Starting phenix.real_space_refine on Tue Aug 26 13:49:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5lkh_4068/08_2025/5lkh_4068.cif Found real_map, /net/cci-nas-00/data/ceres_data/5lkh_4068/08_2025/5lkh_4068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5lkh_4068/08_2025/5lkh_4068.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5lkh_4068/08_2025/5lkh_4068.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5lkh_4068/08_2025/5lkh_4068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5lkh_4068/08_2025/5lkh_4068.map" } resolution = 3.46 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= 1.000 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 100 5.16 5 C 23755 2.51 5 N 6200 2.21 5 O 7290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37345 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7469 Classifications: {'peptide': 948} Link IDs: {'CIS': 2, 'PTRANS': 35, 'TRANS': 910} Chain breaks: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 9.84, per 1000 atoms: 0.26 Number of scatterers: 37345 At special positions: 0 Unit cell: (262.19, 265.33, 152.29, 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 100 16.00 O 7290 8.00 N 6200 7.00 C 23755 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: 3.57 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8950 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 35 sheets defined 45.7% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.515A pdb=" N LEU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 removed outlier: 4.350A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 268 removed outlier: 4.430A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.917A pdb=" N MET A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.671A pdb=" N PHE A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 4.198A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 491 through 499 removed outlier: 3.592A pdb=" N ILE A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.705A pdb=" N THR A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 581 through 598 removed outlier: 3.568A pdb=" N LEU A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 623 through 645 Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.505A pdb=" N MET A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 679 Processing helix chain 'A' and resid 687 through 700 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 704 through 719 Processing helix chain 'A' and resid 726 through 738 Processing helix chain 'A' and resid 748 through 770 Processing helix chain 'A' and resid 772 through 782 Processing helix chain 'A' and resid 797 through 815 Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.632A pdb=" N ALA A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 840 removed outlier: 3.661A pdb=" N ASP A 837 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 856 removed outlier: 3.548A pdb=" N LEU A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 856 " --> pdb=" O GLN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 removed outlier: 4.522A pdb=" N PHE A 868 " --> pdb=" O PRO A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 887 Processing helix chain 'A' and resid 1366 through 1379 removed outlier: 3.594A pdb=" N ASN A1370 " --> pdb=" O GLY A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1465 through 1469 Processing helix chain 'A' and resid 1512 through 1517 removed outlier: 3.706A pdb=" N ASP A1516 " --> pdb=" O THR A1512 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 224 through 231 removed outlier: 3.515A pdb=" N LEU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 241 removed outlier: 4.351A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 256 through 268 removed outlier: 4.429A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.917A pdb=" N MET B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.671A pdb=" N PHE B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 404 removed outlier: 4.198A pdb=" N GLN B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 453 through 465 Processing helix chain 'B' and resid 471 through 488 Processing helix chain 'B' and resid 491 through 499 removed outlier: 3.591A pdb=" N ILE B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.705A pdb=" N THR B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 581 through 598 removed outlier: 3.567A pdb=" N LEU B 585 " --> pdb=" O ASN B 581 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 623 through 645 Processing helix chain 'B' and resid 647 through 656 removed outlier: 3.504A pdb=" N MET B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 Processing helix chain 'B' and resid 687 through 700 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 704 through 719 Processing helix chain 'B' and resid 726 through 738 Processing helix chain 'B' and resid 748 through 770 Processing helix chain 'B' and resid 772 through 782 Processing helix chain 'B' and resid 797 through 815 Processing helix chain 'B' and resid 817 through 827 removed outlier: 3.632A pdb=" N ALA B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 840 removed outlier: 3.660A pdb=" N ASP B 837 " --> pdb=" O GLU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 856 removed outlier: 3.548A pdb=" N LEU B 846 " --> pdb=" O ASP B 842 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 856 " --> pdb=" O GLN B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 868 removed outlier: 4.521A pdb=" N PHE B 868 " --> pdb=" O PRO B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 887 Processing helix chain 'B' and resid 1366 through 1379 removed outlier: 3.593A pdb=" N ASN B1370 " --> pdb=" O GLY B1366 " (cutoff:3.500A) Processing helix chain 'B' and resid 1465 through 1469 Processing helix chain 'B' and resid 1512 through 1517 removed outlier: 3.705A pdb=" N ASP B1516 " --> pdb=" O THR B1512 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.515A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET C 231 " --> pdb=" O ILE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 removed outlier: 4.351A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 256 through 268 removed outlier: 4.430A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.916A pdb=" N MET C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.670A pdb=" N PHE C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 404 removed outlier: 4.198A pdb=" N GLN C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 453 through 465 Processing helix chain 'C' and resid 471 through 488 Processing helix chain 'C' and resid 491 through 499 removed outlier: 3.592A pdb=" N ILE C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 545 through 556 removed outlier: 3.705A pdb=" N THR C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.568A pdb=" N LEU C 585 " --> pdb=" O ASN C 581 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS C 598 " --> pdb=" O LEU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 613 Processing helix chain 'C' and resid 623 through 645 Processing helix chain 'C' and resid 647 through 656 removed outlier: 3.504A pdb=" N MET C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 679 Processing helix chain 'C' and resid 687 through 700 Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 704 through 719 Processing helix chain 'C' and resid 726 through 738 Processing helix chain 'C' and resid 748 through 770 Processing helix chain 'C' and resid 772 through 782 Processing helix chain 'C' and resid 797 through 815 Processing helix chain 'C' and resid 817 through 827 removed outlier: 3.631A pdb=" N ALA C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 840 removed outlier: 3.660A pdb=" N ASP C 837 " --> pdb=" O GLU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 856 removed outlier: 3.548A pdb=" N LEU C 846 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 856 " --> pdb=" O GLN C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 868 removed outlier: 4.521A pdb=" N PHE C 868 " --> pdb=" O PRO C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 887 Processing helix chain 'C' and resid 1366 through 1379 removed outlier: 3.593A pdb=" N ASN C1370 " --> pdb=" O GLY C1366 " (cutoff:3.500A) Processing helix chain 'C' and resid 1465 through 1469 Processing helix chain 'C' and resid 1512 through 1517 removed outlier: 3.705A pdb=" N ASP C1516 " --> pdb=" O THR C1512 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 224 through 231 removed outlier: 3.516A pdb=" N LEU D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 241 removed outlier: 4.351A pdb=" N GLY D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 253 Processing helix chain 'D' and resid 256 through 268 removed outlier: 4.430A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU D 262 " --> pdb=" O GLY D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.917A pdb=" N MET D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'D' and resid 289 through 297 removed outlier: 3.671A pdb=" N PHE D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 404 removed outlier: 4.198A pdb=" N GLN D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 453 through 465 Processing helix chain 'D' and resid 471 through 488 Processing helix chain 'D' and resid 491 through 499 removed outlier: 3.591A pdb=" N ILE D 497 " --> pdb=" O GLU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 545 through 556 removed outlier: 3.705A pdb=" N THR D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.568A pdb=" N LEU D 585 " --> pdb=" O ASN D 581 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS D 598 " --> pdb=" O LEU D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 623 through 645 Processing helix chain 'D' and resid 647 through 656 removed outlier: 3.504A pdb=" N MET D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 679 Processing helix chain 'D' and resid 687 through 700 Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 704 through 719 Processing helix chain 'D' and resid 726 through 738 Processing helix chain 'D' and resid 748 through 770 Processing helix chain 'D' and resid 772 through 782 Processing helix chain 'D' and resid 797 through 815 Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.631A pdb=" N ALA D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 840 removed outlier: 3.660A pdb=" N ASP D 837 " --> pdb=" O GLU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 856 removed outlier: 3.548A pdb=" N LEU D 846 " --> pdb=" O ASP D 842 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 856 " --> pdb=" O GLN D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 868 removed outlier: 4.520A pdb=" N PHE D 868 " --> pdb=" O PRO D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 887 Processing helix chain 'D' and resid 1366 through 1379 removed outlier: 3.592A pdb=" N ASN D1370 " --> pdb=" O GLY D1366 " (cutoff:3.500A) Processing helix chain 'D' and resid 1465 through 1469 Processing helix chain 'D' and resid 1512 through 1517 removed outlier: 3.706A pdb=" N ASP D1516 " --> pdb=" O THR D1512 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 224 through 231 removed outlier: 3.516A pdb=" N LEU E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 241 removed outlier: 4.351A pdb=" N GLY E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 253 Processing helix chain 'E' and resid 256 through 268 removed outlier: 4.429A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU E 262 " --> pdb=" O GLY E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 278 removed outlier: 3.917A pdb=" N MET E 278 " --> pdb=" O ALA E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 287 Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.671A pdb=" N PHE E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 404 removed outlier: 4.198A pdb=" N GLN E 404 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 451 Processing helix chain 'E' and resid 453 through 465 Processing helix chain 'E' and resid 471 through 488 Processing helix chain 'E' and resid 491 through 499 removed outlier: 3.592A pdb=" N ILE E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 545 through 556 removed outlier: 3.704A pdb=" N THR E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 570 Processing helix chain 'E' and resid 581 through 598 removed outlier: 3.568A pdb=" N LEU E 585 " --> pdb=" O ASN E 581 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS E 598 " --> pdb=" O LEU E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 Processing helix chain 'E' and resid 623 through 645 Processing helix chain 'E' and resid 647 through 656 removed outlier: 3.505A pdb=" N MET E 654 " --> pdb=" O GLN E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 679 Processing helix chain 'E' and resid 687 through 700 Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 704 through 719 Processing helix chain 'E' and resid 726 through 738 Processing helix chain 'E' and resid 748 through 770 Processing helix chain 'E' and resid 772 through 782 Processing helix chain 'E' and resid 797 through 815 Processing helix chain 'E' and resid 817 through 827 removed outlier: 3.632A pdb=" N ALA E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 840 removed outlier: 3.660A pdb=" N ASP E 837 " --> pdb=" O GLU E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 856 removed outlier: 3.548A pdb=" N LEU E 846 " --> pdb=" O ASP E 842 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E 856 " --> pdb=" O GLN E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 868 removed outlier: 4.521A pdb=" N PHE E 868 " --> pdb=" O PRO E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 870 through 887 Processing helix chain 'E' and resid 1366 through 1379 removed outlier: 3.593A pdb=" N ASN E1370 " --> pdb=" O GLY E1366 " (cutoff:3.500A) Processing helix chain 'E' and resid 1465 through 1469 Processing helix chain 'E' and resid 1512 through 1517 removed outlier: 3.706A pdb=" N ASP E1516 " --> pdb=" O THR E1512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 319 removed outlier: 3.718A pdb=" N ASN A 319 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 324 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 413 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A 367 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 342 through 349 removed outlier: 7.069A pdb=" N ASN A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA4, first strand: chain 'A' and resid 1319 through 1324 removed outlier: 7.115A pdb=" N ARG A1319 " --> pdb=" O SER A1571 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER A1571 " --> pdb=" O ARG A1319 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A1566 " --> pdb=" O ALA A1557 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A1557 " --> pdb=" O GLY A1566 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A1556 " --> pdb=" O GLN A1499 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A1504 " --> pdb=" O LYS A1507 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A1507 " --> pdb=" O ALA A1504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1340 through 1344 Processing sheet with id=AA6, first strand: chain 'A' and resid 1357 through 1359 Processing sheet with id=AA7, first strand: chain 'A' and resid 1444 through 1450 removed outlier: 6.039A pdb=" N SER A1432 " --> pdb=" O ASN A1449 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A1471 " --> pdb=" O VAL A1483 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR A1388 " --> pdb=" O PRO A1486 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU A1488 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A1386 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN A1490 " --> pdb=" O LYS A1384 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS A1384 " --> pdb=" O ASN A1490 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS A1384 " --> pdb=" O TYR A1410 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A1410 " --> pdb=" O LYS A1384 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A1388 " --> pdb=" O PRO A1406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 319 removed outlier: 3.718A pdb=" N ASN B 319 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 324 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 413 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR B 367 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 342 through 349 removed outlier: 7.069A pdb=" N ASN B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 536 through 537 Processing sheet with id=AB2, first strand: chain 'B' and resid 1319 through 1324 removed outlier: 7.115A pdb=" N ARG B1319 " --> pdb=" O SER B1571 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER B1571 " --> pdb=" O ARG B1319 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY B1566 " --> pdb=" O ALA B1557 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B1557 " --> pdb=" O GLY B1566 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B1556 " --> pdb=" O GLN B1499 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA B1504 " --> pdb=" O LYS B1507 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B1507 " --> pdb=" O ALA B1504 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1340 through 1344 Processing sheet with id=AB4, first strand: chain 'B' and resid 1357 through 1359 Processing sheet with id=AB5, first strand: chain 'B' and resid 1444 through 1450 removed outlier: 6.039A pdb=" N SER B1432 " --> pdb=" O ASN B1449 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B1471 " --> pdb=" O VAL B1483 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR B1388 " --> pdb=" O PRO B1486 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU B1488 " --> pdb=" O ILE B1386 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE B1386 " --> pdb=" O GLU B1488 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN B1490 " --> pdb=" O LYS B1384 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS B1384 " --> pdb=" O ASN B1490 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS B1384 " --> pdb=" O TYR B1410 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B1410 " --> pdb=" O LYS B1384 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B1388 " --> pdb=" O PRO B1406 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 313 through 319 removed outlier: 3.719A pdb=" N ASN C 319 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR C 324 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 413 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR C 367 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 342 through 349 removed outlier: 7.069A pdb=" N ASN C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AB9, first strand: chain 'C' and resid 1319 through 1324 removed outlier: 7.116A pdb=" N ARG C1319 " --> pdb=" O SER C1571 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER C1571 " --> pdb=" O ARG C1319 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY C1566 " --> pdb=" O ALA C1557 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C1557 " --> pdb=" O GLY C1566 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C1556 " --> pdb=" O GLN C1499 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA C1504 " --> pdb=" O LYS C1507 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS C1507 " --> pdb=" O ALA C1504 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1340 through 1344 Processing sheet with id=AC2, first strand: chain 'C' and resid 1357 through 1359 Processing sheet with id=AC3, first strand: chain 'C' and resid 1444 through 1450 removed outlier: 6.038A pdb=" N SER C1432 " --> pdb=" O ASN C1449 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C1471 " --> pdb=" O VAL C1483 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR C1388 " --> pdb=" O PRO C1486 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU C1488 " --> pdb=" O ILE C1386 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C1386 " --> pdb=" O GLU C1488 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN C1490 " --> pdb=" O LYS C1384 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS C1384 " --> pdb=" O ASN C1490 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS C1384 " --> pdb=" O TYR C1410 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C1410 " --> pdb=" O LYS C1384 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR C1388 " --> pdb=" O PRO C1406 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 313 through 319 removed outlier: 3.718A pdb=" N ASN D 319 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR D 324 " --> pdb=" O ASN D 319 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 413 " --> pdb=" O TYR D 367 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR D 367 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 342 through 349 removed outlier: 7.069A pdb=" N ASN D 352 " --> pdb=" O PHE D 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 536 through 537 Processing sheet with id=AC7, first strand: chain 'D' and resid 1319 through 1324 removed outlier: 7.115A pdb=" N ARG D1319 " --> pdb=" O SER D1571 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER D1571 " --> pdb=" O ARG D1319 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY D1566 " --> pdb=" O ALA D1557 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D1557 " --> pdb=" O GLY D1566 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D1556 " --> pdb=" O GLN D1499 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA D1504 " --> pdb=" O LYS D1507 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D1507 " --> pdb=" O ALA D1504 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 1340 through 1344 Processing sheet with id=AC9, first strand: chain 'D' and resid 1357 through 1359 Processing sheet with id=AD1, first strand: chain 'D' and resid 1444 through 1450 removed outlier: 6.038A pdb=" N SER D1432 " --> pdb=" O ASN D1449 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE D1471 " --> pdb=" O VAL D1483 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR D1388 " --> pdb=" O PRO D1486 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU D1488 " --> pdb=" O ILE D1386 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE D1386 " --> pdb=" O GLU D1488 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN D1490 " --> pdb=" O LYS D1384 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS D1384 " --> pdb=" O ASN D1490 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS D1384 " --> pdb=" O TYR D1410 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR D1410 " --> pdb=" O LYS D1384 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR D1388 " --> pdb=" O PRO D1406 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 313 through 319 removed outlier: 3.717A pdb=" N ASN E 319 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR E 324 " --> pdb=" O ASN E 319 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER E 418 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 413 " --> pdb=" O TYR E 367 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR E 367 " --> pdb=" O VAL E 413 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 342 through 349 removed outlier: 7.069A pdb=" N ASN E 352 " --> pdb=" O PHE E 348 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 536 through 537 Processing sheet with id=AD5, first strand: chain 'E' and resid 1319 through 1324 removed outlier: 7.116A pdb=" N ARG E1319 " --> pdb=" O SER E1571 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER E1571 " --> pdb=" O ARG E1319 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY E1566 " --> pdb=" O ALA E1557 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E1557 " --> pdb=" O GLY E1566 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR E1556 " --> pdb=" O GLN E1499 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA E1504 " --> pdb=" O LYS E1507 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS E1507 " --> pdb=" O ALA E1504 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1340 through 1344 Processing sheet with id=AD7, first strand: chain 'E' and resid 1357 through 1359 Processing sheet with id=AD8, first strand: chain 'E' and resid 1444 through 1450 removed outlier: 6.039A pdb=" N SER E1432 " --> pdb=" O ASN E1449 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E1471 " --> pdb=" O VAL E1483 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR E1388 " --> pdb=" O PRO E1486 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU E1488 " --> pdb=" O ILE E1386 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE E1386 " --> pdb=" O GLU E1488 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASN E1490 " --> pdb=" O LYS E1384 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS E1384 " --> pdb=" O ASN E1490 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS E1384 " --> pdb=" O TYR E1410 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR E1410 " --> pdb=" O LYS E1384 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR E1388 " --> pdb=" O PRO E1406 " (cutoff:3.500A) 1880 hydrogen bonds defined for protein. 5475 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: 11.27 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6650 1.33 - 1.45: 14654 1.45 - 1.58: 16651 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 38135 Sorted by residual: bond pdb=" CA THR C 790 " pdb=" C THR C 790 " ideal model delta sigma weight residual 1.532 1.475 0.058 9.60e-03 1.09e+04 3.63e+01 bond pdb=" CA THR E 790 " pdb=" C THR E 790 " ideal model delta sigma weight residual 1.532 1.475 0.058 9.60e-03 1.09e+04 3.61e+01 bond pdb=" CA THR A 790 " pdb=" C THR A 790 " ideal model delta sigma weight residual 1.532 1.475 0.057 9.60e-03 1.09e+04 3.57e+01 bond pdb=" CA THR D 790 " pdb=" C THR D 790 " ideal model delta sigma weight residual 1.532 1.476 0.057 9.60e-03 1.09e+04 3.51e+01 bond pdb=" CA THR B 790 " pdb=" C THR B 790 " ideal model delta sigma weight residual 1.532 1.476 0.057 9.60e-03 1.09e+04 3.49e+01 ... (remaining 38130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 49245 4.80 - 9.61: 2414 9.61 - 14.41: 136 14.41 - 19.21: 10 19.21 - 24.01: 5 Bond angle restraints: 51810 Sorted by residual: angle pdb=" N LYS C 616 " pdb=" CA LYS C 616 " pdb=" C LYS C 616 " ideal model delta sigma weight residual 113.12 97.21 15.91 1.25e+00 6.40e-01 1.62e+02 angle pdb=" N LYS D 616 " pdb=" CA LYS D 616 " pdb=" C LYS D 616 " ideal model delta sigma weight residual 113.12 97.22 15.90 1.25e+00 6.40e-01 1.62e+02 angle pdb=" N LYS E 616 " pdb=" CA LYS E 616 " pdb=" C LYS E 616 " ideal model delta sigma weight residual 113.12 97.23 15.89 1.25e+00 6.40e-01 1.62e+02 angle pdb=" N LYS B 616 " pdb=" CA LYS B 616 " pdb=" C LYS B 616 " ideal model delta sigma weight residual 113.12 97.23 15.89 1.25e+00 6.40e-01 1.62e+02 angle pdb=" N LYS A 616 " pdb=" CA LYS A 616 " pdb=" C LYS A 616 " ideal model delta sigma weight residual 113.12 97.23 15.89 1.25e+00 6.40e-01 1.62e+02 ... (remaining 51805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 21426 17.60 - 35.19: 1124 35.19 - 52.79: 140 52.79 - 70.38: 80 70.38 - 87.98: 65 Dihedral angle restraints: 22835 sinusoidal: 8920 harmonic: 13915 Sorted by residual: dihedral pdb=" CA GLY D 615 " pdb=" C GLY D 615 " pdb=" N LYS D 616 " pdb=" CA LYS D 616 " ideal model delta harmonic sigma weight residual 180.00 138.60 41.40 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLY A 615 " pdb=" C GLY A 615 " pdb=" N LYS A 616 " pdb=" CA LYS A 616 " ideal model delta harmonic sigma weight residual 180.00 138.63 41.37 0 5.00e+00 4.00e-02 6.85e+01 dihedral pdb=" CA GLY C 615 " pdb=" C GLY C 615 " pdb=" N LYS C 616 " pdb=" CA LYS C 616 " ideal model delta harmonic sigma weight residual 180.00 138.64 41.36 0 5.00e+00 4.00e-02 6.84e+01 ... (remaining 22832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 4924 0.151 - 0.303: 719 0.303 - 0.454: 147 0.454 - 0.606: 35 0.606 - 0.757: 5 Chirality restraints: 5830 Sorted by residual: chirality pdb=" CA GLN B 848 " pdb=" N GLN B 848 " pdb=" C GLN B 848 " pdb=" CB GLN B 848 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA GLN D 848 " pdb=" N GLN D 848 " pdb=" C GLN D 848 " pdb=" CB GLN D 848 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA GLN E 848 " pdb=" N GLN E 848 " pdb=" C GLN E 848 " pdb=" CB GLN E 848 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 5827 not shown) Planarity restraints: 6700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D1572 " -0.096 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO D1573 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO D1573 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO D1573 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1572 " -0.096 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO A1573 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO A1573 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO A1573 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C1572 " 0.096 5.00e-02 4.00e+02 1.45e-01 3.34e+01 pdb=" N PRO C1573 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO C1573 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO C1573 " 0.075 5.00e-02 4.00e+02 ... (remaining 6697 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 10850 2.78 - 3.31: 41374 3.31 - 3.84: 61529 3.84 - 4.37: 76894 4.37 - 4.90: 118033 Nonbonded interactions: 308680 Sorted by model distance: nonbonded pdb=" N TYR D 339 " pdb=" O TYR D 339 " model vdw 2.255 2.496 nonbonded pdb=" N TYR E 339 " pdb=" O TYR E 339 " model vdw 2.255 2.496 nonbonded pdb=" N TYR C 339 " pdb=" O TYR C 339 " model vdw 2.255 2.496 nonbonded pdb=" N TYR B 339 " pdb=" O TYR B 339 " model vdw 2.256 2.496 nonbonded pdb=" N TYR A 339 " pdb=" O TYR A 339 " model vdw 2.256 2.496 ... (remaining 308675 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 40.060 Find NCS groups from input model: 0.380 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1614 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 : 0.018 0.067 38135 Z= 1.277 Angle : 2.369 24.013 51810 Z= 1.608 Chirality : 0.121 0.757 5830 Planarity : 0.016 0.145 6700 Dihedral : 12.658 87.978 13885 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 87.16 Ramachandran Plot: Outliers : 1.38 % Allowed : 3.39 % Favored : 95.23 % Rotamer: Outliers : 1.96 % Allowed : 5.75 % Favored : 92.29 % Cbeta Deviations : 1.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.11), residues: 4720 helix: 0.96 (0.11), residues: 1820 sheet: 0.71 (0.16), residues: 980 loop : -1.82 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1563 TYR 0.021 0.003 TYR D1306 PHE 0.014 0.002 PHE E 563 TRP 0.038 0.006 TRP C 810 HIS 0.003 0.000 HIS D 796 Details of bonding type rmsd covalent geometry : bond 0.01816 (38135) covalent geometry : angle 2.36869 (51810) hydrogen bonds : bond 0.18824 ( 1880) hydrogen bonds : angle 9.01505 ( 5475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: -0.1356 (tpp) cc_final: -0.2893 (ttp) REVERT: A 654 MET cc_start: 0.5395 (ttt) cc_final: 0.4711 (ttp) REVERT: A 803 MET cc_start: 0.2663 (tmm) cc_final: 0.2080 (ttt) REVERT: B 803 MET cc_start: 0.5617 (tmm) cc_final: 0.5148 (tmm) REVERT: C 341 MET cc_start: -0.2198 (tpp) cc_final: -0.4357 (ttp) REVERT: C 649 PHE cc_start: 0.5393 (m-80) cc_final: 0.5180 (m-10) REVERT: C 692 MET cc_start: -0.5397 (OUTLIER) cc_final: -0.5654 (tmt) REVERT: D 649 PHE cc_start: 0.5969 (m-80) cc_final: 0.5500 (m-10) REVERT: E 341 MET cc_start: -0.4109 (tpp) cc_final: -0.5173 (tmm) REVERT: E 692 MET cc_start: -0.4970 (OUTLIER) cc_final: -0.5676 (ttt) outliers start: 80 outliers final: 27 residues processed: 397 average time/residue: 0.2818 time to fit residues: 173.7429 Evaluate side-chains 220 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 462 ARG Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1563 ARG Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 701 GLN Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1563 ARG Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 462 ARG Chi-restraints excluded: chain E residue 692 MET Chi-restraints excluded: chain E residue 847 LEU Chi-restraints excluded: chain E residue 1329 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 40.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 240 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 598 HIS A 642 HIS A 650 GLN A 709 HIS ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 HIS A 885 GLN A1361 HIS A1462 ASN B 222 ASN B 337 ASN ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS B 642 HIS B 650 GLN B 709 HIS ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 HIS B 885 GLN B1361 HIS B1462 ASN C 222 ASN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 HIS ** C 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 HIS ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 885 GLN C1361 HIS C1370 ASN C1462 ASN D 222 ASN ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 HIS ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 885 GLN D1370 ASN D1462 ASN E 222 ASN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 HIS E 650 GLN E 709 HIS ** E 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 767 HIS ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 885 GLN E1370 ASN E1462 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5556 r_free = 0.5556 target = 0.169060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.135708 restraints weight = 369109.454| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 24.69 r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4784 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 38135 Z= 0.230 Angle : 0.997 18.224 51810 Z= 0.504 Chirality : 0.052 0.303 5830 Planarity : 0.008 0.078 6700 Dihedral : 7.686 75.602 5178 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.41 % Favored : 96.27 % Rotamer: Outliers : 2.59 % Allowed : 8.47 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.11), residues: 4720 helix: 0.25 (0.11), residues: 1850 sheet: 0.43 (0.16), residues: 920 loop : -1.45 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 284 TYR 0.024 0.002 TYR E1410 PHE 0.031 0.003 PHE A1525 TRP 0.026 0.003 TRP C1324 HIS 0.008 0.002 HIS E1361 Details of bonding type rmsd covalent geometry : bond 0.00485 (38135) covalent geometry : angle 0.99700 (51810) hydrogen bonds : bond 0.05743 ( 1880) hydrogen bonds : angle 6.80226 ( 5475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 220 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: -0.2153 (tpp) cc_final: -0.4580 (tpp) REVERT: A 654 MET cc_start: 0.5045 (ttt) cc_final: 0.4459 (ttm) REVERT: A 803 MET cc_start: 0.1528 (tmm) cc_final: 0.0831 (ttt) REVERT: A 1306 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.5247 (t80) REVERT: A 1320 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7589 (pttt) REVERT: A 1528 MET cc_start: 0.7708 (mmm) cc_final: 0.7488 (mmt) REVERT: A 1551 ILE cc_start: 0.7835 (mm) cc_final: 0.7617 (tp) REVERT: B 341 MET cc_start: -0.2216 (tpp) cc_final: -0.3059 (tpp) REVERT: C 231 MET cc_start: 0.4618 (tpp) cc_final: 0.3212 (ttm) REVERT: C 341 MET cc_start: -0.2094 (tpp) cc_final: -0.3194 (ttt) REVERT: C 654 MET cc_start: -0.0258 (ttt) cc_final: -0.0471 (ttt) REVERT: C 839 MET cc_start: 0.4002 (mmm) cc_final: 0.3723 (mmt) REVERT: D 839 MET cc_start: 0.6079 (mmm) cc_final: 0.5800 (mmt) REVERT: D 1329 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7891 (pp) REVERT: E 299 LYS cc_start: 0.8423 (mmtm) cc_final: 0.7711 (mmtt) REVERT: E 341 MET cc_start: -0.5365 (tpp) cc_final: -0.5879 (tpp) REVERT: E 462 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7557 (mpt180) REVERT: E 491 HIS cc_start: 0.8444 (t70) cc_final: 0.8220 (t-90) REVERT: E 785 MET cc_start: 0.1772 (mtt) cc_final: 0.1341 (mtt) REVERT: E 1327 TYR cc_start: 0.8099 (m-10) cc_final: 0.7894 (m-80) REVERT: E 1375 MET cc_start: 0.2272 (ptm) cc_final: 0.1831 (ptm) outliers start: 106 outliers final: 55 residues processed: 306 average time/residue: 0.2482 time to fit residues: 122.4123 Evaluate side-chains 230 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 171 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 1306 TYR Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1320 LYS Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1322 TYR Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1563 ARG Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 1359 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 462 ARG Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 616 LYS Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1324 TRP Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1403 MET Chi-restraints excluded: chain E residue 1531 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 459 optimal weight: 20.0000 chunk 239 optimal weight: 50.0000 chunk 424 optimal weight: 9.9990 chunk 411 optimal weight: 40.0000 chunk 36 optimal weight: 30.0000 chunk 389 optimal weight: 5.9990 chunk 398 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 417 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 290 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS A 749 GLN A 751 HIS ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 ASN ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN B 642 HIS B 644 GLN B 749 GLN B 751 HIS B1370 ASN C 311 ASN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C 644 GLN C 749 GLN C 774 ASN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 GLN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN D 709 HIS D 749 GLN D 751 HIS D 767 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 GLN E 749 GLN E 751 HIS E 774 ASN ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5484 r_free = 0.5484 target = 0.162253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.127003 restraints weight = 378901.559| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 23.42 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 38135 Z= 0.235 Angle : 0.863 12.361 51810 Z= 0.442 Chirality : 0.048 0.267 5830 Planarity : 0.006 0.090 6700 Dihedral : 6.862 69.142 5145 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.34 % Favored : 95.34 % Rotamer: Outliers : 3.53 % Allowed : 11.06 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.11), residues: 4720 helix: 0.05 (0.11), residues: 1875 sheet: -0.16 (0.16), residues: 905 loop : -1.35 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG D 777 TYR 0.031 0.003 TYR C 285 PHE 0.077 0.003 PHE B1525 TRP 0.042 0.002 TRP B 419 HIS 0.009 0.001 HIS D 642 Details of bonding type rmsd covalent geometry : bond 0.00505 (38135) covalent geometry : angle 0.86258 (51810) hydrogen bonds : bond 0.05214 ( 1880) hydrogen bonds : angle 6.50903 ( 5475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 184 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 654 MET cc_start: 0.5120 (ttt) cc_final: 0.4800 (ttm) REVERT: A 803 MET cc_start: 0.1942 (tmm) cc_final: 0.1382 (ttt) REVERT: A 1551 ILE cc_start: 0.8331 (mm) cc_final: 0.8088 (tp) REVERT: A 1568 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: A 1570 PHE cc_start: 0.8191 (m-10) cc_final: 0.7712 (m-10) REVERT: B 491 HIS cc_start: 0.9519 (t-90) cc_final: 0.9309 (t70) REVERT: B 654 MET cc_start: 0.0012 (ttp) cc_final: -0.1002 (ttm) REVERT: B 840 ASN cc_start: 0.9017 (t0) cc_final: 0.8702 (m110) REVERT: C 231 MET cc_start: 0.4140 (tpp) cc_final: 0.2852 (ttm) REVERT: C 839 MET cc_start: 0.4567 (mmm) cc_final: 0.4210 (mmm) REVERT: C 1316 VAL cc_start: 0.1882 (OUTLIER) cc_final: 0.1668 (m) REVERT: D 391 TYR cc_start: 0.6362 (m-80) cc_final: 0.5217 (t80) REVERT: D 627 LEU cc_start: 0.4946 (OUTLIER) cc_final: 0.4718 (mp) REVERT: D 654 MET cc_start: 0.2663 (ppp) cc_final: 0.0943 (ppp) REVERT: D 764 MET cc_start: 0.5921 (ttt) cc_final: 0.5510 (ptm) REVERT: D 1356 LYS cc_start: 0.8933 (tmmt) cc_final: 0.8601 (tptp) REVERT: E 462 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7719 (mmt-90) REVERT: E 633 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5757 (mmtt) outliers start: 144 outliers final: 67 residues processed: 308 average time/residue: 0.2388 time to fit residues: 121.0616 Evaluate side-chains 237 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 583 LYS Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain A residue 1568 GLU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1563 ARG Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 657 THR Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1498 VAL Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 796 HIS Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 462 ARG Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1324 TRP Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1531 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 97 optimal weight: 4.9990 chunk 467 optimal weight: 6.9990 chunk 422 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 242 optimal weight: 30.0000 chunk 237 optimal weight: 20.0000 chunk 344 optimal weight: 0.5980 chunk 342 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 282 optimal weight: 50.0000 chunk 194 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 364 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 GLN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1533 ASN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN E 467 GLN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.144079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.127244 restraints weight = 87369.783| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 3.89 r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3232 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 38135 Z= 0.172 Angle : 0.737 13.670 51810 Z= 0.373 Chirality : 0.044 0.258 5830 Planarity : 0.005 0.087 6700 Dihedral : 6.430 66.636 5132 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.92 % Favored : 95.76 % Rotamer: Outliers : 2.89 % Allowed : 12.78 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.12), residues: 4720 helix: 0.28 (0.11), residues: 1875 sheet: -0.38 (0.17), residues: 870 loop : -1.16 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1563 TYR 0.020 0.002 TYR E 353 PHE 0.029 0.002 PHE B1525 TRP 0.015 0.002 TRP B 419 HIS 0.006 0.001 HIS D 642 Details of bonding type rmsd covalent geometry : bond 0.00351 (38135) covalent geometry : angle 0.73652 (51810) hydrogen bonds : bond 0.04417 ( 1880) hydrogen bonds : angle 6.20621 ( 5475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 173 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 654 MET cc_start: 0.6053 (ttt) cc_final: 0.5075 (ttm) REVERT: A 803 MET cc_start: 0.1393 (tmm) cc_final: 0.0626 (ttt) REVERT: A 1568 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6239 (pt0) REVERT: A 1570 PHE cc_start: 0.7490 (m-10) cc_final: 0.7134 (m-10) REVERT: B 341 MET cc_start: -0.2475 (tpp) cc_final: -0.2823 (tpp) REVERT: B 654 MET cc_start: 0.2459 (ttp) cc_final: 0.1330 (ttm) REVERT: B 725 MET cc_start: -0.5007 (OUTLIER) cc_final: -0.5884 (ttt) REVERT: B 803 MET cc_start: 0.4022 (ppp) cc_final: 0.3637 (ppp) REVERT: B 840 ASN cc_start: 0.8483 (t0) cc_final: 0.8098 (m110) REVERT: C 231 MET cc_start: 0.4589 (tpp) cc_final: 0.3699 (ttm) REVERT: C 341 MET cc_start: -0.4506 (tpp) cc_final: -0.5476 (ttt) REVERT: D 627 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4871 (mp) REVERT: D 654 MET cc_start: 0.1849 (ppp) cc_final: 0.1347 (ppp) REVERT: D 839 MET cc_start: 0.4653 (mmm) cc_final: 0.4427 (mmm) REVERT: E 341 MET cc_start: -0.5301 (tpp) cc_final: -0.5866 (tmm) REVERT: E 633 LYS cc_start: 0.4695 (OUTLIER) cc_final: 0.4314 (mmtt) outliers start: 118 outliers final: 67 residues processed: 269 average time/residue: 0.2489 time to fit residues: 110.5607 Evaluate side-chains 223 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 152 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1327 TYR Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain A residue 1568 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1563 ARG Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 627 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 796 HIS Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1351 ILE Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 1324 TRP Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1332 VAL Chi-restraints excluded: chain E residue 1403 MET Chi-restraints excluded: chain E residue 1531 GLN Chi-restraints excluded: chain E residue 1542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 421 optimal weight: 40.0000 chunk 405 optimal weight: 5.9990 chunk 172 optimal weight: 50.0000 chunk 457 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 chunk 388 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 385 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 chunk 342 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1533 ASN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS C 709 HIS ** C 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 ASN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 GLN E 467 GLN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 644 GLN ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.138464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.121751 restraints weight = 68551.419| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 3.94 r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3272 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38135 Z= 0.184 Angle : 0.757 20.652 51810 Z= 0.380 Chirality : 0.044 0.582 5830 Planarity : 0.005 0.117 6700 Dihedral : 6.143 43.934 5117 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.62 % Favored : 95.08 % Rotamer: Outliers : 3.45 % Allowed : 13.05 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.12), residues: 4720 helix: 0.21 (0.11), residues: 1885 sheet: -0.66 (0.16), residues: 900 loop : -1.15 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1358 TYR 0.022 0.002 TYR E 353 PHE 0.054 0.002 PHE A1525 TRP 0.014 0.002 TRP D 871 HIS 0.038 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00391 (38135) covalent geometry : angle 0.75739 (51810) hydrogen bonds : bond 0.04569 ( 1880) hydrogen bonds : angle 6.31046 ( 5475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 165 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ILE cc_start: -0.6103 (OUTLIER) cc_final: -0.6396 (mm) REVERT: A 654 MET cc_start: 0.5854 (ttt) cc_final: 0.4753 (ttm) REVERT: A 785 MET cc_start: 0.0941 (ttt) cc_final: -0.1252 (tmt) REVERT: A 803 MET cc_start: 0.1664 (tmm) cc_final: 0.1046 (ttt) REVERT: A 1331 MET cc_start: 0.7881 (tpp) cc_final: 0.7525 (tpp) REVERT: A 1357 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8434 (tt) REVERT: B 725 MET cc_start: -0.5756 (OUTLIER) cc_final: -0.6662 (ttt) REVERT: B 803 MET cc_start: 0.3591 (ppp) cc_final: 0.3200 (ppp) REVERT: B 840 ASN cc_start: 0.8740 (t0) cc_final: 0.8384 (m110) REVERT: C 231 MET cc_start: 0.4297 (tpp) cc_final: 0.4062 (ttm) REVERT: D 1551 ILE cc_start: 0.5051 (OUTLIER) cc_final: 0.4705 (mt) REVERT: E 633 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4673 (mmtt) outliers start: 141 outliers final: 88 residues processed: 281 average time/residue: 0.2322 time to fit residues: 109.3421 Evaluate side-chains 251 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 158 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1327 TYR Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1337 ILE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1315 SER Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1319 ARG Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1563 ARG Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1334 ASN Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1387 VAL Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 796 HIS Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1351 ILE Chi-restraints excluded: chain D residue 1358 ARG Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1509 GLN Chi-restraints excluded: chain D residue 1525 PHE Chi-restraints excluded: chain D residue 1551 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1324 TRP Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1332 VAL Chi-restraints excluded: chain E residue 1334 ASN Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1542 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 376 optimal weight: 50.0000 chunk 349 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 366 optimal weight: 50.0000 chunk 292 optimal weight: 20.0000 chunk 257 optimal weight: 40.0000 chunk 246 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 overall best weight: 10.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN A 644 GLN ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN B 394 ASN ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS B 642 HIS B 812 ASN B 834 GLN B 856 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1361 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 858 HIS ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1334 ASN D 220 GLN ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 885 GLN ** D1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1533 ASN E 394 ASN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1362 ASN ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1533 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.115875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.101135 restraints weight = 75241.928| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 3.52 r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3646 moved from start: 0.8682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 38135 Z= 0.325 Angle : 0.983 19.496 51810 Z= 0.501 Chirality : 0.051 0.292 5830 Planarity : 0.007 0.121 6700 Dihedral : 6.893 55.474 5117 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 40.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.31 % Favored : 93.50 % Rotamer: Outliers : 4.19 % Allowed : 14.12 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.11), residues: 4720 helix: -0.63 (0.11), residues: 1850 sheet: -1.49 (0.16), residues: 920 loop : -1.17 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 564 TYR 0.034 0.003 TYR D 391 PHE 0.045 0.004 PHE D1555 TRP 0.024 0.002 TRP D 714 HIS 0.055 0.003 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00693 (38135) covalent geometry : angle 0.98300 (51810) hydrogen bonds : bond 0.06390 ( 1880) hydrogen bonds : angle 7.82634 ( 5475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 195 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 654 MET cc_start: 0.5765 (ttt) cc_final: 0.4855 (ttm) REVERT: A 725 MET cc_start: -0.5063 (OUTLIER) cc_final: -0.6051 (ttt) REVERT: A 785 MET cc_start: 0.0113 (ttt) cc_final: -0.0508 (ttt) REVERT: A 803 MET cc_start: 0.1437 (tmm) cc_final: 0.0847 (ttp) REVERT: A 1473 MET cc_start: 0.1914 (OUTLIER) cc_final: 0.1627 (mtm) REVERT: A 1528 MET cc_start: 0.6265 (mpp) cc_final: 0.4885 (mpp) REVERT: B 341 MET cc_start: -0.1014 (tpp) cc_final: -0.5038 (tpp) REVERT: B 725 MET cc_start: -0.4152 (OUTLIER) cc_final: -0.4867 (ttt) REVERT: B 840 ASN cc_start: 0.8332 (t0) cc_final: 0.8107 (m110) REVERT: B 1528 MET cc_start: 0.5839 (mtm) cc_final: 0.4908 (mpp) REVERT: C 231 MET cc_start: 0.5084 (tpp) cc_final: 0.4343 (ttm) REVERT: C 839 MET cc_start: 0.3358 (mmm) cc_final: 0.2902 (mmm) REVERT: C 1343 LYS cc_start: 0.1646 (tptt) cc_final: 0.1220 (tmtt) REVERT: C 1360 ILE cc_start: 0.6208 (OUTLIER) cc_final: 0.5991 (mp) REVERT: D 654 MET cc_start: 0.2441 (ppp) cc_final: 0.2217 (ppp) REVERT: E 428 VAL cc_start: 0.5561 (OUTLIER) cc_final: 0.5168 (m) outliers start: 171 outliers final: 93 residues processed: 330 average time/residue: 0.2253 time to fit residues: 125.4992 Evaluate side-chains 269 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 171 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1320 LYS Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1356 LYS Chi-restraints excluded: chain A residue 1357 LEU Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain A residue 1533 ASN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 287 ASN Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1315 SER Chi-restraints excluded: chain B residue 1319 ARG Chi-restraints excluded: chain B residue 1327 TYR Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1551 ILE Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain B residue 1574 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1334 ASN Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1360 ILE Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 796 HIS Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain D residue 1327 TYR Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1358 ARG Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 868 PHE Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1327 TYR Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1530 TYR Chi-restraints excluded: chain E residue 1551 ILE Chi-restraints excluded: chain E residue 1563 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 339 optimal weight: 8.9990 chunk 415 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 403 optimal weight: 4.9990 chunk 173 optimal weight: 30.0000 chunk 323 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 351 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS C 754 GLN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN D 337 ASN ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1362 ASN ** D1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 857 GLN ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.126595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.110476 restraints weight = 71544.916| |-----------------------------------------------------------------------------| r_work (start): 0.4587 rms_B_bonded: 3.16 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3618 moved from start: 0.8913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38135 Z= 0.195 Angle : 0.805 21.271 51810 Z= 0.403 Chirality : 0.046 0.295 5830 Planarity : 0.005 0.064 6700 Dihedral : 6.403 41.398 5113 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.11 % Allowed : 16.30 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.12), residues: 4720 helix: -0.45 (0.11), residues: 1870 sheet: -1.53 (0.16), residues: 895 loop : -1.13 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 354 TYR 0.031 0.002 TYR C 353 PHE 0.031 0.003 PHE A1525 TRP 0.041 0.002 TRP A 546 HIS 0.007 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00423 (38135) covalent geometry : angle 0.80532 (51810) hydrogen bonds : bond 0.04936 ( 1880) hydrogen bonds : angle 7.26786 ( 5475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 181 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TYR cc_start: 0.4366 (OUTLIER) cc_final: 0.4084 (m-80) REVERT: A 654 MET cc_start: 0.5615 (ttt) cc_final: 0.4886 (ttm) REVERT: A 725 MET cc_start: -0.5018 (OUTLIER) cc_final: -0.5948 (ttt) REVERT: A 785 MET cc_start: 0.0490 (ttt) cc_final: 0.0147 (ttt) REVERT: A 803 MET cc_start: 0.1444 (tmm) cc_final: 0.0923 (ttt) REVERT: A 1473 MET cc_start: 0.2300 (OUTLIER) cc_final: 0.1976 (mtm) REVERT: A 1568 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: B 764 MET cc_start: 0.6810 (tmm) cc_final: 0.6588 (ppp) REVERT: B 840 ASN cc_start: 0.8711 (t0) cc_final: 0.8364 (m110) REVERT: B 1473 MET cc_start: 0.0118 (mmt) cc_final: -0.1742 (mmt) REVERT: B 1502 VAL cc_start: 0.8522 (t) cc_final: 0.8261 (t) REVERT: C 341 MET cc_start: -0.2847 (tpp) cc_final: -0.3112 (tpp) REVERT: C 839 MET cc_start: 0.2858 (mmm) cc_final: 0.2526 (mmm) REVERT: C 1343 LYS cc_start: 0.2457 (tptt) cc_final: 0.1753 (tmtt) REVERT: C 1360 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.5246 (mp) REVERT: D 645 LYS cc_start: 0.8951 (tppt) cc_final: 0.8682 (tppt) REVERT: E 654 MET cc_start: 0.3954 (tmm) cc_final: 0.3718 (tmm) REVERT: E 1551 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8349 (tp) outliers start: 127 outliers final: 88 residues processed: 276 average time/residue: 0.2278 time to fit residues: 105.6934 Evaluate side-chains 259 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 165 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1320 LYS Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1524 SER Chi-restraints excluded: chain A residue 1552 ASP Chi-restraints excluded: chain A residue 1568 GLU Chi-restraints excluded: chain A residue 1574 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1315 SER Chi-restraints excluded: chain B residue 1319 ARG Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1327 TYR Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1553 VAL Chi-restraints excluded: chain B residue 1574 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 642 HIS Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1334 ASN Chi-restraints excluded: chain C residue 1360 ILE Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1387 VAL Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1327 TYR Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1358 ARG Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1542 LEU Chi-restraints excluded: chain E residue 1551 ILE Chi-restraints excluded: chain E residue 1563 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 303 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 328 optimal weight: 0.0050 chunk 102 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 404 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 GLN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS B 834 GLN B1361 HIS B1409 GLN C 312 GLN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1334 ASN D 337 ASN ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 GLN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 HIS D 635 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 885 GLN ** D1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.139921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.120149 restraints weight = 71122.714| |-----------------------------------------------------------------------------| r_work (start): 0.4621 rms_B_bonded: 3.93 r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3524 moved from start: 0.8808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 38135 Z= 0.141 Angle : 0.741 18.325 51810 Z= 0.372 Chirality : 0.044 0.255 5830 Planarity : 0.005 0.060 6700 Dihedral : 5.932 43.182 5113 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.55 % Allowed : 16.70 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.12), residues: 4720 helix: 0.07 (0.11), residues: 1880 sheet: -1.26 (0.16), residues: 885 loop : -1.09 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 354 TYR 0.039 0.002 TYR E 391 PHE 0.030 0.002 PHE A1532 TRP 0.035 0.002 TRP A 546 HIS 0.042 0.001 HIS B 642 Details of bonding type rmsd covalent geometry : bond 0.00307 (38135) covalent geometry : angle 0.74107 (51810) hydrogen bonds : bond 0.04192 ( 1880) hydrogen bonds : angle 6.47572 ( 5475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 178 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.5477 (tmm) cc_final: 0.5217 (tmm) REVERT: A 330 ILE cc_start: -0.3626 (OUTLIER) cc_final: -0.3830 (mm) REVERT: A 363 TYR cc_start: 0.3870 (OUTLIER) cc_final: 0.3548 (m-80) REVERT: A 654 MET cc_start: 0.5529 (ttt) cc_final: 0.4953 (ttm) REVERT: A 725 MET cc_start: -0.5549 (OUTLIER) cc_final: -0.6366 (ttt) REVERT: A 803 MET cc_start: 0.0971 (tmm) cc_final: 0.0326 (ttt) REVERT: A 1319 ARG cc_start: 0.6461 (ttt180) cc_final: 0.5387 (ttt180) REVERT: A 1473 MET cc_start: 0.2576 (OUTLIER) cc_final: 0.2220 (mtm) REVERT: A 1568 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6554 (mm-30) REVERT: B 291 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8748 (tm-30) REVERT: B 341 MET cc_start: -0.4535 (tpp) cc_final: -0.4977 (ttm) REVERT: B 725 MET cc_start: -0.5138 (OUTLIER) cc_final: -0.5467 (ttt) REVERT: B 764 MET cc_start: 0.6794 (tmm) cc_final: 0.6391 (ppp) REVERT: B 840 ASN cc_start: 0.8694 (t0) cc_final: 0.8355 (m110) REVERT: B 1356 LYS cc_start: 0.6494 (tptp) cc_final: 0.6052 (tptp) REVERT: B 1473 MET cc_start: 0.0223 (mmt) cc_final: -0.1494 (mmt) REVERT: B 1503 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6337 (tppt) REVERT: B 1528 MET cc_start: 0.4815 (mtm) cc_final: 0.4043 (mpp) REVERT: C 341 MET cc_start: -0.3382 (tpp) cc_final: -0.4027 (tpp) REVERT: C 1343 LYS cc_start: 0.2154 (tptt) cc_final: 0.1577 (tmtt) REVERT: C 1555 PHE cc_start: 0.4740 (m-80) cc_final: 0.4321 (m-80) REVERT: D 231 MET cc_start: -0.0490 (ttm) cc_final: -0.0805 (ttp) REVERT: D 645 LYS cc_start: 0.9178 (tppt) cc_final: 0.8806 (tppt) REVERT: D 764 MET cc_start: 0.6651 (ppp) cc_final: 0.6044 (ppp) REVERT: E 341 MET cc_start: -0.5886 (tpp) cc_final: -0.6399 (tmm) REVERT: E 410 LEU cc_start: -0.2862 (OUTLIER) cc_final: -0.3702 (mp) REVERT: E 428 VAL cc_start: 0.5678 (OUTLIER) cc_final: 0.5319 (m) REVERT: E 1531 GLN cc_start: 0.7913 (pm20) cc_final: 0.7267 (pm20) REVERT: E 1551 ILE cc_start: 0.8427 (mm) cc_final: 0.8216 (tp) outliers start: 104 outliers final: 77 residues processed: 257 average time/residue: 0.2378 time to fit residues: 102.4280 Evaluate side-chains 252 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 166 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1320 LYS Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1331 MET Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1568 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1574 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 642 HIS Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1387 VAL Chi-restraints excluded: chain C residue 1423 LEU Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain C residue 1554 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 796 HIS Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1358 ARG Chi-restraints excluded: chain D residue 1359 ILE Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1554 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1563 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 194 optimal weight: 3.9990 chunk 267 optimal weight: 50.0000 chunk 297 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 371 optimal weight: 0.4980 chunk 241 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 428 optimal weight: 30.0000 chunk 372 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN D 761 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.126758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.113200 restraints weight = 81767.250| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 3.58 r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3513 moved from start: 0.9247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 38135 Z= 0.167 Angle : 0.745 20.206 51810 Z= 0.371 Chirality : 0.043 0.254 5830 Planarity : 0.005 0.067 6700 Dihedral : 5.837 45.518 5111 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.28 % Allowed : 17.33 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.12), residues: 4720 helix: 0.12 (0.11), residues: 1875 sheet: -1.50 (0.15), residues: 1020 loop : -0.96 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1358 TYR 0.030 0.002 TYR C 353 PHE 0.028 0.002 PHE B1525 TRP 0.030 0.002 TRP A 546 HIS 0.008 0.001 HIS D 796 Details of bonding type rmsd covalent geometry : bond 0.00363 (38135) covalent geometry : angle 0.74549 (51810) hydrogen bonds : bond 0.04274 ( 1880) hydrogen bonds : angle 6.58178 ( 5475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 170 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 654 MET cc_start: 0.5686 (ttt) cc_final: 0.4921 (ttm) REVERT: A 725 MET cc_start: -0.5264 (OUTLIER) cc_final: -0.6021 (ttt) REVERT: A 803 MET cc_start: 0.0789 (tmm) cc_final: 0.0133 (ttt) REVERT: A 1473 MET cc_start: 0.2266 (OUTLIER) cc_final: 0.1922 (mtm) REVERT: A 1568 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7324 (mm-30) REVERT: B 725 MET cc_start: -0.4333 (ttt) cc_final: -0.5323 (ttt) REVERT: B 764 MET cc_start: 0.6218 (tmm) cc_final: 0.5933 (ppp) REVERT: B 840 ASN cc_start: 0.8442 (t0) cc_final: 0.8176 (m110) REVERT: B 1473 MET cc_start: -0.0255 (mmt) cc_final: -0.1807 (mmt) REVERT: B 1528 MET cc_start: 0.5178 (mtm) cc_final: 0.4096 (mpp) REVERT: C 1343 LYS cc_start: 0.2131 (tptt) cc_final: 0.1553 (tmtt) REVERT: C 1555 PHE cc_start: 0.4570 (m-80) cc_final: 0.4245 (m-80) REVERT: D 645 LYS cc_start: 0.8995 (tppt) cc_final: 0.8627 (tppt) REVERT: D 764 MET cc_start: 0.7020 (ppp) cc_final: 0.6408 (ppp) REVERT: E 341 MET cc_start: -0.4803 (tpp) cc_final: -0.5795 (tmm) REVERT: E 428 VAL cc_start: 0.6089 (OUTLIER) cc_final: 0.5807 (m) REVERT: E 764 MET cc_start: 0.3287 (tmm) cc_final: 0.2623 (tmm) outliers start: 93 outliers final: 77 residues processed: 244 average time/residue: 0.2360 time to fit residues: 96.3739 Evaluate side-chains 246 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 165 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1568 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1315 SER Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1574 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 642 HIS Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1360 ILE Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1387 VAL Chi-restraints excluded: chain C residue 1423 LEU Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain C residue 1554 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 796 HIS Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1358 ARG Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1554 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1327 TYR Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1334 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1563 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 364 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 74 optimal weight: 40.0000 chunk 72 optimal weight: 6.9990 chunk 463 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 332 optimal weight: 50.0000 chunk 174 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1499 GLN ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.128609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.114322 restraints weight = 72629.304| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 3.27 r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3560 moved from start: 0.9655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 38135 Z= 0.162 Angle : 0.741 18.680 51810 Z= 0.370 Chirality : 0.044 0.207 5830 Planarity : 0.005 0.066 6700 Dihedral : 5.835 45.826 5111 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.20 % Allowed : 17.38 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.12), residues: 4720 helix: 0.18 (0.11), residues: 1875 sheet: -1.37 (0.16), residues: 895 loop : -1.01 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 354 TYR 0.024 0.002 TYR C 353 PHE 0.025 0.002 PHE B1525 TRP 0.031 0.002 TRP A 546 HIS 0.008 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00352 (38135) covalent geometry : angle 0.74060 (51810) hydrogen bonds : bond 0.04253 ( 1880) hydrogen bonds : angle 6.61024 ( 5475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 164 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TYR cc_start: 0.3951 (OUTLIER) cc_final: 0.3536 (m-80) REVERT: A 654 MET cc_start: 0.5457 (ttt) cc_final: 0.4902 (ttm) REVERT: A 725 MET cc_start: -0.5186 (OUTLIER) cc_final: -0.5892 (ttt) REVERT: A 803 MET cc_start: 0.0690 (tmm) cc_final: -0.0031 (ttt) REVERT: A 1319 ARG cc_start: 0.6603 (ttt180) cc_final: 0.6324 (tpt170) REVERT: A 1473 MET cc_start: 0.2246 (OUTLIER) cc_final: 0.1891 (mtm) REVERT: B 725 MET cc_start: -0.3867 (ttt) cc_final: -0.4140 (ttt) REVERT: B 764 MET cc_start: 0.6105 (tmm) cc_final: 0.5217 (ppp) REVERT: B 840 ASN cc_start: 0.8613 (t0) cc_final: 0.8285 (m110) REVERT: B 1473 MET cc_start: -0.0137 (mmt) cc_final: -0.1689 (mmt) REVERT: B 1528 MET cc_start: 0.5749 (mtm) cc_final: 0.5012 (mpp) REVERT: B 1555 PHE cc_start: 0.8352 (m-80) cc_final: 0.8030 (m-80) REVERT: C 654 MET cc_start: 0.2544 (tpt) cc_final: 0.1940 (tpp) REVERT: C 1331 MET cc_start: 0.5629 (tpp) cc_final: 0.5343 (tmm) REVERT: C 1343 LYS cc_start: 0.1947 (tptt) cc_final: 0.1609 (tmtt) REVERT: C 1555 PHE cc_start: 0.4703 (m-80) cc_final: 0.4444 (m-80) REVERT: D 764 MET cc_start: 0.5436 (ppp) cc_final: 0.4616 (ppp) REVERT: D 1509 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5558 (pm20) REVERT: E 341 MET cc_start: -0.4871 (tpp) cc_final: -0.5921 (tmm) REVERT: E 428 VAL cc_start: 0.6044 (OUTLIER) cc_final: 0.5738 (m) REVERT: E 764 MET cc_start: 0.3176 (tmm) cc_final: 0.2883 (ttp) REVERT: E 1331 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.2888 (tmm) REVERT: E 1568 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6868 (mm-30) outliers start: 90 outliers final: 72 residues processed: 233 average time/residue: 0.2365 time to fit residues: 92.3888 Evaluate side-chains 241 residues out of total 4085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 163 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 363 TYR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1321 ASP Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1568 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1329 LEU Chi-restraints excluded: chain B residue 1332 VAL Chi-restraints excluded: chain B residue 1358 ARG Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain B residue 1524 SER Chi-restraints excluded: chain B residue 1574 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 642 HIS Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1360 ILE Chi-restraints excluded: chain C residue 1375 MET Chi-restraints excluded: chain C residue 1423 LEU Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain C residue 1554 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1509 GLN Chi-restraints excluded: chain D residue 1554 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 419 TRP Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 623 SER Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 726 THR Chi-restraints excluded: chain E residue 748 THR Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1327 TYR Chi-restraints excluded: chain E residue 1329 LEU Chi-restraints excluded: chain E residue 1331 MET Chi-restraints excluded: chain E residue 1334 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1563 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 443 optimal weight: 5.9990 chunk 280 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 279 optimal weight: 0.4980 chunk 428 optimal weight: 30.0000 chunk 73 optimal weight: 40.0000 chunk 160 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 464 optimal weight: 0.9980 chunk 39 optimal weight: 50.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.130752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.113783 restraints weight = 75105.252| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 3.81 r_work (final): 0.4610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3616 moved from start: 0.9741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38135 Z= 0.133 Angle : 0.718 18.066 51810 Z= 0.356 Chirality : 0.043 0.233 5830 Planarity : 0.005 0.066 6700 Dihedral : 5.628 48.082 5111 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.03 % Allowed : 17.45 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.12), residues: 4720 helix: 0.38 (0.11), residues: 1880 sheet: -1.51 (0.15), residues: 990 loop : -0.84 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 354 TYR 0.022 0.001 TYR A 339 PHE 0.018 0.002 PHE E1532 TRP 0.031 0.002 TRP A 546 HIS 0.008 0.001 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00289 (38135) covalent geometry : angle 0.71784 (51810) hydrogen bonds : bond 0.03976 ( 1880) hydrogen bonds : angle 6.31128 ( 5475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12054.59 seconds wall clock time: 207 minutes 33.44 seconds (12453.44 seconds total)