Starting phenix.real_space_refine on Sun Sep 29 11:42:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/09_2024/6bwf_7298.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/09_2024/6bwf_7298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/09_2024/6bwf_7298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/09_2024/6bwf_7298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/09_2024/6bwf_7298.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bwf_7298/09_2024/6bwf_7298.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 14320 2.51 5 N 3789 2.21 5 O 3949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5546 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 234} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 685 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Chain: "B" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5532 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 237} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 700 Unresolved non-hydrogen angles: 946 Unresolved non-hydrogen dihedrals: 510 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 7, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 348 Chain: "C" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5550 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 233} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 681 Unresolved non-hydrogen angles: 922 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Chain: "D" Number of atoms: 5546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5546 Classifications: {'peptide': 766} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 234} Link IDs: {'CIS': 43, 'PTRANS': 27, 'TRANS': 695} Chain breaks: 18 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 685 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'UNK:plan-1': 120, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 337 Time building chain proxies: 12.94, per 1000 atoms: 0.58 Number of scatterers: 22174 At special positions: 0 Unit cell: (135.3, 135.3, 153.75, 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 116 16.00 O 3949 8.00 N 3789 7.00 C 14320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.4 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 0 sheets defined 69.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK A 35 " --> pdb=" O UNK A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK A 52 " --> pdb=" O UNK A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.516A pdb=" N UNK A 64 " --> pdb=" O UNK A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.689A pdb=" N LEU A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN A 133 " --> pdb=" O GLU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.370A pdb=" N GLN A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 286 removed outlier: 4.982A pdb=" N ILE A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 322 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 337 through 354 removed outlier: 4.440A pdb=" N LEU A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 390 through 397 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.583A pdb=" N SER A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 429 removed outlier: 4.298A pdb=" N MET A 427 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 428 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU A 429 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 554 removed outlier: 3.964A pdb=" N VAL A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 595 removed outlier: 3.525A pdb=" N PHE A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 633 removed outlier: 3.756A pdb=" N ASP A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR A 643 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE A 657 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 660 " --> pdb=" O TYR A 656 " (cutoff:3.500A) Proline residue: A 671 - end of helix removed outlier: 4.219A pdb=" N ILE A 675 " --> pdb=" O PRO A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE A 707 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 738 removed outlier: 3.606A pdb=" N ALA A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS A 771 " --> pdb=" O TYR A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 790 removed outlier: 3.922A pdb=" N LEU A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 885 removed outlier: 3.864A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 27 through 35 removed outlier: 3.817A pdb=" N UNK B 35 " --> pdb=" O UNK B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK B 52 " --> pdb=" O UNK B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK B 64 " --> pdb=" O UNK B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'B' and resid 123 through 133 removed outlier: 3.689A pdb=" N LEU B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN B 133 " --> pdb=" O GLU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS B 233 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.983A pdb=" N ILE B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 323 removed outlier: 4.746A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 341 through 354 removed outlier: 4.008A pdb=" N VAL B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 346 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 390 through 397 Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.582A pdb=" N SER B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET B 427 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 428 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU B 429 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 574 removed outlier: 4.002A pdb=" N TRP B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.674A pdb=" N ILE B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 633 removed outlier: 3.755A pdb=" N ASP B 632 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR B 643 " --> pdb=" O GLN B 639 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY B 648 " --> pdb=" O VAL B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE B 657 " --> pdb=" O ASN B 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 660 " --> pdb=" O TYR B 656 " (cutoff:3.500A) Proline residue: B 671 - end of helix removed outlier: 4.219A pdb=" N ILE B 675 " --> pdb=" O PRO B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.806A pdb=" N ASP B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE B 707 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 738 removed outlier: 3.607A pdb=" N ALA B 732 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR B 770 " --> pdb=" O LYS B 766 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS B 771 " --> pdb=" O TYR B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 790 removed outlier: 3.923A pdb=" N LEU B 789 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASP B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 885 removed outlier: 3.864A pdb=" N ILE B 851 " --> pdb=" O SER B 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK C 35 " --> pdb=" O UNK C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK C 52 " --> pdb=" O UNK C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 49 through 52' Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK C 64 " --> pdb=" O UNK C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.690A pdb=" N LEU C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN C 211 " --> pdb=" O SER C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 4.394A pdb=" N HIS C 233 " --> pdb=" O ARG C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 286 removed outlier: 4.982A pdb=" N ILE C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 322 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 337 through 354 removed outlier: 5.294A pdb=" N LEU C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 345 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 346 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 390 through 397 Processing helix chain 'C' and resid 413 through 421 removed outlier: 3.582A pdb=" N SER C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET C 427 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 428 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU C 429 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 Processing helix chain 'C' and resid 505 through 529 removed outlier: 4.394A pdb=" N LEU C 518 " --> pdb=" O THR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL C 543 " --> pdb=" O GLN C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE C 618 " --> pdb=" O ALA C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 633 removed outlier: 3.755A pdb=" N ASP C 632 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR C 643 " --> pdb=" O GLN C 639 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE C 657 " --> pdb=" O ASN C 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE C 660 " --> pdb=" O TYR C 656 " (cutoff:3.500A) Proline residue: C 671 - end of helix removed outlier: 4.219A pdb=" N ILE C 675 " --> pdb=" O PRO C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS C 693 " --> pdb=" O ASP C 689 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE C 707 " --> pdb=" O ALA C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 738 removed outlier: 3.607A pdb=" N ALA C 732 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 749 Processing helix chain 'C' and resid 754 through 774 removed outlier: 4.060A pdb=" N ILE C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR C 770 " --> pdb=" O LYS C 766 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS C 771 " --> pdb=" O TYR C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 790 removed outlier: 3.923A pdb=" N LEU C 789 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 844 removed outlier: 4.426A pdb=" N GLU C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 840 " --> pdb=" O PHE C 836 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 885 removed outlier: 3.865A pdb=" N ILE C 851 " --> pdb=" O SER C 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.818A pdb=" N UNK D 35 " --> pdb=" O UNK D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 49 through 52 removed outlier: 4.152A pdb=" N UNK D 52 " --> pdb=" O UNK D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 55 through 64 removed outlier: 3.515A pdb=" N UNK D 64 " --> pdb=" O UNK D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 123 through 133 removed outlier: 3.690A pdb=" N LEU D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN D 133 " --> pdb=" O GLU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 171 through 176 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.369A pdb=" N GLN D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 234 removed outlier: 4.395A pdb=" N HIS D 233 " --> pdb=" O ARG D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 275 through 286 removed outlier: 4.983A pdb=" N ILE D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 323 removed outlier: 4.745A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 322 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 337 through 354 removed outlier: 5.295A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 345 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 346 " --> pdb=" O GLN D 342 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 354 " --> pdb=" O GLN D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 390 through 397 Processing helix chain 'D' and resid 413 through 421 removed outlier: 3.583A pdb=" N SER D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 420 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 429 removed outlier: 4.299A pdb=" N MET D 427 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 428 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 429 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 505 through 529 removed outlier: 4.393A pdb=" N LEU D 518 " --> pdb=" O THR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 554 removed outlier: 3.963A pdb=" N VAL D 543 " --> pdb=" O GLN D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 574 removed outlier: 4.001A pdb=" N TRP D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 595 removed outlier: 3.524A pdb=" N PHE D 593 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 622 removed outlier: 3.673A pdb=" N ILE D 618 " --> pdb=" O ALA D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 633 removed outlier: 3.756A pdb=" N ASP D 632 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 648 removed outlier: 4.237A pdb=" N TYR D 643 " --> pdb=" O GLN D 639 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 677 removed outlier: 6.151A pdb=" N TYR D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ILE D 657 " --> pdb=" O ASN D 653 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE D 660 " --> pdb=" O TYR D 656 " (cutoff:3.500A) Proline residue: D 671 - end of helix removed outlier: 4.219A pdb=" N ILE D 675 " --> pdb=" O PRO D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 removed outlier: 3.807A pdb=" N ASP D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 703 through 707 removed outlier: 3.556A pdb=" N ILE D 707 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 738 removed outlier: 3.606A pdb=" N ALA D 732 " --> pdb=" O PRO D 728 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE D 736 " --> pdb=" O ALA D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 749 Processing helix chain 'D' and resid 754 through 774 removed outlier: 4.059A pdb=" N ILE D 760 " --> pdb=" O GLN D 756 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 763 " --> pdb=" O ALA D 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR D 770 " --> pdb=" O LYS D 766 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS D 771 " --> pdb=" O TYR D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 790 removed outlier: 3.922A pdb=" N LEU D 789 " --> pdb=" O PRO D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 844 removed outlier: 4.425A pdb=" N GLU D 833 " --> pdb=" O GLU D 829 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 847 through 885 removed outlier: 3.865A pdb=" N ILE D 851 " --> pdb=" O SER D 847 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2808 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: 5.88 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6355 1.34 - 1.45: 4381 1.45 - 1.57: 11665 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 22601 Sorted by residual: bond pdb=" C ARG C 242 " pdb=" N PRO C 243 " ideal model delta sigma weight residual 1.332 1.378 -0.046 8.90e-03 1.26e+04 2.66e+01 bond pdb=" C ARG B 242 " pdb=" N PRO B 243 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.90e-03 1.26e+04 2.61e+01 bond pdb=" C ARG D 242 " pdb=" N PRO D 243 " ideal model delta sigma weight residual 1.332 1.378 -0.045 8.90e-03 1.26e+04 2.60e+01 bond pdb=" C ARG A 242 " pdb=" N PRO A 243 " ideal model delta sigma weight residual 1.332 1.377 -0.044 8.90e-03 1.26e+04 2.50e+01 bond pdb=" C GLN A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.337 1.376 -0.040 1.11e-02 8.12e+03 1.29e+01 ... (remaining 22596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 29516 3.42 - 6.85: 969 6.85 - 10.27: 131 10.27 - 13.69: 69 13.69 - 17.11: 11 Bond angle restraints: 30696 Sorted by residual: angle pdb=" N HIS A 777 " pdb=" CA HIS A 777 " pdb=" C HIS A 777 " ideal model delta sigma weight residual 110.80 127.91 -17.11 2.13e+00 2.20e-01 6.46e+01 angle pdb=" N HIS B 777 " pdb=" CA HIS B 777 " pdb=" C HIS B 777 " ideal model delta sigma weight residual 110.80 127.90 -17.10 2.13e+00 2.20e-01 6.44e+01 angle pdb=" N HIS D 777 " pdb=" CA HIS D 777 " pdb=" C HIS D 777 " ideal model delta sigma weight residual 110.80 127.87 -17.07 2.13e+00 2.20e-01 6.43e+01 angle pdb=" N HIS C 777 " pdb=" CA HIS C 777 " pdb=" C HIS C 777 " ideal model delta sigma weight residual 110.80 127.86 -17.06 2.13e+00 2.20e-01 6.41e+01 angle pdb=" C TRP B 601 " pdb=" N ASN B 602 " pdb=" CA ASN B 602 " ideal model delta sigma weight residual 121.70 135.86 -14.16 1.80e+00 3.09e-01 6.19e+01 ... (remaining 30691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 12933 26.67 - 53.34: 319 53.34 - 80.00: 24 80.00 - 106.67: 0 106.67 - 133.34: 8 Dihedral angle restraints: 13284 sinusoidal: 4269 harmonic: 9015 Sorted by residual: dihedral pdb=" CA TYR C 776 " pdb=" C TYR C 776 " pdb=" N HIS C 777 " pdb=" CA HIS C 777 " ideal model delta harmonic sigma weight residual -180.00 -46.66 -133.34 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA TYR B 776 " pdb=" C TYR B 776 " pdb=" N HIS B 777 " pdb=" CA HIS B 777 " ideal model delta harmonic sigma weight residual -180.00 -46.68 -133.32 0 5.00e+00 4.00e-02 7.11e+02 dihedral pdb=" CA TYR A 776 " pdb=" C TYR A 776 " pdb=" N HIS A 777 " pdb=" CA HIS A 777 " ideal model delta harmonic sigma weight residual -180.00 -46.69 -133.31 0 5.00e+00 4.00e-02 7.11e+02 ... (remaining 13281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3077 0.093 - 0.186: 380 0.186 - 0.279: 58 0.279 - 0.372: 9 0.372 - 0.465: 7 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CA HIS D 777 " pdb=" N HIS D 777 " pdb=" C HIS D 777 " pdb=" CB HIS D 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA HIS B 777 " pdb=" N HIS B 777 " pdb=" C HIS B 777 " pdb=" CB HIS B 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA HIS C 777 " pdb=" N HIS C 777 " pdb=" C HIS C 777 " pdb=" CB HIS C 777 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.35e+00 ... (remaining 3528 not shown) Planarity restraints: 3910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 512 " -0.033 2.00e-02 2.50e+03 3.18e-02 1.76e+01 pdb=" CG PHE D 512 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE D 512 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE D 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 512 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE D 512 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 512 " 0.033 2.00e-02 2.50e+03 3.18e-02 1.76e+01 pdb=" CG PHE C 512 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE C 512 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE C 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 512 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE C 512 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 512 " -0.033 2.00e-02 2.50e+03 3.17e-02 1.75e+01 pdb=" CG PHE A 512 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 512 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 512 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 512 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 512 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 512 " 0.005 2.00e-02 2.50e+03 ... (remaining 3907 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5649 2.79 - 3.32: 21152 3.32 - 3.85: 34490 3.85 - 4.37: 38935 4.37 - 4.90: 62040 Nonbonded interactions: 162266 Sorted by model distance: nonbonded pdb=" O SER B 337 " pdb=" N ASP B 339 " model vdw 2.263 3.120 nonbonded pdb=" O PHE B 578 " pdb=" OG SER B 581 " model vdw 2.272 3.040 nonbonded pdb=" O PHE C 578 " pdb=" OG SER C 581 " model vdw 2.272 3.040 nonbonded pdb=" O PHE A 578 " pdb=" OG SER A 581 " model vdw 2.273 3.040 nonbonded pdb=" O PHE D 578 " pdb=" OG SER D 581 " model vdw 2.273 3.040 ... (remaining 162261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) selection = (chain 'D' and (resid 1 through 331 or (resid 332 through 334 and (name N or nam \ e CA or name C or name O or name CB )) or resid 335 or (resid 336 and (name N or \ name CA or name C or name O or name CB )) or resid 337 through 886)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.750 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: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 46.730 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 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 : 0.008 0.081 22601 Z= 0.481 Angle : 1.514 17.114 30696 Z= 0.885 Chirality : 0.070 0.465 3531 Planarity : 0.008 0.076 3910 Dihedral : 12.820 133.338 7388 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 1.32 % Allowed : 12.10 % Favored : 86.58 % Rotamer: Outliers : 0.59 % Allowed : 5.20 % Favored : 94.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 4.93 % Twisted Proline : 11.11 % Twisted General : 2.80 % 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: -5.34 (0.14), residues: 2496 helix: -3.42 (0.10), residues: 1504 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 282 HIS 0.007 0.002 HIS B 693 PHE 0.071 0.004 PHE D 512 TYR 0.026 0.003 TYR A 643 ARG 0.009 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 803 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.9276 (mt) cc_final: 0.8964 (tp) REVERT: A 213 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6836 (mtt180) REVERT: A 303 MET cc_start: 0.8458 (tmt) cc_final: 0.8037 (tmm) REVERT: A 634 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7350 (tt) REVERT: A 665 LEU cc_start: 0.8051 (tm) cc_final: 0.7806 (tp) REVERT: A 825 HIS cc_start: 0.6449 (m-70) cc_final: 0.6091 (m-70) REVERT: B 159 TYR cc_start: 0.5768 (p90) cc_final: 0.5561 (p90) REVERT: B 249 MET cc_start: 0.7770 (ptp) cc_final: 0.6894 (ptp) REVERT: B 251 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7429 (mm-30) REVERT: B 289 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6929 (tp40) REVERT: B 301 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6191 (mt-10) REVERT: B 509 LYS cc_start: 0.8852 (mttt) cc_final: 0.8302 (tttp) REVERT: B 548 PHE cc_start: 0.7378 (t80) cc_final: 0.7102 (t80) REVERT: B 583 THR cc_start: 0.8360 (p) cc_final: 0.8137 (p) REVERT: B 634 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6769 (tt) REVERT: B 651 VAL cc_start: 0.9114 (t) cc_final: 0.8871 (t) REVERT: B 661 MET cc_start: 0.6828 (mmp) cc_final: 0.6147 (tpp) REVERT: B 673 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8783 (mttp) REVERT: C 169 VAL cc_start: 0.7162 (t) cc_final: 0.6667 (t) REVERT: C 249 MET cc_start: 0.7843 (ptp) cc_final: 0.7559 (ptp) REVERT: C 313 TYR cc_start: 0.8109 (m-10) cc_final: 0.7022 (m-10) REVERT: C 349 GLU cc_start: 0.8191 (tt0) cc_final: 0.7867 (tt0) REVERT: C 634 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7941 (tm) REVERT: C 649 LYS cc_start: 0.8320 (ttmp) cc_final: 0.6802 (tptt) REVERT: C 684 TRP cc_start: 0.6678 (p-90) cc_final: 0.3985 (m-10) REVERT: C 756 GLN cc_start: 0.8643 (pt0) cc_final: 0.8080 (pp30) REVERT: C 830 GLN cc_start: 0.8542 (tt0) cc_final: 0.8118 (tm-30) REVERT: C 859 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6058 (tp30) REVERT: D 213 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6821 (mtt180) REVERT: D 289 GLN cc_start: 0.6188 (mm-40) cc_final: 0.5781 (mm-40) REVERT: D 297 GLN cc_start: 0.7943 (tp40) cc_final: 0.7358 (tp40) REVERT: D 303 MET cc_start: 0.8475 (tmt) cc_final: 0.7789 (tmm) REVERT: D 634 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7779 (tp) REVERT: D 825 HIS cc_start: 0.6423 (m-70) cc_final: 0.6068 (m-70) REVERT: D 859 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6523 (tp30) outliers start: 11 outliers final: 0 residues processed: 814 average time/residue: 0.3370 time to fit residues: 426.5119 Evaluate side-chains 523 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 519 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 144 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 406 ASN A 504 HIS ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 HIS ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 ASN C 390 HIS ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 504 HIS C 568 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 GLN C 825 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN D 738 GLN ** D 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 HIS D 864 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22601 Z= 0.232 Angle : 0.918 12.484 30696 Z= 0.486 Chirality : 0.047 0.302 3531 Planarity : 0.005 0.065 3910 Dihedral : 8.390 57.594 3211 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.58 % Favored : 89.90 % Rotamer: Outliers : 0.59 % Allowed : 3.38 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.76 % Twisted Proline : 10.19 % Twisted General : 1.11 % 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: -3.58 (0.15), residues: 2496 helix: -1.65 (0.12), residues: 1588 sheet: None (None), residues: 0 loop : -3.62 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 296 HIS 0.012 0.001 HIS C 825 PHE 0.040 0.002 PHE B 815 TYR 0.026 0.002 TYR A 336 ARG 0.008 0.001 ARG D 871 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 641 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.9354 (mt) cc_final: 0.9061 (tp) REVERT: A 213 ARG cc_start: 0.7470 (mtt180) cc_final: 0.6716 (mtt180) REVERT: A 394 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8078 (tp40) REVERT: A 509 LYS cc_start: 0.8737 (mttt) cc_final: 0.8442 (tttp) REVERT: A 532 MET cc_start: 0.7572 (tpp) cc_final: 0.7009 (tpp) REVERT: A 558 VAL cc_start: 0.6962 (m) cc_final: 0.6606 (m) REVERT: A 673 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8685 (mtpp) REVERT: A 689 ASP cc_start: 0.8339 (t0) cc_final: 0.7796 (t0) REVERT: A 825 HIS cc_start: 0.6472 (m-70) cc_final: 0.6152 (m-70) REVERT: B 125 ILE cc_start: 0.9013 (mm) cc_final: 0.8387 (mm) REVERT: B 300 GLU cc_start: 0.6217 (tm-30) cc_final: 0.5801 (tm-30) REVERT: B 558 VAL cc_start: 0.7027 (m) cc_final: 0.6779 (m) REVERT: B 654 MET cc_start: 0.7029 (ptm) cc_final: 0.6432 (ptm) REVERT: B 697 MET cc_start: 0.8666 (mmm) cc_final: 0.8456 (mmm) REVERT: B 706 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7416 (mm-30) REVERT: B 761 SER cc_start: 0.9030 (p) cc_final: 0.8170 (t) REVERT: B 830 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8133 (tm-30) REVERT: C 303 MET cc_start: 0.8499 (ttp) cc_final: 0.8233 (ttm) REVERT: C 311 LYS cc_start: 0.8111 (tptp) cc_final: 0.7910 (tptp) REVERT: C 313 TYR cc_start: 0.8518 (m-10) cc_final: 0.8142 (m-10) REVERT: C 540 GLU cc_start: 0.6864 (tt0) cc_final: 0.6509 (tt0) REVERT: C 654 MET cc_start: 0.7298 (ptt) cc_final: 0.6966 (ptt) REVERT: C 673 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8636 (mttp) REVERT: C 697 MET cc_start: 0.8808 (mmm) cc_final: 0.8457 (mmm) REVERT: C 713 ASP cc_start: 0.7514 (m-30) cc_final: 0.7194 (t0) REVERT: C 724 THR cc_start: 0.8951 (p) cc_final: 0.8742 (t) REVERT: C 756 GLN cc_start: 0.8719 (pt0) cc_final: 0.8120 (pp30) REVERT: C 830 GLN cc_start: 0.8446 (tt0) cc_final: 0.8157 (tm-30) REVERT: C 834 MET cc_start: 0.7999 (ttm) cc_final: 0.7788 (ttm) REVERT: C 866 LYS cc_start: 0.6011 (ttmm) cc_final: 0.5783 (mtmm) REVERT: D 213 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6750 (mtt180) REVERT: D 249 MET cc_start: 0.7490 (ptp) cc_final: 0.7280 (ptm) REVERT: D 314 ARG cc_start: 0.7495 (tpp80) cc_final: 0.7261 (tpp80) REVERT: D 349 GLU cc_start: 0.7882 (tt0) cc_final: 0.7626 (pt0) REVERT: D 417 LEU cc_start: 0.8213 (tt) cc_final: 0.7770 (tp) REVERT: D 509 LYS cc_start: 0.8673 (mttt) cc_final: 0.8369 (tttp) REVERT: D 622 ASN cc_start: 0.7641 (t0) cc_final: 0.7404 (t0) REVERT: D 673 LYS cc_start: 0.8753 (mttm) cc_final: 0.8400 (mmtp) REVERT: D 825 HIS cc_start: 0.6550 (m-70) cc_final: 0.6221 (m-70) outliers start: 11 outliers final: 4 residues processed: 649 average time/residue: 0.3106 time to fit residues: 311.0539 Evaluate side-chains 509 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 505 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 276 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN B 231 HIS B 751 ASN B 777 HIS B 821 GLN C 192 ASN C 231 HIS C 504 HIS C 731 GLN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 HIS D 693 HIS ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 22601 Z= 0.600 Angle : 1.196 14.249 30696 Z= 0.620 Chirality : 0.058 0.319 3531 Planarity : 0.006 0.068 3910 Dihedral : 8.885 48.775 3211 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.02 % Favored : 87.50 % Rotamer: Outliers : 0.27 % Allowed : 7.02 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.39 % Twisted Proline : 11.11 % Twisted General : 2.01 % 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: -3.68 (0.15), residues: 2496 helix: -1.70 (0.12), residues: 1664 sheet: None (None), residues: 0 loop : -3.84 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 511 HIS 0.014 0.003 HIS B 693 PHE 0.052 0.004 PHE D 815 TYR 0.043 0.003 TYR D 703 ARG 0.008 0.001 ARG D 672 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 587 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ILE cc_start: 0.8378 (mt) cc_final: 0.8103 (mm) REVERT: A 249 MET cc_start: 0.7358 (ptt) cc_final: 0.7133 (ptt) REVERT: A 532 MET cc_start: 0.8325 (tpp) cc_final: 0.7933 (tpp) REVERT: A 541 TRP cc_start: 0.8399 (m100) cc_final: 0.7534 (m100) REVERT: A 622 ASN cc_start: 0.8368 (t0) cc_final: 0.7792 (t0) REVERT: A 649 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7214 (tptt) REVERT: A 654 MET cc_start: 0.8155 (ptm) cc_final: 0.7532 (ttp) REVERT: A 744 ASN cc_start: 0.8371 (t0) cc_final: 0.8028 (m-40) REVERT: A 756 GLN cc_start: 0.8837 (pt0) cc_final: 0.8006 (pp30) REVERT: A 774 MET cc_start: 0.7684 (mmm) cc_final: 0.7462 (mmm) REVERT: A 777 HIS cc_start: 0.8423 (m-70) cc_final: 0.7877 (m170) REVERT: A 825 HIS cc_start: 0.6805 (m-70) cc_final: 0.5922 (m-70) REVERT: A 829 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 125 ILE cc_start: 0.9005 (mm) cc_final: 0.8485 (mm) REVERT: B 303 MET cc_start: 0.9011 (ttt) cc_final: 0.8596 (ttm) REVERT: B 530 VAL cc_start: 0.9291 (t) cc_final: 0.9084 (t) REVERT: B 541 TRP cc_start: 0.8283 (m100) cc_final: 0.7513 (m100) REVERT: B 622 ASN cc_start: 0.8298 (t0) cc_final: 0.7845 (t0) REVERT: B 649 LYS cc_start: 0.8985 (tmtt) cc_final: 0.8372 (tptt) REVERT: B 654 MET cc_start: 0.8170 (ptm) cc_final: 0.7750 (ttp) REVERT: B 756 GLN cc_start: 0.8885 (pt0) cc_final: 0.8309 (pp30) REVERT: B 820 ASP cc_start: 0.8169 (m-30) cc_final: 0.7868 (m-30) REVERT: B 830 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 301 GLU cc_start: 0.7470 (mp0) cc_final: 0.7129 (mp0) REVERT: C 303 MET cc_start: 0.8916 (ttp) cc_final: 0.8613 (ttp) REVERT: C 313 TYR cc_start: 0.9016 (m-10) cc_final: 0.8794 (m-10) REVERT: C 349 GLU cc_start: 0.7970 (pt0) cc_final: 0.7542 (tt0) REVERT: C 518 LEU cc_start: 0.8955 (mp) cc_final: 0.8058 (mp) REVERT: C 522 MET cc_start: 0.8195 (mtm) cc_final: 0.7961 (mtm) REVERT: C 590 PHE cc_start: 0.8348 (m-80) cc_final: 0.8131 (m-10) REVERT: C 684 TRP cc_start: 0.6914 (p-90) cc_final: 0.6465 (p-90) REVERT: C 690 ILE cc_start: 0.8321 (mt) cc_final: 0.8112 (mt) REVERT: C 751 ASN cc_start: 0.8620 (t0) cc_final: 0.8100 (t0) REVERT: C 756 GLN cc_start: 0.8772 (pt0) cc_final: 0.8132 (pp30) REVERT: C 866 LYS cc_start: 0.6275 (ttmm) cc_final: 0.5915 (mtmm) REVERT: D 400 MET cc_start: 0.8503 (mtp) cc_final: 0.8242 (ttm) REVERT: D 420 LEU cc_start: 0.9324 (tp) cc_final: 0.9113 (tp) REVERT: D 541 TRP cc_start: 0.8318 (m100) cc_final: 0.7538 (m100) REVERT: D 622 ASN cc_start: 0.8466 (t0) cc_final: 0.8178 (t0) REVERT: D 644 VAL cc_start: 0.9446 (t) cc_final: 0.9216 (p) REVERT: D 649 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7466 (tptt) REVERT: D 750 PHE cc_start: 0.8258 (m-80) cc_final: 0.8032 (m-80) REVERT: D 756 GLN cc_start: 0.8819 (pt0) cc_final: 0.8114 (pp30) REVERT: D 829 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8354 (mt-10) outliers start: 5 outliers final: 1 residues processed: 592 average time/residue: 0.3219 time to fit residues: 293.2568 Evaluate side-chains 478 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 477 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.9980 chunk 207 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 185 optimal weight: 0.2980 chunk 277 optimal weight: 1.9990 chunk 293 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 864 GLN C 751 ASN C 771 HIS C 777 HIS C 864 GLN ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22601 Z= 0.217 Angle : 0.893 14.896 30696 Z= 0.467 Chirality : 0.046 0.316 3531 Planarity : 0.004 0.063 3910 Dihedral : 7.462 40.181 3211 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.62 % Favored : 89.90 % Rotamer: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 7.41 % Twisted General : 0.70 % 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: -2.69 (0.17), residues: 2496 helix: -0.79 (0.13), residues: 1604 sheet: None (None), residues: 0 loop : -3.65 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 765 HIS 0.008 0.001 HIS B 825 PHE 0.053 0.002 PHE C 512 TYR 0.018 0.001 TYR A 336 ARG 0.009 0.001 ARG B 857 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 614 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 TYR cc_start: 0.7413 (t80) cc_final: 0.7168 (t80) REVERT: A 509 LYS cc_start: 0.8577 (mttt) cc_final: 0.8325 (mmmt) REVERT: A 532 MET cc_start: 0.8182 (tpp) cc_final: 0.7350 (tpp) REVERT: A 622 ASN cc_start: 0.7781 (t0) cc_final: 0.7444 (t0) REVERT: A 654 MET cc_start: 0.8096 (ptm) cc_final: 0.7325 (ttm) REVERT: A 744 ASN cc_start: 0.8037 (t0) cc_final: 0.7820 (m-40) REVERT: A 756 GLN cc_start: 0.8745 (pt0) cc_final: 0.8079 (pp30) REVERT: A 774 MET cc_start: 0.7577 (mmm) cc_final: 0.7260 (mmm) REVERT: A 825 HIS cc_start: 0.6675 (m-70) cc_final: 0.6354 (m-70) REVERT: A 830 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 125 ILE cc_start: 0.8798 (mm) cc_final: 0.8414 (mm) REVERT: B 303 MET cc_start: 0.9031 (ttt) cc_final: 0.8446 (ttm) REVERT: B 589 PHE cc_start: 0.8503 (t80) cc_final: 0.8264 (t80) REVERT: B 622 ASN cc_start: 0.7934 (t0) cc_final: 0.7548 (t0) REVERT: B 649 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8309 (tptt) REVERT: B 654 MET cc_start: 0.7611 (ptm) cc_final: 0.7199 (ptm) REVERT: B 756 GLN cc_start: 0.8655 (pt0) cc_final: 0.8028 (pp30) REVERT: B 820 ASP cc_start: 0.7994 (m-30) cc_final: 0.7501 (m-30) REVERT: B 829 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 830 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 301 GLU cc_start: 0.7451 (mp0) cc_final: 0.6389 (mp0) REVERT: C 340 PHE cc_start: 0.7598 (t80) cc_final: 0.7292 (t80) REVERT: C 509 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7901 (tttm) REVERT: C 556 ARG cc_start: 0.7644 (tpp80) cc_final: 0.6557 (mmt90) REVERT: C 649 LYS cc_start: 0.8383 (mttm) cc_final: 0.7362 (tptt) REVERT: C 654 MET cc_start: 0.8278 (ppp) cc_final: 0.6791 (ppp) REVERT: C 756 GLN cc_start: 0.8770 (pt0) cc_final: 0.8140 (pp30) REVERT: C 763 ILE cc_start: 0.9269 (tp) cc_final: 0.9036 (mt) REVERT: C 776 TYR cc_start: 0.7516 (p90) cc_final: 0.6625 (p90) REVERT: C 866 LYS cc_start: 0.6244 (ttmm) cc_final: 0.5940 (mtmm) REVERT: D 297 GLN cc_start: 0.8258 (tp40) cc_final: 0.7437 (tp40) REVERT: D 509 LYS cc_start: 0.8554 (mttt) cc_final: 0.8336 (mmmt) REVERT: D 622 ASN cc_start: 0.7942 (t0) cc_final: 0.7523 (t0) REVERT: D 693 HIS cc_start: 0.8110 (t70) cc_final: 0.7910 (t-90) REVERT: D 701 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8024 (tm-30) REVERT: D 756 GLN cc_start: 0.8737 (pt0) cc_final: 0.8137 (pp30) REVERT: D 825 HIS cc_start: 0.6735 (m-70) cc_final: 0.5972 (m-70) outliers start: 1 outliers final: 0 residues processed: 614 average time/residue: 0.3026 time to fit residues: 291.6229 Evaluate side-chains 490 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 250 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 263 optimal weight: 0.1980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 864 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 756 GLN D 731 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22601 Z= 0.204 Angle : 0.852 14.222 30696 Z= 0.447 Chirality : 0.045 0.321 3531 Planarity : 0.004 0.055 3910 Dihedral : 6.852 35.393 3211 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.62 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 4.63 % Twisted General : 0.53 % 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: -2.12 (0.17), residues: 2496 helix: -0.34 (0.14), residues: 1584 sheet: None (None), residues: 0 loop : -3.38 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 541 HIS 0.017 0.001 HIS B 825 PHE 0.055 0.002 PHE D 815 TYR 0.028 0.001 TYR C 336 ARG 0.005 0.000 ARG A 857 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 576 time to evaluate : 2.406 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: A 356 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 509 LYS cc_start: 0.8578 (mttt) cc_final: 0.8337 (tttp) REVERT: A 532 MET cc_start: 0.8267 (tpp) cc_final: 0.7534 (tpp) REVERT: A 622 ASN cc_start: 0.8010 (t0) cc_final: 0.7587 (t0) REVERT: A 739 TYR cc_start: 0.7214 (t80) cc_final: 0.6918 (t80) REVERT: A 756 GLN cc_start: 0.8732 (pt0) cc_final: 0.8114 (pp30) REVERT: A 774 MET cc_start: 0.7503 (mmm) cc_final: 0.7175 (mmm) REVERT: A 825 HIS cc_start: 0.6626 (m-70) cc_final: 0.5910 (m-70) REVERT: A 829 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8222 (mt-10) REVERT: A 830 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 125 ILE cc_start: 0.8747 (mm) cc_final: 0.8347 (mm) REVERT: B 303 MET cc_start: 0.8956 (ttt) cc_final: 0.8548 (ttm) REVERT: B 400 MET cc_start: 0.8340 (ttm) cc_final: 0.8115 (ttm) REVERT: B 620 CYS cc_start: 0.9107 (t) cc_final: 0.8861 (t) REVERT: B 649 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8316 (tptt) REVERT: B 654 MET cc_start: 0.7611 (ptm) cc_final: 0.7135 (ptm) REVERT: B 756 GLN cc_start: 0.8634 (pt0) cc_final: 0.8058 (pp30) REVERT: B 774 MET cc_start: 0.7286 (mmm) cc_final: 0.6957 (mtt) REVERT: B 820 ASP cc_start: 0.8229 (m-30) cc_final: 0.7760 (m-30) REVERT: B 830 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 297 GLN cc_start: 0.8458 (tp40) cc_final: 0.7477 (tp40) REVERT: C 420 LEU cc_start: 0.8927 (tp) cc_final: 0.8715 (tt) REVERT: C 649 LYS cc_start: 0.8416 (mttm) cc_final: 0.7473 (tptt) REVERT: C 654 MET cc_start: 0.8069 (ppp) cc_final: 0.6488 (ppp) REVERT: C 724 THR cc_start: 0.9373 (p) cc_final: 0.9017 (t) REVERT: C 756 GLN cc_start: 0.8703 (pt0) cc_final: 0.7962 (pp30) REVERT: C 866 LYS cc_start: 0.6009 (ttmm) cc_final: 0.5755 (mtmm) REVERT: D 297 GLN cc_start: 0.8194 (tp40) cc_final: 0.7614 (tp-100) REVERT: D 509 LYS cc_start: 0.8578 (mttt) cc_final: 0.8328 (tttp) REVERT: D 542 ILE cc_start: 0.8936 (mp) cc_final: 0.8699 (mt) REVERT: D 622 ASN cc_start: 0.7909 (t0) cc_final: 0.7545 (t0) REVERT: D 702 VAL cc_start: 0.9334 (t) cc_final: 0.9041 (t) REVERT: D 756 GLN cc_start: 0.8735 (pt0) cc_final: 0.8028 (pp30) REVERT: D 825 HIS cc_start: 0.6622 (m-70) cc_final: 0.6215 (m-70) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.3010 time to fit residues: 273.5324 Evaluate side-chains 484 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.0370 chunk 264 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN A 394 GLN A 751 ASN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 864 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 756 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22601 Z= 0.199 Angle : 0.832 13.250 30696 Z= 0.436 Chirality : 0.045 0.296 3531 Planarity : 0.004 0.054 3910 Dihedral : 6.516 34.023 3211 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.38 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 3.70 % Twisted General : 0.37 % 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: -2.05 (0.17), residues: 2496 helix: -0.24 (0.14), residues: 1616 sheet: None (None), residues: 0 loop : -3.56 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 370 HIS 0.011 0.001 HIS B 825 PHE 0.040 0.002 PHE B 815 TYR 0.017 0.001 TYR A 336 ARG 0.005 0.000 ARG A 857 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 2.317 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: A 245 MET cc_start: 0.7747 (tpp) cc_final: 0.7519 (tpp) REVERT: A 500 TYR cc_start: 0.7360 (t80) cc_final: 0.7137 (t80) REVERT: A 532 MET cc_start: 0.8023 (tpp) cc_final: 0.7443 (tpp) REVERT: A 595 LEU cc_start: 0.6769 (tp) cc_final: 0.6492 (tp) REVERT: A 622 ASN cc_start: 0.7971 (t0) cc_final: 0.7579 (t0) REVERT: A 654 MET cc_start: 0.7984 (ptm) cc_final: 0.7137 (ptm) REVERT: A 739 TYR cc_start: 0.7122 (t80) cc_final: 0.6862 (t80) REVERT: A 756 GLN cc_start: 0.8747 (pt0) cc_final: 0.8138 (pp30) REVERT: A 825 HIS cc_start: 0.6654 (m-70) cc_final: 0.6315 (m-70) REVERT: A 830 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 125 ILE cc_start: 0.8793 (mm) cc_final: 0.8383 (mt) REVERT: B 303 MET cc_start: 0.8943 (ttt) cc_final: 0.8514 (ttm) REVERT: B 400 MET cc_start: 0.8419 (ttm) cc_final: 0.8188 (ttm) REVERT: B 589 PHE cc_start: 0.8226 (t80) cc_final: 0.7987 (t80) REVERT: B 620 CYS cc_start: 0.9095 (t) cc_final: 0.8805 (t) REVERT: B 622 ASN cc_start: 0.7997 (t0) cc_final: 0.7435 (t0) REVERT: B 649 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8340 (tptt) REVERT: B 756 GLN cc_start: 0.8656 (pt0) cc_final: 0.8119 (pp30) REVERT: B 774 MET cc_start: 0.7547 (mmm) cc_final: 0.6998 (mtt) REVERT: B 820 ASP cc_start: 0.8153 (m-30) cc_final: 0.7666 (m-30) REVERT: B 830 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 297 GLN cc_start: 0.8321 (tp40) cc_final: 0.7864 (tm-30) REVERT: C 301 GLU cc_start: 0.6828 (mp0) cc_final: 0.6480 (mp0) REVERT: C 303 MET cc_start: 0.8195 (ttm) cc_final: 0.7932 (tpt) REVERT: C 420 LEU cc_start: 0.8777 (tp) cc_final: 0.8547 (tt) REVERT: C 571 LYS cc_start: 0.7548 (mttp) cc_final: 0.6830 (tptt) REVERT: C 649 LYS cc_start: 0.8247 (mttm) cc_final: 0.7373 (tptt) REVERT: C 654 MET cc_start: 0.8009 (ppp) cc_final: 0.6466 (ppp) REVERT: C 673 LYS cc_start: 0.9131 (mtpp) cc_final: 0.8859 (mtpp) REVERT: C 713 ASP cc_start: 0.7714 (m-30) cc_final: 0.7170 (t0) REVERT: C 724 THR cc_start: 0.9407 (p) cc_final: 0.9096 (t) REVERT: C 739 TYR cc_start: 0.7123 (t80) cc_final: 0.6790 (t80) REVERT: C 756 GLN cc_start: 0.8635 (pt0) cc_final: 0.8102 (pp30) REVERT: C 866 LYS cc_start: 0.6098 (ttmm) cc_final: 0.5843 (mtmm) REVERT: D 297 GLN cc_start: 0.8084 (tp40) cc_final: 0.7622 (tp40) REVERT: D 509 LYS cc_start: 0.8515 (mttt) cc_final: 0.8299 (mmmt) REVERT: D 532 MET cc_start: 0.7723 (tpp) cc_final: 0.7522 (mmm) REVERT: D 622 ASN cc_start: 0.7933 (t0) cc_final: 0.7560 (t0) REVERT: D 825 HIS cc_start: 0.6625 (m-70) cc_final: 0.6320 (m-70) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.3036 time to fit residues: 267.9423 Evaluate side-chains 474 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 167 optimal weight: 0.0050 chunk 214 optimal weight: 0.3980 chunk 166 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 293 optimal weight: 0.9980 chunk 183 optimal weight: 0.0870 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 0.0980 overall best weight: 0.1290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 864 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 298 HIS D 756 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22601 Z= 0.181 Angle : 0.802 13.532 30696 Z= 0.417 Chirality : 0.043 0.279 3531 Planarity : 0.004 0.052 3910 Dihedral : 6.122 32.563 3211 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.01 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 3.70 % Twisted General : 0.16 % 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: -1.72 (0.17), residues: 2496 helix: 0.03 (0.14), residues: 1564 sheet: None (None), residues: 0 loop : -3.25 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 370 HIS 0.008 0.001 HIS B 825 PHE 0.039 0.002 PHE C 234 TYR 0.016 0.001 TYR A 336 ARG 0.006 0.000 ARG A 857 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 2.336 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: A 532 MET cc_start: 0.7814 (tpp) cc_final: 0.7326 (tpp) REVERT: A 622 ASN cc_start: 0.7729 (t0) cc_final: 0.7449 (t0) REVERT: A 654 MET cc_start: 0.7783 (ptm) cc_final: 0.7089 (ptm) REVERT: A 706 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7808 (mm-30) REVERT: A 739 TYR cc_start: 0.7058 (t80) cc_final: 0.6596 (t80) REVERT: A 830 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 125 ILE cc_start: 0.8751 (mm) cc_final: 0.8418 (mt) REVERT: B 622 ASN cc_start: 0.7628 (t0) cc_final: 0.7320 (t0) REVERT: B 654 MET cc_start: 0.7074 (ptm) cc_final: 0.6753 (ptm) REVERT: B 677 TYR cc_start: 0.8836 (m-80) cc_final: 0.8510 (m-10) REVERT: B 776 TYR cc_start: 0.6716 (p90) cc_final: 0.6370 (p90) REVERT: B 820 ASP cc_start: 0.8241 (m-30) cc_final: 0.7696 (m-30) REVERT: B 830 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 301 GLU cc_start: 0.6832 (mp0) cc_final: 0.6459 (mp0) REVERT: C 420 LEU cc_start: 0.8772 (tp) cc_final: 0.8563 (tt) REVERT: C 571 LYS cc_start: 0.7542 (mttp) cc_final: 0.6854 (tptt) REVERT: C 649 LYS cc_start: 0.7930 (mttm) cc_final: 0.7259 (tptt) REVERT: C 654 MET cc_start: 0.7996 (ppp) cc_final: 0.6988 (ppp) REVERT: C 713 ASP cc_start: 0.7661 (m-30) cc_final: 0.7100 (t0) REVERT: C 724 THR cc_start: 0.9413 (p) cc_final: 0.9076 (t) REVERT: C 739 TYR cc_start: 0.6974 (t80) cc_final: 0.6609 (t80) REVERT: C 756 GLN cc_start: 0.8683 (pt0) cc_final: 0.8134 (pp30) REVERT: C 866 LYS cc_start: 0.6097 (ttmm) cc_final: 0.5872 (mtmm) REVERT: D 297 GLN cc_start: 0.7965 (tp40) cc_final: 0.7603 (tp40) REVERT: D 622 ASN cc_start: 0.7906 (t0) cc_final: 0.7548 (t0) REVERT: D 825 HIS cc_start: 0.6658 (m-70) cc_final: 0.6309 (m-70) outliers start: 0 outliers final: 0 residues processed: 546 average time/residue: 0.2969 time to fit residues: 260.4224 Evaluate side-chains 465 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 2.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.0020 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.0060 chunk 56 optimal weight: 0.6980 chunk 186 optimal weight: 0.0170 chunk 199 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 overall best weight: 0.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 756 GLN A 777 HIS ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN B 756 GLN C 406 ASN C 731 GLN C 751 ASN C 756 GLN C 777 HIS D 744 ASN D 756 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22601 Z= 0.178 Angle : 0.782 13.440 30696 Z= 0.408 Chirality : 0.043 0.236 3531 Planarity : 0.004 0.050 3910 Dihedral : 5.908 32.813 3211 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.89 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 0.93 % Twisted General : 0.25 % 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: -1.67 (0.17), residues: 2496 helix: 0.16 (0.14), residues: 1560 sheet: None (None), residues: 0 loop : -3.40 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 370 HIS 0.011 0.001 HIS A 825 PHE 0.036 0.001 PHE C 234 TYR 0.024 0.001 TYR C 336 ARG 0.006 0.000 ARG A 857 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 2.309 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: A 622 ASN cc_start: 0.7845 (t0) cc_final: 0.7495 (t0) REVERT: A 654 MET cc_start: 0.7528 (ptm) cc_final: 0.7049 (ptm) REVERT: A 724 THR cc_start: 0.9278 (p) cc_final: 0.8895 (t) REVERT: A 739 TYR cc_start: 0.6987 (t80) cc_final: 0.6592 (t80) REVERT: A 830 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 125 ILE cc_start: 0.8751 (mm) cc_final: 0.8482 (mt) REVERT: B 400 MET cc_start: 0.8436 (ttm) cc_final: 0.8227 (ttm) REVERT: B 526 PHE cc_start: 0.7822 (t80) cc_final: 0.7513 (t80) REVERT: B 622 ASN cc_start: 0.7955 (t0) cc_final: 0.7511 (t0) REVERT: B 629 ARG cc_start: 0.7698 (ttt90) cc_final: 0.7480 (ttt-90) REVERT: B 774 MET cc_start: 0.7351 (mmm) cc_final: 0.6996 (mtt) REVERT: B 776 TYR cc_start: 0.6374 (p90) cc_final: 0.6120 (p90) REVERT: B 830 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 311 LYS cc_start: 0.8964 (tttm) cc_final: 0.8683 (tttm) REVERT: C 536 PRO cc_start: 0.7272 (Cg_exo) cc_final: 0.6847 (Cg_endo) REVERT: C 571 LYS cc_start: 0.7520 (mttp) cc_final: 0.6834 (tptt) REVERT: C 654 MET cc_start: 0.7916 (ppp) cc_final: 0.6982 (ppp) REVERT: C 673 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9024 (mmtt) REVERT: C 713 ASP cc_start: 0.7490 (m-30) cc_final: 0.7017 (t0) REVERT: C 724 THR cc_start: 0.9414 (p) cc_final: 0.9125 (t) REVERT: C 739 TYR cc_start: 0.6934 (t80) cc_final: 0.6516 (t80) REVERT: C 827 PHE cc_start: 0.8377 (t80) cc_final: 0.8175 (t80) REVERT: C 866 LYS cc_start: 0.6131 (ttmm) cc_final: 0.5781 (mtmm) REVERT: D 213 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6946 (mtp180) REVERT: D 245 MET cc_start: 0.7828 (tpp) cc_final: 0.7544 (tpp) REVERT: D 297 GLN cc_start: 0.7940 (tp40) cc_final: 0.7545 (tp40) REVERT: D 622 ASN cc_start: 0.7851 (t0) cc_final: 0.7572 (t0) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.2932 time to fit residues: 254.1920 Evaluate side-chains 466 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 20.0000 chunk 280 optimal weight: 0.8980 chunk 256 optimal weight: 0.6980 chunk 273 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 214 optimal weight: 0.0060 chunk 83 optimal weight: 10.0000 chunk 246 optimal weight: 0.0870 chunk 258 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A 756 GLN A 821 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN C 751 ASN C 756 GLN D 298 HIS D 756 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22601 Z= 0.191 Angle : 0.793 14.997 30696 Z= 0.413 Chirality : 0.044 0.272 3531 Planarity : 0.004 0.049 3910 Dihedral : 5.900 33.308 3211 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.93 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.57 (0.17), residues: 2496 helix: 0.17 (0.14), residues: 1576 sheet: None (None), residues: 0 loop : -3.29 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 401 HIS 0.013 0.001 HIS D 825 PHE 0.029 0.002 PHE C 234 TYR 0.021 0.001 TYR B 739 ARG 0.008 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 2.119 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: A 349 GLU cc_start: 0.7959 (pt0) cc_final: 0.7745 (pt0) REVERT: A 377 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8217 (mttt) REVERT: A 522 MET cc_start: 0.8054 (mtt) cc_final: 0.7810 (mtt) REVERT: A 622 ASN cc_start: 0.7868 (t0) cc_final: 0.7506 (t0) REVERT: A 654 MET cc_start: 0.7705 (ptm) cc_final: 0.7268 (ptm) REVERT: A 724 THR cc_start: 0.9283 (p) cc_final: 0.9047 (t) REVERT: A 739 TYR cc_start: 0.7099 (t80) cc_final: 0.6769 (t80) REVERT: B 125 ILE cc_start: 0.8842 (mm) cc_final: 0.8611 (mt) REVERT: B 400 MET cc_start: 0.8542 (ttm) cc_final: 0.8283 (ttm) REVERT: B 622 ASN cc_start: 0.7886 (t0) cc_final: 0.7608 (t0) REVERT: B 629 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7465 (ttt-90) REVERT: B 649 LYS cc_start: 0.7527 (tmtt) cc_final: 0.6474 (ttmm) REVERT: B 654 MET cc_start: 0.7062 (ptm) cc_final: 0.6837 (ptm) REVERT: B 693 HIS cc_start: 0.7921 (t-90) cc_final: 0.7067 (t-170) REVERT: B 774 MET cc_start: 0.7433 (mmm) cc_final: 0.7023 (mtt) REVERT: B 830 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8240 (tm-30) REVERT: C 303 MET cc_start: 0.8689 (tpp) cc_final: 0.8106 (tpt) REVERT: C 536 PRO cc_start: 0.7094 (Cg_exo) cc_final: 0.6775 (Cg_endo) REVERT: C 571 LYS cc_start: 0.7497 (mttp) cc_final: 0.6919 (tptt) REVERT: C 654 MET cc_start: 0.7963 (ppp) cc_final: 0.6997 (ppp) REVERT: C 673 LYS cc_start: 0.9361 (mmmm) cc_final: 0.9086 (mmtt) REVERT: C 713 ASP cc_start: 0.7486 (m-30) cc_final: 0.6989 (t0) REVERT: C 739 TYR cc_start: 0.7187 (t80) cc_final: 0.6485 (t80) REVERT: C 866 LYS cc_start: 0.6097 (ttmm) cc_final: 0.5732 (mtmm) REVERT: D 213 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6965 (mtp180) REVERT: D 245 MET cc_start: 0.7882 (tpp) cc_final: 0.7581 (tpp) REVERT: D 297 GLN cc_start: 0.7983 (tp40) cc_final: 0.7562 (tp40) REVERT: D 506 PRO cc_start: 0.8979 (Cg_exo) cc_final: 0.8706 (Cg_endo) REVERT: D 622 ASN cc_start: 0.7951 (t0) cc_final: 0.7661 (t0) outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.2909 time to fit residues: 245.4610 Evaluate side-chains 443 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.0040 chunk 288 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 136 optimal weight: 0.4980 chunk 200 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 HIS A 751 ASN A 756 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 HIS B 744 ASN B 756 GLN C 197 ASN ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 756 GLN D 298 HIS ** D 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 ASN D 756 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.7410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22601 Z= 0.197 Angle : 0.790 14.670 30696 Z= 0.413 Chirality : 0.044 0.247 3531 Planarity : 0.004 0.049 3910 Dihedral : 5.886 33.288 3211 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.50 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.45 (0.17), residues: 2496 helix: 0.30 (0.14), residues: 1580 sheet: None (None), residues: 0 loop : -3.35 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 401 HIS 0.011 0.001 HIS C 825 PHE 0.023 0.002 PHE B 234 TYR 0.017 0.001 TYR B 739 ARG 0.007 0.000 ARG B 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 2.409 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: A 522 MET cc_start: 0.8048 (mtt) cc_final: 0.7843 (mtt) REVERT: A 622 ASN cc_start: 0.8017 (t0) cc_final: 0.7619 (t0) REVERT: A 629 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7581 (ttt-90) REVERT: A 654 MET cc_start: 0.7866 (ptm) cc_final: 0.7386 (ptm) REVERT: A 724 THR cc_start: 0.9408 (p) cc_final: 0.9064 (t) REVERT: B 125 ILE cc_start: 0.8835 (mm) cc_final: 0.8610 (mt) REVERT: B 400 MET cc_start: 0.8470 (ttm) cc_final: 0.8252 (ttm) REVERT: B 629 ARG cc_start: 0.7777 (ttt90) cc_final: 0.7552 (ttt-90) REVERT: B 693 HIS cc_start: 0.7864 (t70) cc_final: 0.7319 (t70) REVERT: B 756 GLN cc_start: 0.8738 (pt0) cc_final: 0.8324 (pp30) REVERT: B 774 MET cc_start: 0.7447 (mmm) cc_final: 0.7017 (mtt) REVERT: B 830 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8262 (tm-30) REVERT: C 548 PHE cc_start: 0.8131 (t80) cc_final: 0.7908 (t80) REVERT: C 571 LYS cc_start: 0.7743 (mttp) cc_final: 0.6993 (tptt) REVERT: C 654 MET cc_start: 0.8054 (ppp) cc_final: 0.7065 (ppp) REVERT: C 673 LYS cc_start: 0.9355 (mmmm) cc_final: 0.9101 (mmtt) REVERT: C 713 ASP cc_start: 0.7489 (m-30) cc_final: 0.7017 (t0) REVERT: C 739 TYR cc_start: 0.7258 (t80) cc_final: 0.6577 (t80) REVERT: C 866 LYS cc_start: 0.6024 (ttmm) cc_final: 0.5702 (mtmm) REVERT: D 213 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6919 (mtp180) REVERT: D 297 GLN cc_start: 0.7954 (tp40) cc_final: 0.7351 (tp40) REVERT: D 622 ASN cc_start: 0.8098 (t0) cc_final: 0.7791 (t0) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.2847 time to fit residues: 237.5256 Evaluate side-chains 445 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 241 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A 731 GLN A 751 ASN A 821 GLN B 298 HIS C 231 HIS ** C 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** D 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.153795 restraints weight = 37097.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156852 restraints weight = 23433.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.158990 restraints weight = 16653.559| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22601 Z= 0.260 Angle : 0.850 14.917 30696 Z= 0.444 Chirality : 0.046 0.251 3531 Planarity : 0.004 0.054 3910 Dihedral : 6.243 35.455 3211 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.74 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.51 (0.17), residues: 2496 helix: 0.22 (0.14), residues: 1580 sheet: None (None), residues: 0 loop : -3.27 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 401 HIS 0.013 0.002 HIS D 825 PHE 0.040 0.002 PHE C 234 TYR 0.026 0.002 TYR C 336 ARG 0.008 0.001 ARG B 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5190.30 seconds wall clock time: 92 minutes 18.85 seconds (5538.85 seconds total)