Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:28:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/05_2023/5lkh_4068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/05_2023/5lkh_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_4068/05_2023/5lkh_4068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/05_2023/5lkh_4068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/05_2023/5lkh_4068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/05_2023/5lkh_4068.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 20.04, per 1000 atoms: 0.54 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: 16.60 Conformation dependent library (CDL) restraints added in 6.5 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: 2.49 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: 16.41 Time building geometry restraints manager: 17.72 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: 1.190 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: 0.040 Extract box with map and model: 8.180 Check model and map are aligned: 0.570 Set scattering table: 0.290 Process input model: 98.960 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.200 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.850 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 4.222 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 outliers start: 80 outliers final: 27 residues processed: 397 average time/residue: 0.5718 time to fit residues: 352.8209 Evaluate side-chains 220 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 3.888 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5044 time to fit residues: 26.3913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 396 optimal weight: 10.0000 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... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: