Starting phenix.real_space_refine on Sat Mar 23 14:15:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/03_2024/5lkh_4068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/03_2024/5lkh_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/03_2024/5lkh_4068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/03_2024/5lkh_4068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/03_2024/5lkh_4068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/03_2024/5lkh_4068.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37345 Number of models: 1 Model: "" Number of chains: 5 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Time building chain proxies: 19.37, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 15.38 Conformation dependent library (CDL) restraints added in 6.6 seconds 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: 4.26 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: 15.93 Time building geometry restraints manager: 16.58 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: 93.50 - 103.91: 570 103.91 - 114.32: 22058 114.32 - 124.73: 28265 124.73 - 135.14: 912 135.14 - 145.55: 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 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.130 Check model and map are aligned: 0.580 Set scattering table: 0.390 Process input model: 99.220 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.110 ------------------------------------------------------------------------------- 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= 1.181 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 : 87.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (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 TRP 0.038 0.006 TRP C 810 HIS 0.003 0.000 HIS D 796 PHE 0.014 0.002 PHE E 563 TYR 0.021 0.003 TYR D1306 ARG 0.008 0.001 ARG D1563 *********************** 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 fitting. rotamer outliers: 80 poor density : 330 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.5147 (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: -0.5658 (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: -0.5171 (tmm) REVERT: E 692 MET cc_start: -0.4970 (OUTLIER) cc_final: -0.5675 (ttt) outliers start: 80 outliers final: 27 residues processed: 397 average time/residue: 0.5610 time to fit residues: 344.6393 Evaluate side-chains 222 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 4.273 ------------------------------------------------------------------------------- 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 396 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 368 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 426 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 ASN ** 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN A 598 HIS A 635 ASN A 642 HIS A 650 GLN A 709 HIS A 767 HIS A 885 GLN A1361 HIS A1370 ASN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN A1462 ASN B 222 ASN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 GLN B 598 HIS B 635 ASN B 650 GLN B 709 HIS ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 HIS B 885 GLN B1361 HIS B1370 ASN ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1400 ASN B1462 ASN C 222 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 433 GLN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 598 HIS C 635 ASN ** C 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 885 GLN C1361 HIS C1370 ASN ** C1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1400 ASN C1462 ASN D 222 ASN ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 GLN D 598 HIS D 635 ASN D 767 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 885 GLN D1370 ASN ** D1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1400 ASN D1462 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 GLN E 598 HIS E 635 ASN E 650 GLN ** E 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 E1400 ASN E1462 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1749 moved from start: 0.3187 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= 0.323 Angle : 0.988 18.618 51810 Z= 0.498 Chirality : 0.052 0.304 5830 Planarity : 0.008 0.082 6700 Dihedral : 7.660 80.026 5178 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 27.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.71 % Favored : 95.97 % Rotamer: Outliers : 2.86 % Allowed : 8.59 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 4720 helix: 0.34 (0.11), residues: 1860 sheet: 0.54 (0.17), residues: 885 loop : -1.48 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 419 HIS 0.011 0.002 HIS E1361 PHE 0.031 0.003 PHE C 529 TYR 0.024 0.002 TYR E1410 ARG 0.009 0.001 ARG E1563 *********************** 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 335 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 218 time to evaluate : 4.595 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: A 341 MET cc_start: -0.1719 (tpp) cc_final: -0.2990 (tpp) REVERT: A 654 MET cc_start: 0.5693 (ttt) cc_final: 0.5155 (ttm) REVERT: A 803 MET cc_start: 0.1916 (tmm) cc_final: 0.1135 (ttt) REVERT: A 1306 TYR cc_start: 0.6097 (OUTLIER) cc_final: 0.5663 (t80) REVERT: A 1568 GLU cc_start: 0.4745 (OUTLIER) cc_final: 0.3715 (pt0) REVERT: B 341 MET cc_start: -0.1307 (tpp) cc_final: -0.2603 (tpp) REVERT: C 231 MET cc_start: 0.5329 (tpp) cc_final: 0.3674 (ttt) REVERT: C 341 MET cc_start: -0.3935 (tpp) cc_final: -0.5513 (ttt) REVERT: C 654 MET cc_start: 0.1004 (ttt) cc_final: 0.0702 (ttt) REVERT: C 1375 MET cc_start: -0.0824 (OUTLIER) cc_final: -0.2137 (ppp) REVERT: C 1473 MET cc_start: -0.2878 (mtm) cc_final: -0.3121 (mtt) REVERT: E 341 MET cc_start: -0.4818 (tpp) cc_final: -0.6276 (ttt) REVERT: E 803 MET cc_start: 0.1976 (tmm) cc_final: 0.1614 (tmm) outliers start: 117 outliers final: 59 residues processed: 310 average time/residue: 0.5216 time to fit residues: 259.1130 Evaluate side-chains 233 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 171 time to evaluate : 3.182 ------------------------------------------------------------------------------- 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 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 1322 TYR 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 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 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 1339 THR Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1503 LYS 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 633 LYS Chi-restraints excluded: chain C residue 782 LYS Chi-restraints excluded: chain C residue 1375 MET 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 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 1403 MET Chi-restraints excluded: chain D residue 1462 ASN 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 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 1403 MET Chi-restraints excluded: chain E residue 1462 ASN 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 237 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 117 optimal weight: 0.4980 chunk 427 optimal weight: 50.0000 chunk 461 optimal weight: 0.0870 chunk 380 optimal weight: 6.9990 chunk 424 optimal weight: 0.4980 chunk 145 optimal weight: 3.9990 chunk 343 optimal weight: 40.0000 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 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 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 HIS A 679 GLN A 751 HIS ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS B 644 GLN B 679 GLN ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 HIS ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 HIS ** 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 679 GLN D 709 HIS ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 HIS D 767 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1462 ASN E 222 ASN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 679 GLN E 709 HIS E 751 HIS E1462 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1770 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38135 Z= 0.221 Angle : 0.781 13.436 51810 Z= 0.397 Chirality : 0.045 0.357 5830 Planarity : 0.006 0.069 6700 Dihedral : 6.757 76.734 5143 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.90 % Favored : 95.78 % Rotamer: Outliers : 3.06 % Allowed : 10.75 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 4720 helix: 0.38 (0.11), residues: 1865 sheet: 0.38 (0.17), residues: 905 loop : -1.26 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 419 HIS 0.008 0.001 HIS E1361 PHE 0.023 0.002 PHE A 529 TYR 0.026 0.002 TYR A 421 ARG 0.017 0.001 ARG D 777 *********************** 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 310 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 185 time to evaluate : 4.173 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: A 803 MET cc_start: 0.1949 (tmm) cc_final: 0.1252 (ttt) REVERT: A 1568 GLU cc_start: 0.4257 (OUTLIER) cc_final: 0.3447 (pt0) REVERT: B 341 MET cc_start: -0.1675 (tpp) cc_final: -0.2044 (tpp) REVERT: B 654 MET cc_start: 0.2004 (ttp) cc_final: -0.0761 (ttm) REVERT: C 231 MET cc_start: 0.3884 (tpp) cc_final: 0.2956 (ttt) REVERT: C 341 MET cc_start: -0.3939 (tpp) cc_final: -0.4465 (tpp) REVERT: C 1351 ILE cc_start: -0.0224 (OUTLIER) cc_final: -0.0958 (pt) REVERT: E 341 MET cc_start: -0.5438 (tpp) cc_final: -0.6241 (ttt) REVERT: E 803 MET cc_start: 0.1448 (tmm) cc_final: 0.1061 (tmm) outliers start: 125 outliers final: 59 residues processed: 285 average time/residue: 0.4936 time to fit residues: 231.8369 Evaluate side-chains 221 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 160 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 572 ASP 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 1322 TYR 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 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 642 HIS Chi-restraints excluded: chain B residue 645 LYS 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 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 1565 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1498 VAL Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 701 GLN Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain D residue 1403 MET 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 623 SER 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 422 optimal weight: 50.0000 chunk 321 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 287 optimal weight: 8.9990 chunk 429 optimal weight: 7.9990 chunk 454 optimal weight: 50.0000 chunk 224 optimal weight: 20.0000 chunk 406 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 812 ASN A 844 ASN ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN B 749 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C 644 GLN C 749 GLN C 774 ASN C 844 ASN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 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 433 GLN ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN D 749 GLN ** D 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 844 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 844 ASN E1362 ASN ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1960 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38135 Z= 0.267 Angle : 0.778 14.889 51810 Z= 0.395 Chirality : 0.044 0.230 5830 Planarity : 0.005 0.080 6700 Dihedral : 6.490 73.912 5138 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.53 % Favored : 95.15 % Rotamer: Outliers : 3.21 % Allowed : 12.58 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 4720 helix: 0.33 (0.11), residues: 1885 sheet: -0.06 (0.16), residues: 905 loop : -1.27 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 419 HIS 0.061 0.002 HIS B 642 PHE 0.022 0.002 PHE E1555 TYR 0.052 0.002 TYR B 421 ARG 0.009 0.001 ARG A 564 *********************** 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 305 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 174 time to evaluate : 4.428 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: A 692 MET cc_start: -0.4382 (tmt) cc_final: -0.4630 (tmt) REVERT: A 803 MET cc_start: 0.1819 (tmm) cc_final: 0.1092 (ttt) REVERT: A 1568 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.4962 (pm20) REVERT: C 231 MET cc_start: 0.4170 (tpp) cc_final: 0.2601 (ttm) REVERT: C 1375 MET cc_start: -0.0793 (OUTLIER) cc_final: -0.1664 (ppp) REVERT: D 231 MET cc_start: -0.1226 (ttm) cc_final: -0.1595 (ttm) REVERT: D 645 LYS cc_start: 0.8515 (tppt) cc_final: 0.8301 (tppt) REVERT: E 299 LYS cc_start: 0.2914 (mmtt) cc_final: 0.2283 (mmtm) REVERT: E 633 LYS cc_start: 0.4108 (OUTLIER) cc_final: 0.3528 (mmmt) REVERT: E 803 MET cc_start: 0.1606 (tmm) cc_final: 0.1376 (tmm) outliers start: 131 outliers final: 71 residues processed: 279 average time/residue: 0.5042 time to fit residues: 227.4999 Evaluate side-chains 231 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 157 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 428 VAL 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 785 MET Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1327 TYR Chi-restraints excluded: chain A residue 1329 LEU 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 645 LYS Chi-restraints excluded: chain B residue 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1322 TYR 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 C residue 230 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1351 ILE Chi-restraints excluded: chain C residue 1358 ARG 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 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 657 THR 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 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 524 LEU Chi-restraints excluded: chain E residue 594 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 657 THR Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 839 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 1403 MET Chi-restraints excluded: chain E residue 1525 PHE Chi-restraints excluded: chain E residue 1526 ASP Chi-restraints excluded: chain E residue 1531 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 378 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 387 optimal weight: 5.9990 chunk 314 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 231 optimal weight: 7.9990 chunk 407 optimal weight: 5.9990 chunk 114 optimal weight: 0.3980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 404 GLN ** 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 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN B 305 GLN B 486 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN C 812 ASN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1533 ASN D 249 ASN ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 GLN ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 GLN E 514 GLN ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1946 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38135 Z= 0.196 Angle : 0.692 16.477 51810 Z= 0.349 Chirality : 0.042 0.224 5830 Planarity : 0.005 0.056 6700 Dihedral : 6.147 68.977 5132 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.30 % Favored : 95.40 % Rotamer: Outliers : 3.04 % Allowed : 13.90 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 4720 helix: 0.49 (0.12), residues: 1885 sheet: -0.16 (0.16), residues: 945 loop : -1.17 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 871 HIS 0.007 0.001 HIS E1361 PHE 0.064 0.002 PHE B1525 TYR 0.026 0.002 TYR D1530 ARG 0.007 0.000 ARG D1358 *********************** 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 291 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 167 time to evaluate : 4.186 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: A 803 MET cc_start: 0.1724 (tmm) cc_final: 0.0987 (ttt) REVERT: A 1528 MET cc_start: 0.4489 (OUTLIER) cc_final: 0.3411 (tpp) REVERT: A 1568 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4578 (pt0) REVERT: B 231 MET cc_start: 0.3472 (tpt) cc_final: 0.2932 (tmm) REVERT: B 1375 MET cc_start: -0.1361 (OUTLIER) cc_final: -0.2582 (ppp) REVERT: C 1375 MET cc_start: -0.1100 (OUTLIER) cc_final: -0.1942 (ppp) REVERT: D 231 MET cc_start: -0.0135 (ttm) cc_final: -0.1038 (ttm) REVERT: E 633 LYS cc_start: 0.4052 (OUTLIER) cc_final: 0.3759 (mmtt) outliers start: 124 outliers final: 70 residues processed: 258 average time/residue: 0.4903 time to fit residues: 208.2737 Evaluate side-chains 229 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 154 time to evaluate : 4.074 ------------------------------------------------------------------------------- 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 372 LEU Chi-restraints excluded: chain A residue 524 LEU 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 782 LYS 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 1331 MET Chi-restraints excluded: chain A residue 1351 ILE 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 1528 MET 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 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 725 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 1332 VAL Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1359 ILE Chi-restraints excluded: chain B residue 1375 MET Chi-restraints excluded: chain B residue 1503 LYS Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 725 MET 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 1473 MET 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 657 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 1315 SER Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1473 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 608 LEU Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 657 THR Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 1324 TRP Chi-restraints excluded: chain E residue 1327 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 152 optimal weight: 30.0000 chunk 409 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 266 optimal weight: 40.0000 chunk 112 optimal weight: 20.0000 chunk 454 optimal weight: 0.0670 chunk 377 optimal weight: 20.0000 chunk 210 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 238 optimal weight: 20.0000 overall best weight: 6.4126 ------------------------------------------------------------------------------- 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 305 GLN A 311 ASN ** A 404 GLN ** 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 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B1533 ASN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1533 ASN ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 812 ASN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2130 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 38135 Z= 0.299 Angle : 0.791 21.859 51810 Z= 0.393 Chirality : 0.044 0.379 5830 Planarity : 0.005 0.068 6700 Dihedral : 6.162 52.676 5125 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.60 % Rotamer: Outliers : 3.43 % Allowed : 14.30 % Favored : 82.28 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4720 helix: 0.21 (0.11), residues: 1890 sheet: -0.61 (0.16), residues: 950 loop : -1.15 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 419 HIS 0.047 0.001 HIS B 642 PHE 0.042 0.003 PHE B1525 TYR 0.034 0.002 TYR E1328 ARG 0.006 0.001 ARG E 284 *********************** 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 314 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 174 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: -0.2271 (tpp) cc_final: -0.2869 (tmm) REVERT: A 1528 MET cc_start: 0.4787 (OUTLIER) cc_final: 0.3638 (tpp) REVERT: B 1473 MET cc_start: -0.2878 (mmt) cc_final: -0.3346 (mmt) REVERT: C 341 MET cc_start: -0.4051 (tpp) cc_final: -0.4784 (ttt) REVERT: C 1375 MET cc_start: -0.1184 (OUTLIER) cc_final: -0.2572 (ppp) REVERT: C 1547 ASN cc_start: 0.6628 (OUTLIER) cc_final: 0.5971 (t0) REVERT: D 231 MET cc_start: 0.0115 (ttm) cc_final: -0.0521 (ttm) REVERT: D 1353 ILE cc_start: 0.0505 (OUTLIER) cc_final: -0.0090 (tp) REVERT: D 1357 LEU cc_start: 0.5341 (pp) cc_final: 0.5065 (pp) REVERT: D 1551 ILE cc_start: 0.4880 (OUTLIER) cc_final: 0.4538 (mt) REVERT: E 633 LYS cc_start: 0.4696 (OUTLIER) cc_final: 0.4306 (mmtt) outliers start: 140 outliers final: 84 residues processed: 282 average time/residue: 0.4732 time to fit residues: 221.7260 Evaluate side-chains 252 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 162 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 511 GLN 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 863 THR 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 1473 MET Chi-restraints excluded: chain A residue 1528 MET 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 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 725 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 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 1565 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 725 MET Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 1329 LEU Chi-restraints excluded: chain C residue 1331 MET Chi-restraints excluded: chain C residue 1334 ASN 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 1387 VAL Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain C residue 1535 LEU Chi-restraints excluded: chain C residue 1547 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 462 ARG Chi-restraints excluded: chain D residue 466 LEU 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 1315 SER Chi-restraints excluded: chain D residue 1329 LEU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1547 ASN Chi-restraints excluded: chain D residue 1551 ILE 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 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 1327 TYR Chi-restraints excluded: chain E residue 1403 MET Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1531 GLN Chi-restraints excluded: chain E residue 1547 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 438 optimal weight: 10.0000 chunk 51 optimal weight: 50.0000 chunk 259 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 chunk 257 optimal weight: 1.9990 chunk 382 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 453 optimal weight: 30.0000 chunk 283 optimal weight: 20.0000 chunk 276 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 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 240 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** 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 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 GLN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** E 500 ASN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2126 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 38135 Z= 0.232 Angle : 0.719 16.341 51810 Z= 0.356 Chirality : 0.043 0.201 5830 Planarity : 0.005 0.067 6700 Dihedral : 5.941 54.842 5119 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.55 % Favored : 94.43 % Rotamer: Outliers : 2.77 % Allowed : 15.74 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 4720 helix: 0.33 (0.11), residues: 1890 sheet: -0.81 (0.16), residues: 910 loop : -1.10 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 546 HIS 0.006 0.001 HIS E 491 PHE 0.049 0.002 PHE B1525 TYR 0.025 0.002 TYR E1327 ARG 0.009 0.001 ARG A 517 *********************** 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 280 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 167 time to evaluate : 3.527 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: A 1319 ARG cc_start: 0.4392 (ttt180) cc_final: 0.3926 (ttt180) REVERT: A 1331 MET cc_start: 0.7085 (tmm) cc_final: 0.6360 (tpt) REVERT: A 1528 MET cc_start: 0.5084 (OUTLIER) cc_final: 0.3941 (tpp) REVERT: B 1358 ARG cc_start: 0.5764 (mtm-85) cc_final: 0.5283 (mtm-85) REVERT: B 1473 MET cc_start: -0.3560 (mmt) cc_final: -0.4201 (mmt) REVERT: C 341 MET cc_start: -0.4057 (tpp) cc_final: -0.4728 (ttt) REVERT: C 1343 LYS cc_start: 0.0718 (tttt) cc_final: -0.0133 (tmtt) REVERT: C 1375 MET cc_start: -0.1303 (OUTLIER) cc_final: -0.2643 (ppp) REVERT: D 231 MET cc_start: 0.0890 (ttm) cc_final: 0.0231 (ttm) REVERT: D 761 GLN cc_start: 0.1388 (OUTLIER) cc_final: 0.0769 (tt0) REVERT: D 1353 ILE cc_start: 0.0409 (OUTLIER) cc_final: -0.0133 (tp) outliers start: 113 outliers final: 72 residues processed: 253 average time/residue: 0.4881 time to fit residues: 204.9480 Evaluate side-chains 238 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 162 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 863 THR 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 1528 MET Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain A residue 1547 ASN 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 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 1316 VAL 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 1339 THR 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 1565 LEU Chi-restraints excluded: chain B residue 1574 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 725 MET 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 D residue 341 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 462 ARG 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 761 GLN Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1525 PHE Chi-restraints excluded: chain D residue 1547 ASN 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 654 MET Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET Chi-restraints excluded: chain E residue 868 PHE Chi-restraints excluded: chain E residue 1316 VAL Chi-restraints excluded: chain E residue 1324 TRP Chi-restraints excluded: chain E residue 1334 ASN Chi-restraints excluded: chain E residue 1403 MET Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1547 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 280 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 356 optimal weight: 30.0000 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 240 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** 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 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 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 433 GLN ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN ** E 500 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2171 moved from start: 0.7616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 38135 Z= 0.232 Angle : 0.720 18.284 51810 Z= 0.356 Chirality : 0.042 0.239 5830 Planarity : 0.005 0.061 6700 Dihedral : 5.848 57.440 5119 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 2.47 % Allowed : 16.11 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.12), residues: 4720 helix: 0.38 (0.11), residues: 1890 sheet: -0.91 (0.16), residues: 910 loop : -1.02 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 546 HIS 0.009 0.001 HIS C 751 PHE 0.038 0.002 PHE B1525 TYR 0.022 0.002 TYR C 353 ARG 0.008 0.001 ARG A1563 *********************** 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 270 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 169 time to evaluate : 4.138 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: A 1331 MET cc_start: 0.7103 (tmm) cc_final: 0.6201 (tpt) REVERT: A 1528 MET cc_start: 0.4800 (OUTLIER) cc_final: 0.3737 (tpp) REVERT: B 725 MET cc_start: -0.3271 (OUTLIER) cc_final: -0.4418 (ttt) REVERT: B 803 MET cc_start: 0.3924 (OUTLIER) cc_final: 0.3336 (ppp) REVERT: B 1473 MET cc_start: -0.3759 (mmt) cc_final: -0.4361 (mmt) REVERT: B 1547 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7281 (t0) REVERT: C 231 MET cc_start: 0.4036 (ttm) cc_final: 0.2939 (tmm) REVERT: C 341 MET cc_start: -0.4121 (tpp) cc_final: -0.5110 (ttp) REVERT: C 785 MET cc_start: 0.4550 (pmm) cc_final: 0.2578 (pmm) REVERT: C 1343 LYS cc_start: 0.0833 (tttt) cc_final: -0.0095 (tmtt) REVERT: C 1375 MET cc_start: -0.2078 (OUTLIER) cc_final: -0.3213 (ppp) REVERT: D 231 MET cc_start: 0.1074 (ttm) cc_final: 0.0429 (ttm) REVERT: D 764 MET cc_start: 0.4503 (ppp) cc_final: 0.4252 (ppp) REVERT: D 1353 ILE cc_start: 0.0340 (OUTLIER) cc_final: -0.0155 (tp) REVERT: E 803 MET cc_start: 0.0504 (tmm) cc_final: 0.0103 (tmm) outliers start: 101 outliers final: 72 residues processed: 244 average time/residue: 0.4765 time to fit residues: 193.7202 Evaluate side-chains 243 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 165 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1356 LYS Chi-restraints excluded: chain A residue 1473 MET Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1555 PHE 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 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 803 MET 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 1339 THR 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 1547 ASN Chi-restraints excluded: chain B residue 1565 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 725 MET 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 1423 LEU 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 462 ARG 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 1353 ILE Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1511 PHE Chi-restraints excluded: chain D residue 1525 PHE Chi-restraints excluded: chain D residue 1547 ASN 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 654 MET Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET 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 1334 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1547 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 412 optimal weight: 40.0000 chunk 433 optimal weight: 0.3980 chunk 395 optimal weight: 0.8980 chunk 422 optimal weight: 10.0000 chunk 254 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 331 optimal weight: 5.9990 chunk 129 optimal weight: 30.0000 chunk 381 optimal weight: 0.5980 chunk 399 optimal weight: 9.9990 chunk 420 optimal weight: 4.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN C 467 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** D 500 ASN ** 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 ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2147 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 38135 Z= 0.190 Angle : 0.699 17.545 51810 Z= 0.346 Chirality : 0.042 0.201 5830 Planarity : 0.005 0.073 6700 Dihedral : 5.685 58.589 5115 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 2.25 % Allowed : 16.47 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 4720 helix: 0.55 (0.12), residues: 1880 sheet: -0.96 (0.16), residues: 910 loop : -0.99 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 546 HIS 0.006 0.001 HIS E 491 PHE 0.036 0.002 PHE B1525 TYR 0.021 0.001 TYR C 353 ARG 0.010 0.000 ARG C 462 *********************** 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 265 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 173 time to evaluate : 4.182 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: A 725 MET cc_start: -0.3893 (OUTLIER) cc_final: -0.4761 (ttt) REVERT: A 1331 MET cc_start: 0.7069 (tmm) cc_final: 0.6205 (tpt) REVERT: A 1528 MET cc_start: 0.4441 (OUTLIER) cc_final: 0.3610 (tpp) REVERT: B 803 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.3207 (ppp) REVERT: B 1473 MET cc_start: -0.3589 (mmt) cc_final: -0.4215 (mmt) REVERT: C 231 MET cc_start: 0.4177 (ttm) cc_final: 0.3443 (tmm) REVERT: C 341 MET cc_start: -0.4150 (tpp) cc_final: -0.5399 (ttp) REVERT: C 1375 MET cc_start: -0.2278 (OUTLIER) cc_final: -0.3380 (ppp) REVERT: D 231 MET cc_start: 0.1092 (ttm) cc_final: 0.0452 (ttm) REVERT: D 761 GLN cc_start: 0.1348 (OUTLIER) cc_final: 0.0945 (tm-30) REVERT: D 1353 ILE cc_start: 0.0385 (OUTLIER) cc_final: -0.0152 (tp) outliers start: 92 outliers final: 65 residues processed: 244 average time/residue: 0.4972 time to fit residues: 202.2826 Evaluate side-chains 241 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 170 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1334 ASN Chi-restraints excluded: chain A residue 1356 LYS Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain A residue 1547 ASN 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 657 THR Chi-restraints excluded: chain B residue 692 MET Chi-restraints excluded: chain B residue 725 MET Chi-restraints excluded: chain B residue 785 MET Chi-restraints excluded: chain B residue 803 MET 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 1574 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 372 LEU 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 1423 LEU Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 462 ARG 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 761 GLN Chi-restraints excluded: chain D residue 1334 ASN Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1362 ASN Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1511 PHE Chi-restraints excluded: chain D residue 1525 PHE Chi-restraints excluded: chain D residue 1547 ASN 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 605 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 654 MET Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET 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 1324 TRP Chi-restraints excluded: chain E residue 1334 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1547 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 277 optimal weight: 5.9990 chunk 446 optimal weight: 0.0670 chunk 272 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 468 optimal weight: 20.0000 chunk 430 optimal weight: 6.9990 chunk 372 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 288 optimal weight: 6.9990 chunk 228 optimal weight: 30.0000 overall best weight: 3.1524 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 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 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2151 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.288 38135 Z= 0.318 Angle : 0.792 59.162 51810 Z= 0.411 Chirality : 0.043 0.328 5830 Planarity : 0.005 0.065 6700 Dihedral : 5.645 58.872 5113 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 1.98 % Allowed : 16.84 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.12), residues: 4720 helix: 0.53 (0.12), residues: 1880 sheet: -0.96 (0.16), residues: 910 loop : -0.99 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 546 HIS 0.007 0.001 HIS E 491 PHE 0.037 0.002 PHE E1558 TYR 0.049 0.002 TYR C 363 ARG 0.027 0.001 ARG A1358 ********************** 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 250 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 169 time to evaluate : 4.259 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: A 341 MET cc_start: -0.3180 (tpp) cc_final: -0.3382 (tmm) REVERT: A 725 MET cc_start: -0.3894 (OUTLIER) cc_final: -0.4762 (ttt) REVERT: A 1331 MET cc_start: 0.7085 (tmm) cc_final: 0.6227 (tpt) REVERT: A 1528 MET cc_start: 0.4763 (OUTLIER) cc_final: 0.3870 (tpp) REVERT: B 803 MET cc_start: 0.3829 (OUTLIER) cc_final: 0.3211 (ppp) REVERT: B 1473 MET cc_start: -0.3589 (mmt) cc_final: -0.4215 (mmt) REVERT: C 231 MET cc_start: 0.4185 (ttm) cc_final: 0.3449 (tmm) REVERT: C 341 MET cc_start: -0.4147 (tpp) cc_final: -0.5167 (ttp) REVERT: C 1375 MET cc_start: -0.2273 (OUTLIER) cc_final: -0.3364 (ppp) REVERT: D 231 MET cc_start: 0.1093 (ttm) cc_final: 0.0453 (ttm) REVERT: D 761 GLN cc_start: 0.1347 (OUTLIER) cc_final: 0.0931 (tm-30) REVERT: D 764 MET cc_start: 0.4495 (ppp) cc_final: 0.4048 (ppp) REVERT: D 1353 ILE cc_start: 0.0390 (OUTLIER) cc_final: -0.0140 (tp) outliers start: 81 outliers final: 72 residues processed: 228 average time/residue: 0.4963 time to fit residues: 187.3894 Evaluate side-chains 245 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 167 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1334 ASN Chi-restraints excluded: chain A residue 1356 LYS Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1528 MET Chi-restraints excluded: chain A residue 1531 GLN Chi-restraints excluded: chain A residue 1547 ASN Chi-restraints excluded: chain A residue 1553 VAL 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 627 LEU 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 785 MET Chi-restraints excluded: chain B residue 803 MET Chi-restraints excluded: chain B residue 1327 TYR 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 372 LEU Chi-restraints excluded: chain C residue 725 MET 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 1423 LEU Chi-restraints excluded: chain C residue 1473 MET Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 453 SER Chi-restraints excluded: chain D residue 462 ARG 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 761 GLN Chi-restraints excluded: chain D residue 1324 TRP Chi-restraints excluded: chain D residue 1334 ASN Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1511 PHE Chi-restraints excluded: chain D residue 1525 PHE Chi-restraints excluded: chain D residue 1547 ASN 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 605 LEU Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 654 MET Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 725 MET 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 1324 TRP Chi-restraints excluded: chain E residue 1334 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1502 VAL Chi-restraints excluded: chain E residue 1547 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 296 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 156 optimal weight: 0.2980 chunk 383 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 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 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5438 r_free = 0.5438 target = 0.156937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.119515 restraints weight = 378067.666| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 21.89 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.7862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.288 38135 Z= 0.318 Angle : 0.792 59.162 51810 Z= 0.411 Chirality : 0.043 0.328 5830 Planarity : 0.005 0.065 6700 Dihedral : 5.645 58.872 5113 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 24.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 1.91 % Allowed : 16.92 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.12), residues: 4720 helix: 0.53 (0.12), residues: 1880 sheet: -0.96 (0.16), residues: 910 loop : -0.99 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 546 HIS 0.007 0.001 HIS E 491 PHE 0.037 0.002 PHE E1558 TYR 0.049 0.002 TYR C 363 ARG 0.027 0.001 ARG A1358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9145.73 seconds wall clock time: 169 minutes 30.47 seconds (10170.47 seconds total)