Starting phenix.real_space_refine (version: dev) on Tue Dec 20 01:52:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/12_2022/5lkh_4068.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/12_2022/5lkh_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_4068/12_2022/5lkh_4068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/12_2022/5lkh_4068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/12_2022/5lkh_4068.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lkh_4068/12_2022/5lkh_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 Convert atoms to be neutral 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-4807/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: 19.99, 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: 15.84 Conformation dependent library (CDL) restraints added in 5.3 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: 2.35 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: 15.36 Time building geometry restraints manager: 16.91 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 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. 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.070 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.330 Process input model: 95.360 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1663 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 : 2.368 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 : 87.25 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 : 4.196 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: 0.5474 time to fit residues: 339.2813 Evaluate side-chains 220 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 4.039 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5131 time to fit residues: 27.3209 ------------------------------------------------------------------------------- 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: 8.9990 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 312 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 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 885 GLN C1361 HIS C1370 ASN C1400 ASN C1462 ASN D 222 ASN ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** D 486 GLN ** 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 D1400 ASN D1462 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** 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: 0.1796 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 38135 Z= 0.318 Angle : 0.985 18.485 51810 Z= 0.497 Chirality : 0.051 0.308 5830 Planarity : 0.008 0.079 6700 Dihedral : 6.758 31.309 5095 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.60 % Favored : 96.08 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.52 (0.11), residues: 4720 helix: 0.36 (0.11), residues: 1870 sheet: 0.47 (0.16), residues: 920 loop : -1.42 (0.13), residues: 1930 *********************** 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 311 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 222 time to evaluate : 4.569 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 outliers start: 89 outliers final: 46 residues processed: 293 average time/residue: 0.5047 time to fit residues: 241.4505 Evaluate side-chains 212 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 4.418 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3934 time to fit residues: 37.6450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 237 optimal weight: 30.0000 chunk 132 optimal weight: 0.8980 chunk 355 optimal weight: 0.0070 chunk 290 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 427 optimal weight: 50.0000 chunk 461 optimal weight: 20.0000 chunk 380 optimal weight: 7.9990 chunk 424 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 overall best weight: 5.1804 ------------------------------------------------------------------------------- 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 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN B 642 HIS B 644 GLN B 679 GLN ** B 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 HIS C 311 ASN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN ** C 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 679 GLN ** C 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN 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** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 GLN E 679 GLN E 709 HIS E 751 HIS E 844 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1945 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 38135 Z= 0.273 Angle : 0.801 11.272 51810 Z= 0.409 Chirality : 0.045 0.215 5830 Planarity : 0.006 0.065 6700 Dihedral : 6.162 29.788 5095 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 26.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.26 % Favored : 95.42 % Rotamer Outliers : 2.15 % 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: -0.55 (0.12), residues: 4720 helix: 0.33 (0.11), residues: 1875 sheet: 0.15 (0.17), residues: 905 loop : -1.24 (0.13), residues: 1940 *********************** 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 265 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 177 time to evaluate : 4.367 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 outliers start: 88 outliers final: 27 residues processed: 249 average time/residue: 0.4860 time to fit residues: 203.2024 Evaluate side-chains 184 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 4.282 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3501 time to fit residues: 24.2137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 422 optimal weight: 30.0000 chunk 321 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 429 optimal weight: 40.0000 chunk 454 optimal weight: 0.0980 chunk 224 optimal weight: 20.0000 chunk 406 optimal weight: 0.0020 chunk 122 optimal weight: 6.9990 overall best weight: 6.6196 ------------------------------------------------------------------------------- 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 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 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 749 GLN A 812 ASN A 844 ASN ** A1531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN B 337 ASN B 467 GLN ** B 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 GLN B 812 ASN B1533 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 ASN C 486 GLN C 584 ASN C 642 HIS C 709 HIS C 749 GLN C 774 ASN C 812 ASN C 844 ASN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1533 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 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 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 749 GLN D 812 ASN D 844 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 GLN ** E 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 749 GLN E 812 ASN ** E1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2123 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 38135 Z= 0.309 Angle : 0.815 15.684 51810 Z= 0.414 Chirality : 0.045 0.290 5830 Planarity : 0.006 0.077 6700 Dihedral : 6.096 31.295 5095 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.51 % Favored : 95.17 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.78 (0.12), residues: 4720 helix: 0.13 (0.11), residues: 1890 sheet: -0.42 (0.16), residues: 905 loop : -1.11 (0.14), residues: 1925 *********************** 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 257 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 170 time to evaluate : 5.170 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 outliers start: 87 outliers final: 28 residues processed: 244 average time/residue: 0.5029 time to fit residues: 204.6276 Evaluate side-chains 182 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 4.071 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3799 time to fit residues: 25.2070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 378 optimal weight: 0.4980 chunk 257 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 338 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 387 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 231 optimal weight: 6.9990 chunk 407 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 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** ** A1531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 486 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 337 ASN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS ** C 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1547 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 486 GLN ** 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 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 GLN ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** 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 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2114 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 38135 Z= 0.224 Angle : 0.714 18.795 51810 Z= 0.359 Chirality : 0.042 0.224 5830 Planarity : 0.005 0.059 6700 Dihedral : 5.770 29.300 5095 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.60 % Favored : 95.13 % Rotamer Outliers : 1.54 % 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: -0.71 (0.12), residues: 4720 helix: 0.29 (0.11), residues: 1885 sheet: -0.56 (0.16), residues: 915 loop : -1.08 (0.14), residues: 1920 *********************** 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 232 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 169 time to evaluate : 4.269 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 outliers start: 63 outliers final: 22 residues processed: 219 average time/residue: 0.4980 time to fit residues: 185.0596 Evaluate side-chains 177 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 4.491 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3744 time to fit residues: 20.9789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 152 optimal weight: 5.9990 chunk 409 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 454 optimal weight: 20.0000 chunk 377 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** 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** D1529 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** 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** E1533 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2134 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 38135 Z= 0.209 Angle : 0.692 18.202 51810 Z= 0.345 Chirality : 0.042 0.221 5830 Planarity : 0.005 0.057 6700 Dihedral : 5.609 28.224 5095 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.02 % Favored : 94.83 % Rotamer Outliers : 1.13 % 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: -0.70 (0.12), residues: 4720 helix: 0.37 (0.11), residues: 1890 sheet: -0.78 (0.16), residues: 925 loop : -1.02 (0.14), residues: 1905 *********************** 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 215 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 169 time to evaluate : 4.547 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 outliers start: 46 outliers final: 17 residues processed: 204 average time/residue: 0.5012 time to fit residues: 174.3085 Evaluate side-chains 172 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 4.205 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3854 time to fit residues: 17.7986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 438 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 332 optimal weight: 0.4980 chunk 257 optimal weight: 10.0000 chunk 382 optimal weight: 6.9990 chunk 253 optimal weight: 30.0000 chunk 453 optimal weight: 40.0000 chunk 283 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** 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** ** C1547 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 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1529 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2191 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 38135 Z= 0.226 Angle : 0.704 17.693 51810 Z= 0.352 Chirality : 0.042 0.461 5830 Planarity : 0.005 0.057 6700 Dihedral : 5.554 29.955 5095 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.83 % Favored : 94.11 % Rotamer Outliers : 1.10 % 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: 1880 sheet: -0.86 (0.16), residues: 910 loop : -1.06 (0.14), residues: 1930 *********************** 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 210 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 165 time to evaluate : 4.309 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 outliers start: 45 outliers final: 13 residues processed: 199 average time/residue: 0.4880 time to fit residues: 164.0649 Evaluate side-chains 172 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 4.014 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3387 time to fit residues: 13.9688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 280 optimal weight: 20.0000 chunk 180 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 42 optimal weight: 30.0000 chunk 356 optimal weight: 30.0000 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 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** ** A1531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN B 856 HIS ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1334 ASN ** C1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** 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** D1533 ASN E 222 ASN ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** 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 644 GLN ** E 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1533 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2237 moved from start: 0.8077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 38135 Z= 0.239 Angle : 0.719 17.394 51810 Z= 0.359 Chirality : 0.043 0.269 5830 Planarity : 0.005 0.059 6700 Dihedral : 5.571 26.486 5095 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.00 % Favored : 93.98 % Rotamer Outliers : 0.86 % 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: -0.82 (0.12), residues: 4720 helix: 0.35 (0.11), residues: 1885 sheet: -1.06 (0.16), residues: 945 loop : -1.05 (0.14), residues: 1890 *********************** 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 210 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 4.107 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 outliers start: 35 outliers final: 10 residues processed: 201 average time/residue: 0.4850 time to fit residues: 164.5349 Evaluate side-chains 177 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 4.487 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4098 time to fit residues: 13.6922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 412 optimal weight: 8.9990 chunk 433 optimal weight: 9.9990 chunk 395 optimal weight: 5.9990 chunk 422 optimal weight: 40.0000 chunk 254 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 331 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 381 optimal weight: 3.9990 chunk 399 optimal weight: 9.9990 chunk 420 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 337 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 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** ** A1531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 GLN ** E 486 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2267 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 38135 Z= 0.226 Angle : 0.713 17.135 51810 Z= 0.357 Chirality : 0.043 0.283 5830 Planarity : 0.005 0.063 6700 Dihedral : 5.521 27.530 5095 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.61 % 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: -0.79 (0.12), residues: 4720 helix: 0.40 (0.11), residues: 1875 sheet: -1.07 (0.16), residues: 935 loop : -1.03 (0.14), residues: 1910 *********************** 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 198 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 4.179 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 outliers start: 25 outliers final: 9 residues processed: 190 average time/residue: 0.4999 time to fit residues: 158.8794 Evaluate side-chains 171 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 4.105 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3641 time to fit residues: 11.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 277 optimal weight: 40.0000 chunk 446 optimal weight: 10.0000 chunk 272 optimal weight: 30.0000 chunk 211 optimal weight: 3.9990 chunk 310 optimal weight: 50.0000 chunk 468 optimal weight: 2.9990 chunk 430 optimal weight: 40.0000 chunk 372 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 288 optimal weight: 6.9990 chunk 228 optimal weight: 40.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- 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 337 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS ** C 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 486 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2346 moved from start: 0.9208 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= 0.267 Angle : 0.754 17.020 51810 Z= 0.376 Chirality : 0.044 0.279 5830 Planarity : 0.005 0.068 6700 Dihedral : 5.653 31.827 5095 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.94 (0.12), residues: 4720 helix: 0.27 (0.11), residues: 1880 sheet: -1.27 (0.16), residues: 945 loop : -1.05 (0.14), residues: 1895 ********************** 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 187 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 4.351 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 outliers start: 18 outliers final: 12 residues processed: 180 average time/residue: 0.4965 time to fit residues: 152.7119 Evaluate side-chains 175 residues out of total 4085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 4.292 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3801 time to fit residues: 15.0203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 296 optimal weight: 0.6980 chunk 397 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 343 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 103 optimal weight: 0.0870 chunk 373 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 383 optimal weight: 6.9990 chunk 47 optimal weight: 40.0000 chunk 68 optimal weight: 0.0060 overall best weight: 2.7578 ------------------------------------------------------------------------------- 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 337 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN ** 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** ** C1547 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 337 ASN ** 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 337 ASN E 486 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5396 r_free = 0.5396 target = 0.153487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.118109 restraints weight = 376325.360| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 23.14 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.9347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 38135 Z= 0.211 Angle : 0.716 15.723 51810 Z= 0.356 Chirality : 0.043 0.283 5830 Planarity : 0.005 0.066 6700 Dihedral : 5.528 26.612 5095 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.37 % 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: -0.80 (0.12), residues: 4720 helix: 0.45 (0.12), residues: 1880 sheet: -1.19 (0.16), residues: 935 loop : -1.05 (0.14), residues: 1905 =============================================================================== Job complete usr+sys time: 8169.95 seconds wall clock time: 148 minutes 49.33 seconds (8929.33 seconds total)