REVERT: E 286 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: E 572 LEU cc_start: 0.8959 (mp) cc_final: 0.8609 (mt) REVERT: E 673 MET cc_start: 0.9166 (ttt) cc_final: 0.8813 (ttt) REVERT: F 180 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7592 (mm110) REVERT: F 188 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: F 198 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6963 (tp30) REVERT: F 200 GLU cc_start: 0.7895 (tt0) cc_final: 0.7525 (mt-10) REVERT: I 69 GLU cc_start: 0.7709 (tt0) cc_final: 0.7295 (tt0) REVERT: I 148 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7928 (mtmp) REVERT: I 160 ASP cc_start: 0.8153 (t70) cc_final: 0.7938 (t70) REVERT: I 219 ASP cc_start: 0.8076 (m-30) cc_final: 0.7677 (m-30) REVERT: I 227 ASN cc_start: 0.8157 (t0) cc_final: 0.7356 (m-40) REVERT: I 230 VAL cc_start: 0.8687 (t) cc_final: 0.8413 (p) REVERT: I 286 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: I 338 LYS cc_start: 0.8802 (mttp) cc_final: 0.8504 (mtmt) REVERT: I 374 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8358 (mt) REVERT: I 378 MET cc_start: 0.8970 (ttm) cc_final: 0.8678 (ttp) REVERT: I 518 MET cc_start: 0.8813 (mtp) cc_final: 0.8547 (mtp) REVERT: I 546 ARG cc_start: 0.8691 (mtt180) cc_final: 0.8446 (mtt180) REVERT: I 607 THR cc_start: 0.9323 (t) cc_final: 0.8984 (m) REVERT: I 636 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: I 690 LYS cc_start: 0.8325 (ttpp) cc_final: 0.7950 (ttmm) REVERT: I 694 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6373 (mt-10) REVERT: J 1 MET cc_start: 0.4316 (pp-130) cc_final: 0.3057 (tmm) REVERT: J 36 THR cc_start: 0.7358 (m) cc_final: 0.6964 (p) REVERT: J 88 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7734 (tmmt) REVERT: J 155 GLU cc_start: 0.8035 (pt0) cc_final: 0.7817 (tt0) REVERT: J 219 ASP cc_start: 0.7840 (m-30) cc_final: 0.7487 (m-30) REVERT: K 68 ASP cc_start: 0.8145 (t70) cc_final: 0.7796 (t0) REVERT: K 85 GLU cc_start: 0.7788 (pt0) cc_final: 0.7465 (pt0) REVERT: K 119 ASP cc_start: 0.8275 (t70) cc_final: 0.8009 (t70) REVERT: K 188 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: K 211 MET cc_start: 0.8710 (mtp) cc_final: 0.8310 (mtm) REVERT: K 219 ASP cc_start: 0.8064 (m-30) cc_final: 0.7646 (m-30) REVERT: K 227 ASN cc_start: 0.7879 (t0) cc_final: 0.7293 (m-40) REVERT: K 239 GLN cc_start: 0.8776 (tt0) cc_final: 0.8528 (mt0) REVERT: K 291 MET cc_start: 0.9370 (mmm) cc_final: 0.9057 (mmm) REVERT: K 372 LYS cc_start: 0.8774 (tttm) cc_final: 0.8475 (tttp) REVERT: K 445 MET cc_start: 0.8704 (mtp) cc_final: 0.8461 (mtp) REVERT: K 543 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8011 (ttpp) REVERT: K 550 ASP cc_start: 0.8467 (m-30) cc_final: 0.7873 (m-30) REVERT: K 554 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: K 572 LEU cc_start: 0.8834 (mp) cc_final: 0.8615 (mt) REVERT: K 690 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8093 (tttp) REVERT: L 1 MET cc_start: 0.4853 (mtm) cc_final: 0.4197 (pp-130) REVERT: L 13 ASP cc_start: 0.6946 (p0) cc_final: 0.6552 (m-30) REVERT: L 30 LEU cc_start: 0.7340 (tp) cc_final: 0.7110 (tp) REVERT: L 37 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6479 (mm-30) REVERT: L 54 MET cc_start: 0.7242 (mmt) cc_final: 0.6315 (mpt) REVERT: L 155 GLU cc_start: 0.7817 (pt0) cc_final: 0.7506 (tt0) REVERT: L 163 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8387 (mmtp) REVERT: L 216 GLU cc_start: 0.8352 (pt0) cc_final: 0.8027 (pp20) outliers start: 109 outliers final: 43 residues processed: 756 average time/residue: 0.7808 time to fit residues: 707.5376 Evaluate side-chains 757 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 694 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 298 GLN Chi-restraints excluded: chain H residue 490 MET Chi-restraints excluded: chain H residue 520 MET Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 164 GLN Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain I residue 694 GLU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 554 GLU Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 163 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 474 optimal weight: 0.0770 chunk 327 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 chunk 340 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 324 optimal weight: 0.7980 chunk 251 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 695 ASN G 184 GLN A 191 GLN A 239 GLN A 695 ASN C 88 ASN C 191 GLN C 246 GLN D 153 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 191 GLN E 298 GLN E 308 GLN E 629 ASN I 191 GLN I 410 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110740 restraints weight = 44061.496| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.79 r_work: 0.3044 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 41988 Z= 0.107 Angle : 0.442 9.249 56574 Z= 0.232 Chirality : 0.037 0.195 6078 Planarity : 0.004 0.037 7560 Dihedral : 3.627 18.757 5712 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.16 % Allowed : 12.76 % Favored : 85.08 % 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 are not related in a simple way. whole: 2.41 (0.12), residues: 5244 helix: 2.43 (0.09), residues: 3726 sheet: 1.46 (0.49), residues: 90 loop : -0.68 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 541 TYR 0.014 0.001 TYR L 123 PHE 0.007 0.001 PHE A 404 TRP 0.012 0.001 TRP C 366 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00222 (41988) covalent geometry : angle 0.44215 (56574) hydrogen bonds : bond 0.04652 ( 2677) hydrogen bonds : angle 3.36638 ( 7923) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 709 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 152 GLU cc_start: 0.8220 (pt0) cc_final: 0.7977 (mm-30) REVERT: H 211 MET cc_start: 0.8616 (mtp) cc_final: 0.8413 (mtp) REVERT: H 266 ASP cc_start: 0.8714 (m-30) cc_final: 0.8417 (m-30) REVERT: H 286 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: H 298 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: H 328 MET cc_start: 0.9089 (mtp) cc_final: 0.8837 (mtp) REVERT: H 407 MET cc_start: 0.9295 (mmt) cc_final: 0.8923 (mmt) REVERT: H 520 MET cc_start: 0.8691 (ttp) cc_final: 0.8367 (tpp) REVERT: H 554 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: H 561 LYS cc_start: 0.8256 (mmpt) cc_final: 0.7946 (mmmt) REVERT: H 690 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7912 (ttmm) REVERT: H 694 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6709 (mt-10) REVERT: G 36 THR cc_start: 0.7321 (m) cc_final: 0.6902 (p) REVERT: G 54 MET cc_start: 0.6726 (mpt) cc_final: 0.6319 (mpm) REVERT: G 88 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7711 (ttpt) REVERT: G 219 ASP cc_start: 0.7843 (m-30) cc_final: 0.7520 (m-30) REVERT: A 102 GLU cc_start: 0.7914 (tt0) cc_final: 0.7592 (tt0) REVERT: A 110 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8177 (mtm180) REVERT: A 164 GLN cc_start: 0.8427 (mt0) cc_final: 0.7906 (tp-100) REVERT: A 207 GLN cc_start: 0.8843 (tt0) cc_final: 0.8571 (tt0) REVERT: A 298 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: A 307 GLU cc_start: 0.8781 (tt0) cc_final: 0.8559 (tt0) REVERT: A 451 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7677 (tp40) REVERT: A 543 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8133 (ttpp) REVERT: A 683 TYR cc_start: 0.8913 (m-80) cc_final: 0.8704 (m-80) REVERT: A 690 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7572 (ttmm) REVERT: B 1 MET cc_start: 0.5293 (ppp) cc_final: 0.4162 (mpp) REVERT: B 188 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8007 (pm20) REVERT: B 216 GLU cc_start: 0.8398 (pt0) cc_final: 0.8034 (pt0) REVERT: C 82 GLN cc_start: 0.8258 (mt0) cc_final: 0.7863 (mt0) REVERT: C 102 GLU cc_start: 0.8051 (tt0) cc_final: 0.7680 (tt0) REVERT: C 162 ASP cc_start: 0.8017 (m-30) cc_final: 0.7711 (m-30) REVERT: C 210 ASP cc_start: 0.8400 (m-30) cc_final: 0.8136 (m-30) REVERT: C 219 ASP cc_start: 0.8111 (m-30) cc_final: 0.7645 (m-30) REVERT: C 223 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8085 (mtpt) REVERT: C 226 ASP cc_start: 0.7884 (m-30) cc_final: 0.7409 (m-30) REVERT: C 227 ASN cc_start: 0.8135 (t0) cc_final: 0.7330 (m-40) REVERT: C 266 ASP cc_start: 0.8600 (m-30) cc_final: 0.8377 (m-30) REVERT: C 421 MET cc_start: 0.8943 (mmm) cc_final: 0.8498 (mmt) REVERT: C 510 ASP cc_start: 0.8077 (m-30) cc_final: 0.7835 (m-30) REVERT: C 554 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: C 590 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8010 (mt-10) REVERT: C 602 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8468 (mtpt) REVERT: C 690 LYS cc_start: 0.8289 (ttpp) cc_final: 0.8015 (tttp) REVERT: D 37 GLU cc_start: 0.6361 (mm-30) cc_final: 0.5540 (mm-30) REVERT: D 53 MET cc_start: 0.4065 (tpp) cc_final: 0.3747 (tpp) REVERT: D 179 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7923 (mptp) REVERT: D 180 GLN cc_start: 0.8502 (mm110) cc_final: 0.8229 (mm-40) REVERT: E 121 MET cc_start: 0.9287 (tpp) cc_final: 0.8915 (tpp) REVERT: E 211 MET cc_start: 0.8503 (mtp) cc_final: 0.8183 (mtp) REVERT: E 227 ASN cc_start: 0.8009 (t0) cc_final: 0.7219 (m110) REVERT: E 286 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: E 345 MET cc_start: 0.9346 (mmm) cc_final: 0.9067 (mmm) REVERT: E 374 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (tt) REVERT: E 673 MET cc_start: 0.9144 (ttt) cc_final: 0.8676 (ttt) REVERT: F 180 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7567 (mm110) REVERT: F 188 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7896 (pm20) REVERT: F 198 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6914 (tp30) REVERT: F 200 GLU cc_start: 0.7887 (tt0) cc_final: 0.7506 (mt-10) REVERT: I 160 ASP cc_start: 0.8083 (t70) cc_final: 0.7856 (t70) REVERT: I 219 ASP cc_start: 0.8052 (m-30) cc_final: 0.7635 (m-30) REVERT: I 227 ASN cc_start: 0.8052 (t0) cc_final: 0.7298 (m-40) REVERT: I 230 VAL cc_start: 0.8633 (t) cc_final: 0.8380 (p) REVERT: I 286 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: I 338 LYS cc_start: 0.8731 (mttp) cc_final: 0.8454 (mtmt) REVERT: I 374 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8300 (mt) REVERT: I 378 MET cc_start: 0.8950 (ttm) cc_final: 0.8682 (ttp) REVERT: I 518 MET cc_start: 0.8780 (mtp) cc_final: 0.8522 (mtp) REVERT: I 546 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8387 (mtt180) REVERT: I 607 THR cc_start: 0.9286 (t) cc_final: 0.8945 (m) REVERT: I 636 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: I 690 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8022 (ttmm) REVERT: J 1 MET cc_start: 0.4403 (OUTLIER) cc_final: 0.3062 (tmm) REVERT: J 36 THR cc_start: 0.7373 (m) cc_final: 0.6964 (p) REVERT: J 88 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7989 (tttt) REVERT: J 127 ASP cc_start: 0.7275 (t70) cc_final: 0.6821 (t0) REVERT: J 219 ASP cc_start: 0.7693 (m-30) cc_final: 0.7363 (m-30) REVERT: K 68 ASP cc_start: 0.8075 (t70) cc_final: 0.7726 (t0) REVERT: K 85 GLU cc_start: 0.7752 (pt0) cc_final: 0.7444 (pt0) REVERT: K 119 ASP cc_start: 0.8295 (t70) cc_final: 0.8050 (t70) REVERT: K 145 GLU cc_start: 0.7588 (pt0) cc_final: 0.6946 (mt-10) REVERT: K 188 GLN cc_start: 0.8504 (pp30) cc_final: 0.8216 (pt0) REVERT: K 211 MET cc_start: 0.8613 (mtp) cc_final: 0.8228 (mtm) REVERT: K 219 ASP cc_start: 0.8000 (m-30) cc_final: 0.7585 (m-30) REVERT: K 227 ASN cc_start: 0.7845 (t0) cc_final: 0.7245 (m-40) REVERT: K 239 GLN cc_start: 0.8744 (tt0) cc_final: 0.8498 (mt0) REVERT: K 291 MET cc_start: 0.9343 (mmm) cc_final: 0.8982 (mmm) REVERT: K 372 LYS cc_start: 0.8753 (tttm) cc_final: 0.8446 (tttp) REVERT: K 445 MET cc_start: 0.8687 (mtp) cc_final: 0.8435 (mtp) REVERT: K 543 LYS cc_start: 0.8342 (ttpp) cc_final: 0.7965 (ttpp) REVERT: K 550 ASP cc_start: 0.8422 (m-30) cc_final: 0.7839 (m-30) REVERT: K 690 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8105 (tttp) REVERT: L 1 MET cc_start: 0.4875 (mtm) cc_final: 0.4194 (pp-130) REVERT: L 13 ASP cc_start: 0.6872 (p0) cc_final: 0.6558 (m-30) REVERT: L 54 MET cc_start: 0.7262 (mmt) cc_final: 0.6435 (mpt) REVERT: L 155 GLU cc_start: 0.7818 (pt0) cc_final: 0.7501 (tt0) REVERT: L 163 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8366 (mmtp) REVERT: L 180 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7520 (mm110) REVERT: L 216 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8025 (pp20) outliers start: 94 outliers final: 42 residues processed: 750 average time/residue: 0.7893 time to fit residues: 710.1107 Evaluate side-chains 739 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 681 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 298 GLN Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 490 MET Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 223 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 510 ASP Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 374 LEU Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 163 LYS Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 167 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 439 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 466 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 695 ASN A 191 GLN A 695 ASN C 88 ASN C 191 GLN C 358 GLN D 137 ASN D 153 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN E 629 ASN F 141 ASN I 191 GLN I 410 ASN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110203 restraints weight = 44046.117| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.79 r_work: 0.3036 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41988 Z= 0.115 Angle : 0.454 9.298 56574 Z= 0.237 Chirality : 0.038 0.210 6078 Planarity : 0.004 0.038 7560 Dihedral : 3.632 18.505 5712 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.02 % Allowed : 13.52 % Favored : 84.46 % 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 are not related in a simple way. whole: 2.45 (0.12), residues: 5244 helix: 2.45 (0.08), residues: 3732 sheet: 1.53 (0.50), residues: 90 loop : -0.66 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 541 TYR 0.015 0.001 TYR F 138 PHE 0.009 0.001 PHE A 404 TRP 0.011 0.001 TRP C 366 HIS 0.002 0.001 HIS J 178 Details of bonding type rmsd covalent geometry : bond 0.00246 (41988) covalent geometry : angle 0.45384 (56574) hydrogen bonds : bond 0.04809 ( 2677) hydrogen bonds : angle 3.36314 ( 7923) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 700 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: H 201 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7812 (tm-30) REVERT: H 211 MET cc_start: 0.8648 (mtp) cc_final: 0.8406 (mtp) REVERT: H 266 ASP cc_start: 0.8702 (m-30) cc_final: 0.8408 (m-30) REVERT: H 286 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: H 298 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (pt0) REVERT: H 328 MET cc_start: 0.9092 (mtp) cc_final: 0.8851 (mtp) REVERT: H 407 MET cc_start: 0.9302 (mmt) cc_final: 0.8902 (mmt) REVERT: H 520 MET cc_start: 0.8702 (ttp) cc_final: 0.8387 (tpp) REVERT: H 554 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: H 561 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7916 (mmmt) REVERT: H 636 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: H 690 LYS cc_start: 0.8345 (ttpp) cc_final: 0.7874 (ttmm) REVERT: H 694 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6727 (mt-10) REVERT: G 36 THR cc_start: 0.7318 (m) cc_final: 0.6922 (p) REVERT: G 54 MET cc_start: 0.6661 (mpt) cc_final: 0.6408 (mpm) REVERT: G 88 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7713 (ttpt) REVERT: G 130 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.7997 (m) REVERT: G 216 GLU cc_start: 0.8461 (pt0) cc_final: 0.8138 (pt0) REVERT: G 219 ASP cc_start: 0.7937 (m-30) cc_final: 0.7632 (m-30) REVERT: A 102 GLU cc_start: 0.7938 (tt0) cc_final: 0.7658 (tt0) REVERT: A 110 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8201 (mtm180) REVERT: A 164 GLN cc_start: 0.8398 (mt0) cc_final: 0.7898 (tp-100) REVERT: A 207 GLN cc_start: 0.8836 (tt0) cc_final: 0.8551 (tt0) REVERT: A 298 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: A 307 GLU cc_start: 0.8788 (tt0) cc_final: 0.8569 (tt0) REVERT: A 451 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7694 (tp40) REVERT: A 543 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8163 (ttpp) REVERT: A 554 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: A 572 LEU cc_start: 0.8841 (mp) cc_final: 0.8586 (mt) REVERT: A 636 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: A 683 TYR cc_start: 0.8904 (m-80) cc_final: 0.8697 (m-80) REVERT: A 690 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7578 (ttmm) REVERT: B 1 MET cc_start: 0.5299 (ppp) cc_final: 0.4165 (mpp) REVERT: B 130 SER cc_start: 0.8814 (m) cc_final: 0.8590 (m) REVERT: B 188 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7997 (pm20) REVERT: B 216 GLU cc_start: 0.8408 (pt0) cc_final: 0.8078 (pt0) REVERT: C 102 GLU cc_start: 0.8048 (tt0) cc_final: 0.7690 (tt0) REVERT: C 162 ASP cc_start: 0.8019 (m-30) cc_final: 0.7726 (m-30) REVERT: C 201 GLU cc_start: 0.8203 (tt0) cc_final: 0.7888 (tm-30) REVERT: C 210 ASP cc_start: 0.8462 (m-30) cc_final: 0.8161 (m-30) REVERT: C 219 ASP cc_start: 0.8112 (m-30) cc_final: 0.7649 (m-30) REVERT: C 226 ASP cc_start: 0.7882 (m-30) cc_final: 0.7425 (m-30) REVERT: C 227 ASN cc_start: 0.8161 (t0) cc_final: 0.7346 (m-40) REVERT: C 266 ASP cc_start: 0.8597 (m-30) cc_final: 0.8385 (m-30) REVERT: C 421 MET cc_start: 0.8970 (mmm) cc_final: 0.8526 (mmt) REVERT: C 510 ASP cc_start: 0.8094 (m-30) cc_final: 0.7848 (m-30) REVERT: C 554 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: C 590 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8035 (mt-10) REVERT: C 602 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8481 (mtpt) REVERT: C 690 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8017 (tttp) REVERT: D 53 MET cc_start: 0.3960 (tpp) cc_final: 0.3641 (tpp) REVERT: D 156 THR cc_start: 0.8590 (t) cc_final: 0.8284 (m) REVERT: D 179 LYS cc_start: 0.8380 (mtpt) cc_final: 0.7904 (mptp) REVERT: D 180 GLN cc_start: 0.8512 (mm110) cc_final: 0.8285 (mm-40) REVERT: E 121 MET cc_start: 0.9284 (tpp) cc_final: 0.8910 (tpp) REVERT: E 211 MET cc_start: 0.8522 (mtp) cc_final: 0.8200 (mtp) REVERT: E 227 ASN cc_start: 0.8014 (t0) cc_final: 0.7236 (m110) REVERT: E 286 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: E 592 MET cc_start: 0.9113 (ttt) cc_final: 0.8791 (ttt) REVERT: E 673 MET cc_start: 0.9113 (ttt) cc_final: 0.8616 (ttt) REVERT: F 180 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7586 (mm110) REVERT: F 188 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: F 198 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6921 (tp30) REVERT: F 200 GLU cc_start: 0.7890 (tt0) cc_final: 0.7496 (mt-10) REVERT: I 160 ASP cc_start: 0.8057 (t70) cc_final: 0.7802 (t70) REVERT: I 219 ASP cc_start: 0.8056 (m-30) cc_final: 0.7641 (m-30) REVERT: I 227 ASN cc_start: 0.8059 (t0) cc_final: 0.7301 (m-40) REVERT: I 230 VAL cc_start: 0.8650 (t) cc_final: 0.8391 (p) REVERT: I 286 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: I 338 LYS cc_start: 0.8771 (mttp) cc_final: 0.8488 (mtmt) REVERT: I 374 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8338 (mt) REVERT: I 378 MET cc_start: 0.8946 (ttm) cc_final: 0.8677 (ttp) REVERT: I 510 ASP cc_start: 0.7949 (m-30) cc_final: 0.7561 (m-30) REVERT: I 518 MET cc_start: 0.8784 (mtp) cc_final: 0.8525 (mtp) REVERT: I 546 ARG cc_start: 0.8652 (mtt180) cc_final: 0.8345 (mtt180) REVERT: I 607 THR cc_start: 0.9295 (t) cc_final: 0.8952 (m) REVERT: I 636 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: I 690 LYS cc_start: 0.8316 (ttpp) cc_final: 0.8049 (ttmm) REVERT: J 1 MET cc_start: 0.4327 (OUTLIER) cc_final: 0.2872 (tmm) REVERT: J 36 THR cc_start: 0.7357 (m) cc_final: 0.6962 (p) REVERT: J 127 ASP cc_start: 0.7163 (t70) cc_final: 0.6563 (t0) REVERT: J 219 ASP cc_start: 0.7681 (m-30) cc_final: 0.7361 (m-30) REVERT: K 68 ASP cc_start: 0.8115 (t70) cc_final: 0.7763 (t0) REVERT: K 85 GLU cc_start: 0.7765 (pt0) cc_final: 0.7454 (pt0) REVERT: K 119 ASP cc_start: 0.8268 (t70) cc_final: 0.8015 (t70) REVERT: K 145 GLU cc_start: 0.7629 (pt0) cc_final: 0.6975 (mt-10) REVERT: K 188 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: K 211 MET cc_start: 0.8603 (mtp) cc_final: 0.8228 (mtm) REVERT: K 219 ASP cc_start: 0.8006 (m-30) cc_final: 0.7588 (m-30) REVERT: K 227 ASN cc_start: 0.7850 (t0) cc_final: 0.7245 (m-40) REVERT: K 239 GLN cc_start: 0.8758 (tt0) cc_final: 0.8498 (mt0) REVERT: K 291 MET cc_start: 0.9341 (mmm) cc_final: 0.8949 (mmm) REVERT: K 372 LYS cc_start: 0.8766 (tttm) cc_final: 0.8456 (tttp) REVERT: K 445 MET cc_start: 0.8683 (mtp) cc_final: 0.8429 (mtp) REVERT: K 543 LYS cc_start: 0.8372 (ttpp) cc_final: 0.8006 (ttpp) REVERT: K 550 ASP cc_start: 0.8442 (m-30) cc_final: 0.8104 (m-30) REVERT: K 690 LYS cc_start: 0.8365 (ttpp) cc_final: 0.8105 (tttp) REVERT: L 1 MET cc_start: 0.4933 (mtm) cc_final: 0.4240 (pp-130) REVERT: L 13 ASP cc_start: 0.6830 (p0) cc_final: 0.6573 (m-30) REVERT: L 54 MET cc_start: 0.7262 (mmt) cc_final: 0.6456 (mpt) REVERT: L 155 GLU cc_start: 0.7824 (pt0) cc_final: 0.7473 (tt0) REVERT: L 163 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8369 (mmtp) REVERT: L 180 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7532 (mm110) REVERT: L 216 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8036 (pp20) outliers start: 88 outliers final: 45 residues processed: 734 average time/residue: 0.7856 time to fit residues: 692.7422 Evaluate side-chains 748 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 684 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 298 GLN Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 490 MET Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 616 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 163 LYS Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 437 optimal weight: 0.9980 chunk 321 optimal weight: 0.9980 chunk 404 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 230 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 492 optimal weight: 0.2980 chunk 425 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 471 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 695 ASN G 199 GLN A 695 ASN C 88 ASN C 89 ASN C 191 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 191 GLN E 308 GLN F 141 ASN I 191 GLN I 410 ASN J 180 GLN K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111182 restraints weight = 44063.401| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.81 r_work: 0.3050 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 41988 Z= 0.108 Angle : 0.448 10.849 56574 Z= 0.233 Chirality : 0.038 0.211 6078 Planarity : 0.004 0.038 7560 Dihedral : 3.571 18.041 5712 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.81 % Allowed : 13.87 % Favored : 84.32 % 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 are not related in a simple way. whole: 2.52 (0.12), residues: 5244 helix: 2.50 (0.08), residues: 3732 sheet: 1.59 (0.50), residues: 90 loop : -0.63 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 541 TYR 0.015 0.001 TYR L 138 PHE 0.030 0.001 PHE G 128 TRP 0.011 0.001 TRP E 366 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00226 (41988) covalent geometry : angle 0.44774 (56574) hydrogen bonds : bond 0.04588 ( 2677) hydrogen bonds : angle 3.32793 ( 7923) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 703 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: H 201 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7748 (tm-30) REVERT: H 211 MET cc_start: 0.8630 (mtp) cc_final: 0.8385 (mtp) REVERT: H 266 ASP cc_start: 0.8699 (m-30) cc_final: 0.8402 (m-30) REVERT: H 286 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: H 298 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8585 (pt0) REVERT: H 328 MET cc_start: 0.9084 (mtp) cc_final: 0.8825 (mtp) REVERT: H 407 MET cc_start: 0.9299 (mmt) cc_final: 0.8906 (mmt) REVERT: H 520 MET cc_start: 0.8732 (ttp) cc_final: 0.8424 (tpp) REVERT: H 554 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: H 561 LYS cc_start: 0.8206 (mmpt) cc_final: 0.7893 (mmmt) REVERT: H 636 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: H 690 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7871 (ttmm) REVERT: H 694 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6714 (mt-10) REVERT: G 13 ASP cc_start: 0.7123 (p0) cc_final: 0.6445 (t0) REVERT: G 36 THR cc_start: 0.7287 (m) cc_final: 0.6897 (p) REVERT: G 54 MET cc_start: 0.6852 (mpt) cc_final: 0.6596 (mpm) REVERT: G 88 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7709 (ttpt) REVERT: G 130 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8070 (m) REVERT: G 180 GLN cc_start: 0.8238 (mm110) cc_final: 0.7892 (mm110) REVERT: G 209 ASP cc_start: 0.8273 (t0) cc_final: 0.7789 (t0) REVERT: G 216 GLU cc_start: 0.8443 (pt0) cc_final: 0.8122 (pt0) REVERT: G 219 ASP cc_start: 0.7930 (m-30) cc_final: 0.7638 (m-30) REVERT: A 102 GLU cc_start: 0.7946 (tt0) cc_final: 0.7648 (tt0) REVERT: A 110 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8182 (mtm180) REVERT: A 164 GLN cc_start: 0.8372 (mt0) cc_final: 0.7890 (tp-100) REVERT: A 207 GLN cc_start: 0.8819 (tt0) cc_final: 0.8546 (tt0) REVERT: A 285 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.6868 (tp30) REVERT: A 298 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7766 (mp10) REVERT: A 307 GLU cc_start: 0.8777 (tt0) cc_final: 0.8564 (tt0) REVERT: A 451 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7692 (tp40) REVERT: A 543 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8160 (ttpp) REVERT: A 554 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: A 636 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: A 683 TYR cc_start: 0.8908 (m-80) cc_final: 0.8701 (m-80) REVERT: A 690 LYS cc_start: 0.8102 (ttpp) cc_final: 0.7571 (ttmm) REVERT: B 1 MET cc_start: 0.5291 (ppp) cc_final: 0.4156 (mpp) REVERT: B 188 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7999 (pm20) REVERT: B 216 GLU cc_start: 0.8387 (pt0) cc_final: 0.8008 (pt0) REVERT: C 81 GLU cc_start: 0.7929 (tt0) cc_final: 0.7477 (mp0) REVERT: C 102 GLU cc_start: 0.8027 (tt0) cc_final: 0.7670 (tt0) REVERT: C 162 ASP cc_start: 0.8004 (m-30) cc_final: 0.7705 (m-30) REVERT: C 201 GLU cc_start: 0.8181 (tt0) cc_final: 0.7871 (tm-30) REVERT: C 210 ASP cc_start: 0.8453 (m-30) cc_final: 0.8146 (m-30) REVERT: C 219 ASP cc_start: 0.8102 (m-30) cc_final: 0.7655 (m-30) REVERT: C 226 ASP cc_start: 0.7870 (m-30) cc_final: 0.7403 (m-30) REVERT: C 227 ASN cc_start: 0.8154 (t0) cc_final: 0.7346 (m-40) REVERT: C 266 ASP cc_start: 0.8612 (m-30) cc_final: 0.8391 (m-30) REVERT: C 421 MET cc_start: 0.8954 (mmm) cc_final: 0.8588 (mmt) REVERT: C 510 ASP cc_start: 0.8026 (m-30) cc_final: 0.7794 (m-30) REVERT: C 554 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: C 590 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8025 (mt-10) REVERT: C 602 LYS cc_start: 0.8785 (mtmm) cc_final: 0.8507 (mtpt) REVERT: C 690 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8013 (tttp) REVERT: D 53 MET cc_start: 0.3939 (tpp) cc_final: 0.3578 (tpp) REVERT: D 179 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7915 (mptp) REVERT: D 180 GLN cc_start: 0.8443 (mm110) cc_final: 0.8197 (mm-40) REVERT: E 121 MET cc_start: 0.9282 (tpp) cc_final: 0.8902 (tpp) REVERT: E 152 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7730 (mm-30) REVERT: E 211 MET cc_start: 0.8489 (mtp) cc_final: 0.8173 (mtp) REVERT: E 227 ASN cc_start: 0.8010 (t0) cc_final: 0.7234 (m110) REVERT: E 286 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7765 (mp10) REVERT: E 345 MET cc_start: 0.9357 (mmm) cc_final: 0.9075 (mmm) REVERT: E 374 LEU cc_start: 0.8711 (tp) cc_final: 0.8471 (tt) REVERT: E 592 MET cc_start: 0.9106 (ttt) cc_final: 0.8815 (ttt) REVERT: E 616 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7347 (t0) REVERT: E 673 MET cc_start: 0.9132 (ttt) cc_final: 0.8661 (ttt) REVERT: F 180 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7584 (mm110) REVERT: F 188 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: F 198 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6910 (tp30) REVERT: I 160 ASP cc_start: 0.8047 (t70) cc_final: 0.7794 (t70) REVERT: I 219 ASP cc_start: 0.8068 (m-30) cc_final: 0.7656 (m-30) REVERT: I 227 ASN cc_start: 0.8021 (t0) cc_final: 0.7272 (m-40) REVERT: I 230 VAL cc_start: 0.8652 (t) cc_final: 0.8401 (p) REVERT: I 286 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: I 338 LYS cc_start: 0.8636 (mttp) cc_final: 0.8345 (mtmt) REVERT: I 374 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8299 (mt) REVERT: I 378 MET cc_start: 0.8938 (ttm) cc_final: 0.8669 (ttp) REVERT: I 510 ASP cc_start: 0.7920 (m-30) cc_final: 0.7525 (m-30) REVERT: I 518 MET cc_start: 0.8777 (mtp) cc_final: 0.8519 (mtp) REVERT: I 546 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8282 (mtt180) REVERT: I 607 THR cc_start: 0.9287 (t) cc_final: 0.8937 (m) REVERT: I 636 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: I 690 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8034 (ttmm) REVERT: J 1 MET cc_start: 0.4315 (OUTLIER) cc_final: 0.2867 (tmm) REVERT: J 36 THR cc_start: 0.7370 (m) cc_final: 0.6938 (p) REVERT: J 127 ASP cc_start: 0.7053 (t70) cc_final: 0.6723 (t0) REVERT: J 155 GLU cc_start: 0.8126 (pt0) cc_final: 0.7894 (tt0) REVERT: J 180 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7454 (tp40) REVERT: J 219 ASP cc_start: 0.7656 (m-30) cc_final: 0.7343 (m-30) REVERT: K 68 ASP cc_start: 0.8088 (t70) cc_final: 0.7742 (t0) REVERT: K 85 GLU cc_start: 0.7758 (pt0) cc_final: 0.7446 (pt0) REVERT: K 119 ASP cc_start: 0.8310 (t70) cc_final: 0.8077 (t70) REVERT: K 145 GLU cc_start: 0.7567 (pt0) cc_final: 0.6953 (mt-10) REVERT: K 152 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7838 (mp0) REVERT: K 188 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: K 211 MET cc_start: 0.8589 (mtp) cc_final: 0.8222 (mtm) REVERT: K 219 ASP cc_start: 0.7984 (m-30) cc_final: 0.7563 (m-30) REVERT: K 227 ASN cc_start: 0.7836 (t0) cc_final: 0.7258 (m-40) REVERT: K 239 GLN cc_start: 0.8743 (tt0) cc_final: 0.8484 (mt0) REVERT: K 291 MET cc_start: 0.9336 (mmm) cc_final: 0.8936 (mmm) REVERT: K 372 LYS cc_start: 0.8743 (tttm) cc_final: 0.8434 (tttp) REVERT: K 445 MET cc_start: 0.8693 (mtp) cc_final: 0.8437 (mtp) REVERT: K 543 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7976 (ttpp) REVERT: K 550 ASP cc_start: 0.8438 (m-30) cc_final: 0.8111 (m-30) REVERT: K 690 LYS cc_start: 0.8353 (ttpp) cc_final: 0.8091 (tttp) REVERT: L 1 MET cc_start: 0.4871 (mtm) cc_final: 0.4210 (pp-130) REVERT: L 54 MET cc_start: 0.7307 (mmt) cc_final: 0.6544 (mpt) REVERT: L 155 GLU cc_start: 0.7819 (pt0) cc_final: 0.7462 (tt0) REVERT: L 163 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8364 (mmtp) REVERT: L 180 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7551 (mm110) REVERT: L 216 GLU cc_start: 0.8265 (pt0) cc_final: 0.8019 (pp20) outliers start: 79 outliers final: 43 residues processed: 736 average time/residue: 0.7829 time to fit residues: 691.5257 Evaluate side-chains 743 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 680 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 298 GLN Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 490 MET Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 616 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 163 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 222 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 174 optimal weight: 30.0000 chunk 249 optimal weight: 1.9990 chunk 418 optimal weight: 20.0000 chunk 283 optimal weight: 3.9990 chunk 417 optimal weight: 10.0000 chunk 313 optimal weight: 0.7980 chunk 395 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 164 GLN H 695 ASN G 214 HIS A 191 GLN A 695 ASN C 88 ASN C 191 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 GLN F 141 ASN I 191 GLN I 410 ASN K 246 GLN K 340 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107024 restraints weight = 44016.469| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.78 r_work: 0.3009 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41988 Z= 0.161 Angle : 0.506 11.133 56574 Z= 0.264 Chirality : 0.040 0.228 6078 Planarity : 0.004 0.055 7560 Dihedral : 3.858 20.944 5712 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.86 % Allowed : 13.98 % Favored : 84.16 % 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 are not related in a simple way. whole: 2.26 (0.12), residues: 5244 helix: 2.31 (0.08), residues: 3738 sheet: 1.58 (0.50), residues: 90 loop : -0.75 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 349 TYR 0.019 0.002 TYR F 138 PHE 0.012 0.001 PHE E 404 TRP 0.010 0.001 TRP K 399 HIS 0.003 0.001 HIS J 178 Details of bonding type rmsd covalent geometry : bond 0.00376 (41988) covalent geometry : angle 0.50570 (56574) hydrogen bonds : bond 0.05790 ( 2677) hydrogen bonds : angle 3.49376 ( 7923) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 675 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: H 201 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7823 (tm-30) REVERT: H 266 ASP cc_start: 0.8769 (m-30) cc_final: 0.8490 (m-30) REVERT: H 286 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: H 328 MET cc_start: 0.9109 (mtp) cc_final: 0.8856 (mtp) REVERT: H 407 MET cc_start: 0.9306 (mmt) cc_final: 0.8887 (mmt) REVERT: H 520 MET cc_start: 0.8737 (ttp) cc_final: 0.8421 (tpp) REVERT: H 554 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: H 564 GLU cc_start: 0.7600 (pm20) cc_final: 0.7323 (pm20) REVERT: H 636 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: H 690 LYS cc_start: 0.8400 (ttpp) cc_final: 0.7918 (ttmm) REVERT: H 694 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6682 (mt-10) REVERT: G 54 MET cc_start: 0.6866 (mpt) cc_final: 0.6626 (mpm) REVERT: G 88 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7667 (ttpt) REVERT: G 180 GLN cc_start: 0.8251 (mm110) cc_final: 0.7935 (mm110) REVERT: G 219 ASP cc_start: 0.7846 (m-30) cc_final: 0.7613 (m-30) REVERT: A 102 GLU cc_start: 0.8136 (tt0) cc_final: 0.7733 (tt0) REVERT: A 110 ARG cc_start: 0.8543 (mtp180) cc_final: 0.8294 (mtm180) REVERT: A 207 GLN cc_start: 0.8860 (tt0) cc_final: 0.8581 (tt0) REVERT: A 298 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: A 307 GLU cc_start: 0.8837 (tt0) cc_final: 0.8602 (tt0) REVERT: A 451 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7753 (tp40) REVERT: A 543 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8249 (ttpp) REVERT: A 554 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7596 (tp30) REVERT: A 572 LEU cc_start: 0.8937 (mp) cc_final: 0.8676 (mt) REVERT: A 636 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: A 683 TYR cc_start: 0.8949 (m-80) cc_final: 0.8746 (m-80) REVERT: A 690 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7648 (ttmm) REVERT: B 188 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7935 (pm20) REVERT: B 216 GLU cc_start: 0.8461 (pt0) cc_final: 0.8078 (pt0) REVERT: C 102 GLU cc_start: 0.8104 (tt0) cc_final: 0.7732 (tt0) REVERT: C 152 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: C 162 ASP cc_start: 0.8060 (m-30) cc_final: 0.7762 (m-30) REVERT: C 201 GLU cc_start: 0.8254 (tt0) cc_final: 0.7953 (tm-30) REVERT: C 210 ASP cc_start: 0.8490 (m-30) cc_final: 0.8171 (m-30) REVERT: C 219 ASP cc_start: 0.8185 (m-30) cc_final: 0.7719 (m-30) REVERT: C 226 ASP cc_start: 0.7939 (m-30) cc_final: 0.7490 (m-30) REVERT: C 227 ASN cc_start: 0.8205 (t0) cc_final: 0.7376 (m-40) REVERT: C 266 ASP cc_start: 0.8604 (m-30) cc_final: 0.8399 (m-30) REVERT: C 421 MET cc_start: 0.8917 (mmm) cc_final: 0.8535 (mmt) REVERT: C 510 ASP cc_start: 0.8043 (m-30) cc_final: 0.7802 (m-30) REVERT: C 554 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: C 602 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8507 (mtpt) REVERT: C 690 LYS cc_start: 0.8305 (ttpp) cc_final: 0.8034 (tttp) REVERT: D 53 MET cc_start: 0.3973 (tpp) cc_final: 0.3509 (tpp) REVERT: D 54 MET cc_start: 0.7329 (mmt) cc_final: 0.7025 (mmp) REVERT: D 88 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7410 (ttmt) REVERT: D 156 THR cc_start: 0.8610 (t) cc_final: 0.8297 (m) REVERT: D 179 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7864 (mptp) REVERT: E 121 MET cc_start: 0.9286 (tpp) cc_final: 0.8986 (tpp) REVERT: E 148 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8113 (mtpt) REVERT: E 152 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7774 (mm-30) REVERT: E 211 MET cc_start: 0.8626 (mtp) cc_final: 0.8276 (mtp) REVERT: E 227 ASN cc_start: 0.8039 (t0) cc_final: 0.7249 (m110) REVERT: E 286 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: E 345 MET cc_start: 0.9374 (mmm) cc_final: 0.8988 (mmm) REVERT: E 564 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6989 (mt-10) REVERT: E 592 MET cc_start: 0.9142 (ttt) cc_final: 0.8855 (ttt) REVERT: E 629 ASN cc_start: 0.8210 (m110) cc_final: 0.7988 (m-40) REVERT: E 673 MET cc_start: 0.9189 (ttt) cc_final: 0.8804 (ttp) REVERT: F 180 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7641 (mm110) REVERT: F 188 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: I 219 ASP cc_start: 0.8118 (m-30) cc_final: 0.7693 (m-30) REVERT: I 227 ASN cc_start: 0.8121 (t0) cc_final: 0.7367 (m-40) REVERT: I 286 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: I 338 LYS cc_start: 0.8794 (mttp) cc_final: 0.8487 (mtmt) REVERT: I 374 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8353 (mt) REVERT: I 378 MET cc_start: 0.8991 (ttm) cc_final: 0.8704 (ttp) REVERT: I 510 ASP cc_start: 0.7966 (m-30) cc_final: 0.7583 (m-30) REVERT: I 518 MET cc_start: 0.8821 (mtp) cc_final: 0.8547 (mtp) REVERT: I 546 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8259 (mtt180) REVERT: I 607 THR cc_start: 0.9343 (t) cc_final: 0.8974 (m) REVERT: I 636 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: I 690 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8072 (ttmm) REVERT: J 1 MET cc_start: 0.4442 (OUTLIER) cc_final: 0.2802 (tmm) REVERT: J 127 ASP cc_start: 0.7204 (t70) cc_final: 0.6618 (t0) REVERT: J 155 GLU cc_start: 0.8186 (pt0) cc_final: 0.7923 (tt0) REVERT: J 219 ASP cc_start: 0.7622 (m-30) cc_final: 0.7302 (m-30) REVERT: K 85 GLU cc_start: 0.7751 (pt0) cc_final: 0.7336 (pt0) REVERT: K 119 ASP cc_start: 0.8320 (t70) cc_final: 0.8038 (t70) REVERT: K 145 GLU cc_start: 0.7657 (pt0) cc_final: 0.7043 (mt-10) REVERT: K 152 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7823 (mp0) REVERT: K 188 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: K 211 MET cc_start: 0.8681 (mtp) cc_final: 0.8276 (mtm) REVERT: K 219 ASP cc_start: 0.8037 (m-30) cc_final: 0.7608 (m-30) REVERT: K 227 ASN cc_start: 0.7912 (t0) cc_final: 0.7268 (m-40) REVERT: K 239 GLN cc_start: 0.8844 (tt0) cc_final: 0.8518 (tt0) REVERT: K 291 MET cc_start: 0.9359 (mmm) cc_final: 0.9034 (mmm) REVERT: K 372 LYS cc_start: 0.8799 (tttm) cc_final: 0.8482 (tttp) REVERT: K 445 MET cc_start: 0.8683 (mtp) cc_final: 0.8432 (mtp) REVERT: K 543 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8091 (ttpp) REVERT: K 550 ASP cc_start: 0.8464 (m-30) cc_final: 0.7969 (m-30) REVERT: K 572 LEU cc_start: 0.8832 (mp) cc_final: 0.8595 (mt) REVERT: K 690 LYS cc_start: 0.8366 (ttpp) cc_final: 0.8112 (tttp) REVERT: L 1 MET cc_start: 0.5059 (mtm) cc_final: 0.4245 (pp-130) REVERT: L 54 MET cc_start: 0.7337 (mmt) cc_final: 0.6545 (mpt) REVERT: L 155 GLU cc_start: 0.7831 (pt0) cc_final: 0.7515 (tt0) REVERT: L 163 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8424 (mmtp) REVERT: L 216 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8067 (pp20) outliers start: 81 outliers final: 46 residues processed: 719 average time/residue: 0.7691 time to fit residues: 663.6060 Evaluate side-chains 722 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 657 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 236 SER Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 298 GLN Chi-restraints excluded: chain H residue 490 MET Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 539 VAL Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain H residue 609 THR Chi-restraints excluded: chain H residue 636 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain E residue 148 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 236 SER Chi-restraints excluded: chain K residue 298 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain K residue 694 GLU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 163 LYS Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 504 optimal weight: 0.9980 chunk 392 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.0040 chunk 503 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 495 optimal weight: 3.9990 chunk 439 optimal weight: 0.8980 chunk 308 optimal weight: 0.0770 chunk 480 optimal weight: 0.6980 chunk 87 optimal weight: 30.0000 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 695 ASN A 82 GLN A 191 GLN A 695 ASN C 88 ASN C 89 ASN C 191 GLN D 180 GLN E 95 GLN E 191 GLN E 246 GLN F 141 ASN I 191 GLN I 392 GLN K 246 GLN K 340 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112214 restraints weight = 43935.777| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.78 r_work: 0.3091 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41988 Z= 0.101 Angle : 0.444 12.018 56574 Z= 0.231 Chirality : 0.037 0.240 6078 Planarity : 0.003 0.037 7560 Dihedral : 3.531 19.823 5712 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.40 % Allowed : 14.37 % Favored : 84.23 % 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 are not related in a simple way. whole: 2.54 (0.12), residues: 5244 helix: 2.50 (0.08), residues: 3732 sheet: 1.67 (0.50), residues: 90 loop : -0.62 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 541 TYR 0.017 0.001 TYR L 138 PHE 0.006 0.001 PHE A 404 TRP 0.013 0.001 TRP H 366 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00205 (41988) covalent geometry : angle 0.44373 (56574) hydrogen bonds : bond 0.04345 ( 2677) hydrogen bonds : angle 3.32335 ( 7923) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10488 Ramachandran restraints generated. 5244 Oldfield, 0 Emsley, 5244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 692 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: H 201 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7726 (tm-30) REVERT: H 266 ASP cc_start: 0.8707 (m-30) cc_final: 0.8358 (m-30) REVERT: H 286 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: H 298 GLN cc_start: 0.8806 (mt0) cc_final: 0.8587 (pt0) REVERT: H 328 MET cc_start: 0.9077 (mtp) cc_final: 0.8830 (mtp) REVERT: H 407 MET cc_start: 0.9290 (mmt) cc_final: 0.8928 (mmt) REVERT: H 520 MET cc_start: 0.8717 (ttp) cc_final: 0.8294 (tpp) REVERT: H 554 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: H 561 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7949 (mmmt) REVERT: H 564 GLU cc_start: 0.7581 (pm20) cc_final: 0.7335 (pm20) REVERT: H 690 LYS cc_start: 0.8337 (ttpp) cc_final: 0.7849 (ttmm) REVERT: H 694 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6717 (mt-10) REVERT: G 36 THR cc_start: 0.7268 (m) cc_final: 0.6861 (p) REVERT: G 54 MET cc_start: 0.6804 (mpt) cc_final: 0.6554 (mpm) REVERT: G 88 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7770 (ttpt) REVERT: G 130 SER cc_start: 0.8490 (m) cc_final: 0.8028 (m) REVERT: G 179 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8092 (mptt) REVERT: G 180 GLN cc_start: 0.8313 (mm110) cc_final: 0.8101 (mm110) REVERT: G 209 ASP cc_start: 0.8265 (t0) cc_final: 0.7729 (t0) REVERT: G 216 GLU cc_start: 0.8435 (pt0) cc_final: 0.8137 (pt0) REVERT: G 219 ASP cc_start: 0.7899 (m-30) cc_final: 0.7622 (m-30) REVERT: A 164 GLN cc_start: 0.8387 (mt0) cc_final: 0.7981 (tp-100) REVERT: A 207 GLN cc_start: 0.8823 (tt0) cc_final: 0.8545 (tt0) REVERT: A 307 GLU cc_start: 0.8749 (tt0) cc_final: 0.8533 (tt0) REVERT: A 451 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7683 (tp40) REVERT: A 466 MET cc_start: 0.9182 (ttm) cc_final: 0.8972 (ttp) REVERT: A 543 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8162 (ttpp) REVERT: A 554 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7451 (tp30) REVERT: A 636 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 690 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7589 (ttmm) REVERT: B 1 MET cc_start: 0.5247 (ppp) cc_final: 0.3965 (mpp) REVERT: B 188 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7875 (pm20) REVERT: B 216 GLU cc_start: 0.8348 (pt0) cc_final: 0.7986 (pt0) REVERT: C 81 GLU cc_start: 0.7967 (tt0) cc_final: 0.7479 (mp0) REVERT: C 102 GLU cc_start: 0.8036 (tt0) cc_final: 0.7529 (tt0) REVERT: C 121 MET cc_start: 0.9217 (tpp) cc_final: 0.8850 (tpt) REVERT: C 152 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: C 162 ASP cc_start: 0.8018 (m-30) cc_final: 0.7701 (m-30) REVERT: C 201 GLU cc_start: 0.8195 (tt0) cc_final: 0.7900 (tm-30) REVERT: C 210 ASP cc_start: 0.8434 (m-30) cc_final: 0.8112 (m-30) REVERT: C 219 ASP cc_start: 0.8090 (m-30) cc_final: 0.7652 (m-30) REVERT: C 226 ASP cc_start: 0.7891 (m-30) cc_final: 0.7432 (m-30) REVERT: C 227 ASN cc_start: 0.8165 (t0) cc_final: 0.7365 (m-40) REVERT: C 266 ASP cc_start: 0.8584 (m-30) cc_final: 0.8364 (m-30) REVERT: C 421 MET cc_start: 0.8976 (mmm) cc_final: 0.8576 (mmt) REVERT: C 510 ASP cc_start: 0.8054 (m-30) cc_final: 0.7806 (m-30) REVERT: C 554 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: C 602 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8522 (mtpt) REVERT: C 690 LYS cc_start: 0.8333 (ttpp) cc_final: 0.8050 (tttp) REVERT: D 53 MET cc_start: 0.3857 (tpp) cc_final: 0.3412 (tpp) REVERT: D 54 MET cc_start: 0.7300 (mmt) cc_final: 0.6975 (mmp) REVERT: D 88 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7430 (ttmt) REVERT: D 156 THR cc_start: 0.8554 (t) cc_final: 0.8257 (m) REVERT: D 179 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7908 (mptp) REVERT: E 121 MET cc_start: 0.9279 (tpp) cc_final: 0.8899 (tpp) REVERT: E 152 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7763 (mm-30) REVERT: E 211 MET cc_start: 0.8510 (mtp) cc_final: 0.8204 (mtp) REVERT: E 227 ASN cc_start: 0.8036 (t0) cc_final: 0.7271 (m110) REVERT: E 286 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7755 (mp10) REVERT: E 345 MET cc_start: 0.9344 (mmm) cc_final: 0.9052 (mmm) REVERT: E 564 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7046 (mt-10) REVERT: E 592 MET cc_start: 0.9079 (ttt) cc_final: 0.8822 (ttt) REVERT: E 673 MET cc_start: 0.9124 (ttt) cc_final: 0.8682 (ttt) REVERT: F 53 MET cc_start: 0.3532 (tpp) cc_final: 0.3093 (tpp) REVERT: F 180 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7597 (mm110) REVERT: F 188 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: F 198 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6890 (tp30) REVERT: F 200 GLU cc_start: 0.7879 (tt0) cc_final: 0.7484 (mt-10) REVERT: I 148 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7884 (mtmp) REVERT: I 219 ASP cc_start: 0.8072 (m-30) cc_final: 0.7741 (m-30) REVERT: I 227 ASN cc_start: 0.8076 (t0) cc_final: 0.7328 (m-40) REVERT: I 230 VAL cc_start: 0.8613 (t) cc_final: 0.8379 (p) REVERT: I 286 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: I 338 LYS cc_start: 0.8712 (mttp) cc_final: 0.8437 (mtmt) REVERT: I 374 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8314 (mt) REVERT: I 378 MET cc_start: 0.8902 (ttm) cc_final: 0.8648 (ttp) REVERT: I 518 MET cc_start: 0.8775 (mtp) cc_final: 0.8516 (mtp) REVERT: I 546 ARG cc_start: 0.8498 (mtt180) cc_final: 0.8226 (mtt180) REVERT: I 607 THR cc_start: 0.9294 (t) cc_final: 0.8932 (m) REVERT: I 636 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: I 690 LYS cc_start: 0.8331 (ttpp) cc_final: 0.8078 (ttmm) REVERT: J 1 MET cc_start: 0.4539 (OUTLIER) cc_final: 0.3941 (ppp) REVERT: J 36 THR cc_start: 0.7604 (m) cc_final: 0.7112 (p) REVERT: J 219 ASP cc_start: 0.7681 (m-30) cc_final: 0.7330 (m-30) REVERT: K 85 GLU cc_start: 0.7763 (pt0) cc_final: 0.7457 (pt0) REVERT: K 119 ASP cc_start: 0.8288 (t70) cc_final: 0.8052 (t70) REVERT: K 145 GLU cc_start: 0.7537 (pt0) cc_final: 0.6927 (mt-10) REVERT: K 152 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7814 (mp0) REVERT: K 188 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: K 211 MET cc_start: 0.8584 (mtp) cc_final: 0.8205 (mtm) REVERT: K 219 ASP cc_start: 0.8046 (m-30) cc_final: 0.7627 (m-30) REVERT: K 227 ASN cc_start: 0.7861 (t0) cc_final: 0.7283 (m-40) REVERT: K 239 GLN cc_start: 0.8741 (tt0) cc_final: 0.8497 (mt0) REVERT: K 291 MET cc_start: 0.9346 (mmm) cc_final: 0.9111 (mmm) REVERT: K 372 LYS cc_start: 0.8750 (tttm) cc_final: 0.8442 (tttp) REVERT: K 445 MET cc_start: 0.8698 (mtp) cc_final: 0.8445 (mtp) REVERT: K 543 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8003 (ttpp) REVERT: K 550 ASP cc_start: 0.8452 (m-30) cc_final: 0.8116 (m-30) REVERT: K 690 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8116 (tttp) REVERT: L 1 MET cc_start: 0.5090 (mtm) cc_final: 0.4287 (pp-130) REVERT: L 30 LEU cc_start: 0.7358 (tp) cc_final: 0.7129 (tp) REVERT: L 54 MET cc_start: 0.7289 (mmt) cc_final: 0.6503 (mpt) REVERT: L 155 GLU cc_start: 0.7815 (pt0) cc_final: 0.7471 (tt0) REVERT: L 163 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8379 (mmtp) REVERT: L 180 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7607 (mm110) REVERT: L 216 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8043 (pp20) outliers start: 61 outliers final: 30 residues processed: 720 average time/residue: 0.7925 time to fit residues: 685.9099 Evaluate side-chains 718 residues out of total 4404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 672 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 286 GLN Chi-restraints excluded: chain H residue 445 MET Chi-restraints excluded: chain H residue 554 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 595 GLU Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 370 GLN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 370 GLN Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 286 GLN Chi-restraints excluded: chain I residue 374 LEU Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 636 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 188 GLN Chi-restraints excluded: chain K residue 368 LYS Chi-restraints excluded: chain K residue 523 LYS Chi-restraints excluded: chain K residue 539 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 ASP Chi-restraints excluded: chain L residue 163 LYS Chi-restraints excluded: chain L residue 216 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 60 optimal weight: 2.9990 chunk 313 optimal weight: 0.6980 chunk 394 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 306 optimal weight: 0.7980 chunk 285 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 482 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 410 ASN H 524 GLN H 695 ASN A 695 ASN C 89 ASN C 191 GLN D 180 GLN E 191 GLN F 141 ASN I 410 ASN K 246 GLN K 695 ASN L 184 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.111239 restraints weight = 44215.116| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.79 r_work: 0.3070 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41988 Z= 0.110 Angle : 0.459 12.064 56574 Z= 0.238 Chirality : 0.038 0.239 6078 Planarity : 0.004 0.037 7560 Dihedral : 3.539 20.169 5712 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.19 % Allowed : 14.90 % Favored : 83.91 % 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 are not related in a simple way. whole: 2.56 (0.12), residues: 5244 helix: 2.50 (0.08), residues: 3738 sheet: 1.63 (0.50), residues: 90 loop : -0.57 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 541 TYR 0.020 0.001 TYR L 138 PHE 0.008 0.001 PHE A 404 TRP 0.011 0.001 TRP H 366 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00231 (41988) covalent geometry : angle 0.45854 (56574) hydrogen bonds : bond 0.04585 ( 2677) hydrogen bonds : angle 3.30790 ( 7923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19078.92 seconds wall clock time: 324 minutes 5.65 seconds (19445.65 seconds total)