Starting phenix.real_space_refine on Fri Sep 19 02:23:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bwf_7298/09_2025/6bwf_7298.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bwf_7298/09_2025/6bwf_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/cci-nas-00/data/ceres_data/6bwf_7298/09_2025/6bwf_7298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bwf_7298/09_2025/6bwf_7298.map" model { file = "/net/cci-nas-00/data/ceres_data/6bwf_7298/09_2025/6bwf_7298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bwf_7298/09_2025/6bwf_7298.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'UNK:plan-1': 120, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 5, 'ASP:plan': 4, 'TRP:plan': 2} 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: {'UNK:plan-1': 120, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 7, 'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 5, 'HIS:plan': 5, 'ASP:plan': 4, 'TRP:plan': 2} 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: {'UNK:plan-1': 120, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 5, 'ASP:plan': 4, 'TRP:plan': 2} 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: {'UNK:plan-1': 120, 'PHE:plan': 2, 'ARG:plan': 9, 'GLU:plan': 6, 'GLN:plan1': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 5, 'ASP:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 337 Time building chain proxies: 5.68, per 1000 atoms: 0.26 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: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.84 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: 3.72 Time building geometry restraints manager: 2.54 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.910 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- 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= 0.394 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.009 0.001 ARG C 293 TYR 0.026 0.003 TYR A 643 PHE 0.071 0.004 PHE D 512 TRP 0.024 0.003 TRP A 282 HIS 0.007 0.002 HIS B 693 Details of bonding type rmsd covalent geometry : bond 0.00759 (22601) covalent geometry : angle 1.51388 (30696) hydrogen bonds : bond 0.19947 ( 974) hydrogen bonds : angle 11.35277 ( 2808) *********************** 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 to be fit. rotamer outliers: 11 poor density : 803 time to evaluate : 0.779 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: 0.8963 (tp) REVERT: A 213 ARG cc_start: 0.7587 (mtt180) cc_final: 0.6840 (mtt180) REVERT: A 303 MET cc_start: 0.8458 (tmt) cc_final: 0.8040 (tmm) REVERT: A 634 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7349 (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: 0.6090 (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: 0.6895 (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: 0.8303 (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: 0.6771 (tt) REVERT: B 651 VAL cc_start: 0.9114 (t) cc_final: 0.8870 (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: 0.6669 (t) REVERT: C 249 MET cc_start: 0.7843 (ptp) cc_final: 0.7558 (ptp) REVERT: C 313 TYR cc_start: 0.8109 (m-10) cc_final: 0.7023 (m-10) REVERT: C 349 GLU cc_start: 0.8191 (tt0) cc_final: 0.7868 (tt0) REVERT: C 634 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7942 (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: 0.3984 (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: 0.6831 (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: 0.7357 (tp40) REVERT: D 303 MET cc_start: 0.8475 (tmt) cc_final: 0.7790 (tmm) REVERT: D 634 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7777 (tp) REVERT: D 825 HIS cc_start: 0.6423 (m-70) cc_final: 0.6067 (m-70) REVERT: D 859 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6522 (tp30) outliers start: 11 outliers final: 0 residues processed: 814 average time/residue: 0.1586 time to fit residues: 201.8757 Evaluate side-chains 523 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 519 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.193083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.165133 restraints weight = 35694.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.168532 restraints weight = 21746.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170742 restraints weight = 15225.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172121 restraints weight = 11953.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172805 restraints weight = 10190.629| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22601 Z= 0.180 Angle : 0.923 12.541 30696 Z= 0.489 Chirality : 0.047 0.309 3531 Planarity : 0.005 0.065 3910 Dihedral : 8.468 58.956 3211 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.46 % Favored : 89.98 % 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 : 11.11 % Twisted General : 1.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.15), residues: 2496 helix: -1.70 (0.12), residues: 1592 sheet: None (None), residues: 0 loop : -3.61 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 871 TYR 0.026 0.002 TYR A 336 PHE 0.041 0.002 PHE B 815 TRP 0.017 0.002 TRP C 296 HIS 0.012 0.001 HIS C 825 Details of bonding type rmsd covalent geometry : bond 0.00372 (22601) covalent geometry : angle 0.92316 (30696) hydrogen bonds : bond 0.04356 ( 974) hydrogen bonds : angle 5.21801 ( 2808) *********************** 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 653 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 642 time to evaluate : 0.838 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 128 LEU cc_start: 0.9370 (mt) cc_final: 0.9093 (tp) REVERT: A 213 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6598 (mtt180) REVERT: A 394 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8011 (tp40) REVERT: A 509 LYS cc_start: 0.8708 (mttt) cc_final: 0.8424 (tttp) REVERT: A 521 LEU cc_start: 0.8863 (tp) cc_final: 0.8658 (tp) REVERT: A 532 MET cc_start: 0.7574 (tpp) cc_final: 0.7062 (tpp) REVERT: A 558 VAL cc_start: 0.7066 (m) cc_final: 0.6722 (m) REVERT: A 673 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8760 (mtpp) REVERT: A 689 ASP cc_start: 0.8313 (t0) cc_final: 0.7713 (t0) REVERT: A 825 HIS cc_start: 0.6238 (m-70) cc_final: 0.6006 (m-70) REVERT: B 125 ILE cc_start: 0.8987 (mm) cc_final: 0.8352 (mm) REVERT: B 159 TYR cc_start: 0.5927 (p90) cc_final: 0.5707 (p90) REVERT: B 300 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5794 (tm-30) REVERT: B 558 VAL cc_start: 0.7004 (m) cc_final: 0.6773 (m) REVERT: B 654 MET cc_start: 0.7053 (ptm) cc_final: 0.6449 (ptm) REVERT: B 697 MET cc_start: 0.8671 (mmm) cc_final: 0.8466 (mmm) REVERT: B 706 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7503 (mm-30) REVERT: B 713 ASP cc_start: 0.6832 (m-30) cc_final: 0.6618 (t70) REVERT: B 761 SER cc_start: 0.9016 (p) cc_final: 0.8150 (t) REVERT: B 819 GLU cc_start: 0.7024 (pm20) cc_final: 0.6626 (tm-30) REVERT: B 830 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 303 MET cc_start: 0.8535 (ttp) cc_final: 0.8210 (ttm) REVERT: C 313 TYR cc_start: 0.8516 (m-10) cc_final: 0.8137 (m-10) REVERT: C 540 GLU cc_start: 0.6809 (tt0) cc_final: 0.6436 (tt0) REVERT: C 654 MET cc_start: 0.7268 (ptt) cc_final: 0.6949 (ptt) REVERT: C 673 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8584 (mttp) REVERT: C 697 MET cc_start: 0.8883 (mmm) cc_final: 0.8469 (mmm) REVERT: C 713 ASP cc_start: 0.7524 (m-30) cc_final: 0.7243 (t0) REVERT: C 756 GLN cc_start: 0.8735 (pt0) cc_final: 0.8129 (pp30) REVERT: C 830 GLN cc_start: 0.8443 (tt0) cc_final: 0.8174 (tm-30) REVERT: C 834 MET cc_start: 0.7978 (ttm) cc_final: 0.7770 (ttm) REVERT: C 866 LYS cc_start: 0.5787 (ttmm) cc_final: 0.5574 (mtmm) REVERT: D 213 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6757 (mtt180) REVERT: D 249 MET cc_start: 0.7460 (ptp) cc_final: 0.7246 (ptm) REVERT: D 311 LYS cc_start: 0.7901 (tptp) cc_final: 0.7551 (tptp) REVERT: D 417 LEU cc_start: 0.8051 (tt) cc_final: 0.7580 (tp) REVERT: D 509 LYS cc_start: 0.8672 (mttt) cc_final: 0.8342 (tttp) REVERT: D 673 LYS cc_start: 0.8740 (mttm) cc_final: 0.8278 (mmtp) REVERT: D 825 HIS cc_start: 0.6437 (m-70) cc_final: 0.6165 (m-70) outliers start: 11 outliers final: 4 residues processed: 650 average time/residue: 0.1522 time to fit residues: 154.7978 Evaluate side-chains 504 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 500 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 49 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 286 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 738 GLN A 751 ASN B 192 ASN B 504 HIS B 731 GLN ** B 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 HIS B 821 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 GLN C 751 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN D 211 GLN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 HIS ** D 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.193611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.165405 restraints weight = 36058.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168986 restraints weight = 21488.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.171381 restraints weight = 14876.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.172749 restraints weight = 11484.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.173940 restraints weight = 9757.978| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4376 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= 0.156 Angle : 0.854 12.329 30696 Z= 0.450 Chirality : 0.045 0.311 3531 Planarity : 0.004 0.055 3910 Dihedral : 7.259 40.475 3211 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.21 % Favored : 90.30 % Rotamer: Outliers : 0.11 % Allowed : 4.72 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.72 % Twisted Proline : 7.41 % Twisted General : 0.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.16), residues: 2496 helix: -0.97 (0.13), residues: 1608 sheet: None (None), residues: 0 loop : -3.41 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 871 TYR 0.024 0.001 TYR A 627 PHE 0.045 0.002 PHE A 815 TRP 0.013 0.001 TRP C 370 HIS 0.009 0.001 HIS B 825 Details of bonding type rmsd covalent geometry : bond 0.00322 (22601) covalent geometry : angle 0.85440 (30696) hydrogen bonds : bond 0.03668 ( 974) hydrogen bonds : angle 4.42210 ( 2808) *********************** 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 600 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 598 time to evaluate : 0.743 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: A 128 LEU cc_start: 0.9415 (mt) cc_final: 0.9213 (mp) REVERT: A 213 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6754 (mtt180) REVERT: A 417 LEU cc_start: 0.8565 (tt) cc_final: 0.8364 (tt) REVERT: A 509 LYS cc_start: 0.8752 (mttt) cc_final: 0.8519 (tttp) REVERT: A 532 MET cc_start: 0.8034 (tpp) cc_final: 0.7744 (tmm) REVERT: A 558 VAL cc_start: 0.6986 (m) cc_final: 0.6768 (m) REVERT: A 622 ASN cc_start: 0.7740 (t0) cc_final: 0.7199 (t0) REVERT: A 654 MET cc_start: 0.7313 (ptm) cc_final: 0.6239 (ptm) REVERT: A 661 MET cc_start: 0.6984 (mmp) cc_final: 0.6490 (mmp) REVERT: A 673 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8675 (mttp) REVERT: A 738 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8282 (mm110) REVERT: A 825 HIS cc_start: 0.6301 (m-70) cc_final: 0.6019 (m-70) REVERT: B 125 ILE cc_start: 0.9019 (mm) cc_final: 0.8454 (mm) REVERT: B 159 TYR cc_start: 0.5540 (p90) cc_final: 0.5291 (p90) REVERT: B 622 ASN cc_start: 0.7733 (t0) cc_final: 0.7204 (t0) REVERT: B 654 MET cc_start: 0.6796 (ptm) cc_final: 0.6402 (ptm) REVERT: B 713 ASP cc_start: 0.7076 (m-30) cc_final: 0.6672 (t70) REVERT: B 758 LYS cc_start: 0.8498 (tppp) cc_final: 0.8261 (tppp) REVERT: B 761 SER cc_start: 0.9000 (p) cc_final: 0.8487 (t) REVERT: B 830 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8267 (tm-30) REVERT: C 405 LEU cc_start: 0.8872 (mp) cc_final: 0.8535 (mp) REVERT: C 509 LYS cc_start: 0.7486 (mmmt) cc_final: 0.7244 (tttt) REVERT: C 649 LYS cc_start: 0.8127 (mttm) cc_final: 0.7499 (tptt) REVERT: C 673 LYS cc_start: 0.9156 (mtpp) cc_final: 0.8752 (ttmm) REVERT: C 713 ASP cc_start: 0.7546 (m-30) cc_final: 0.7221 (t0) REVERT: C 756 GLN cc_start: 0.8873 (pt0) cc_final: 0.8256 (pp30) REVERT: C 834 MET cc_start: 0.7858 (ttm) cc_final: 0.7553 (ttm) REVERT: C 866 LYS cc_start: 0.5918 (ttmm) cc_final: 0.5685 (mtmm) REVERT: D 213 ARG cc_start: 0.7477 (mtt180) cc_final: 0.6605 (mmm160) REVERT: D 249 MET cc_start: 0.7684 (ptp) cc_final: 0.7393 (pmm) REVERT: D 417 LEU cc_start: 0.8455 (tt) cc_final: 0.7879 (tt) REVERT: D 509 LYS cc_start: 0.8674 (mttt) cc_final: 0.8291 (tttp) REVERT: D 532 MET cc_start: 0.7832 (tpp) cc_final: 0.7156 (tpp) REVERT: D 547 ILE cc_start: 0.7756 (mm) cc_final: 0.7388 (mt) REVERT: D 706 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7235 (mm-30) REVERT: D 738 GLN cc_start: 0.8653 (mm110) cc_final: 0.8021 (mm-40) REVERT: D 776 TYR cc_start: 0.7076 (p90) cc_final: 0.6481 (p90) REVERT: D 859 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7287 (tp30) outliers start: 2 outliers final: 0 residues processed: 598 average time/residue: 0.1382 time to fit residues: 130.7227 Evaluate side-chains 485 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 484 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 293 optimal weight: 0.1980 chunk 279 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 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 211 GLN A 289 GLN A 751 ASN A 864 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 825 HIS C 513 ASN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 821 GLN C 864 GLN D 394 GLN D 821 GLN D 825 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.185723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156671 restraints weight = 36413.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.160064 restraints weight = 22184.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162236 restraints weight = 15605.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163696 restraints weight = 12288.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164404 restraints weight = 10449.112| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22601 Z= 0.191 Angle : 0.886 12.795 30696 Z= 0.467 Chirality : 0.047 0.290 3531 Planarity : 0.005 0.069 3910 Dihedral : 7.043 40.761 3211 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.29 % Favored : 90.22 % Rotamer: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.80 % Twisted Proline : 2.78 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.17), residues: 2496 helix: -0.60 (0.13), residues: 1600 sheet: None (None), residues: 0 loop : -3.52 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 857 TYR 0.028 0.002 TYR C 336 PHE 0.042 0.002 PHE C 512 TRP 0.019 0.002 TRP B 401 HIS 0.012 0.002 HIS D 825 Details of bonding type rmsd covalent geometry : bond 0.00413 (22601) covalent geometry : angle 0.88580 (30696) hydrogen bonds : bond 0.03867 ( 974) hydrogen bonds : angle 4.19564 ( 2808) *********************** 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 569 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 568 time to evaluate : 0.704 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: A 213 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7114 (mtt180) REVERT: A 245 MET cc_start: 0.7613 (tpp) cc_final: 0.7365 (tpp) REVERT: A 509 LYS cc_start: 0.8930 (mttt) cc_final: 0.8648 (tttp) REVERT: A 532 MET cc_start: 0.8057 (tpp) cc_final: 0.7681 (tmm) REVERT: A 622 ASN cc_start: 0.8139 (t0) cc_final: 0.7572 (t0) REVERT: A 649 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7065 (tptt) REVERT: A 654 MET cc_start: 0.7124 (ptm) cc_final: 0.6407 (ptm) REVERT: A 673 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8873 (ttmm) REVERT: A 689 ASP cc_start: 0.8131 (t0) cc_final: 0.7802 (t0) REVERT: A 776 TYR cc_start: 0.7265 (p90) cc_final: 0.6764 (p90) REVERT: A 825 HIS cc_start: 0.6532 (m-70) cc_final: 0.6187 (m-70) REVERT: B 125 ILE cc_start: 0.8985 (mm) cc_final: 0.8588 (mm) REVERT: B 291 MET cc_start: 0.8796 (tmm) cc_final: 0.8423 (tmm) REVERT: B 303 MET cc_start: 0.8674 (tpp) cc_final: 0.8377 (ttm) REVERT: B 305 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8727 (mtpp) REVERT: B 622 ASN cc_start: 0.7882 (t0) cc_final: 0.7490 (t0) REVERT: B 713 ASP cc_start: 0.7392 (m-30) cc_final: 0.6915 (t0) REVERT: B 830 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 852 ARG cc_start: 0.8047 (tmm-80) cc_final: 0.7744 (tmm-80) REVERT: C 518 LEU cc_start: 0.8688 (mp) cc_final: 0.8264 (mp) REVERT: C 649 LYS cc_start: 0.8257 (mttm) cc_final: 0.7712 (tptt) REVERT: C 713 ASP cc_start: 0.7816 (m-30) cc_final: 0.7291 (t0) REVERT: C 756 GLN cc_start: 0.8885 (pt0) cc_final: 0.8254 (pp30) REVERT: C 821 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8384 (mm-40) REVERT: C 830 GLN cc_start: 0.8239 (tm-30) cc_final: 0.8013 (tm-30) REVERT: C 866 LYS cc_start: 0.6161 (ttmm) cc_final: 0.5813 (mtmm) REVERT: D 213 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7343 (mtt180) REVERT: D 417 LEU cc_start: 0.8679 (tt) cc_final: 0.8337 (tp) REVERT: D 623 ILE cc_start: 0.8732 (tp) cc_final: 0.8518 (tt) outliers start: 1 outliers final: 0 residues processed: 569 average time/residue: 0.1420 time to fit residues: 129.0395 Evaluate side-chains 461 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 303 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 240 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 GLN D 756 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.189341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161744 restraints weight = 36237.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164942 restraints weight = 22642.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167005 restraints weight = 16032.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.168462 restraints weight = 12688.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.168976 restraints weight = 10813.589| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22601 Z= 0.155 Angle : 0.826 12.738 30696 Z= 0.435 Chirality : 0.045 0.307 3531 Planarity : 0.004 0.051 3910 Dihedral : 6.632 37.934 3211 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.66 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.92 % Twisted Proline : 4.63 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.17), residues: 2496 helix: -0.26 (0.14), residues: 1548 sheet: None (None), residues: 0 loop : -3.38 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 383 TYR 0.015 0.001 TYR D 703 PHE 0.043 0.002 PHE A 815 TRP 0.015 0.001 TRP B 401 HIS 0.007 0.001 HIS D 298 Details of bonding type rmsd covalent geometry : bond 0.00322 (22601) covalent geometry : angle 0.82563 (30696) hydrogen bonds : bond 0.03504 ( 974) hydrogen bonds : angle 3.90198 ( 2808) *********************** 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 559 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 0.863 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 213 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7325 (mtt180) REVERT: A 504 HIS cc_start: 0.8371 (m90) cc_final: 0.8088 (m170) REVERT: A 509 LYS cc_start: 0.8795 (mttt) cc_final: 0.8586 (tttp) REVERT: A 522 MET cc_start: 0.8214 (mtt) cc_final: 0.7867 (mtt) REVERT: A 532 MET cc_start: 0.7934 (tpp) cc_final: 0.7160 (tpp) REVERT: A 622 ASN cc_start: 0.8086 (t0) cc_final: 0.7541 (t0) REVERT: A 654 MET cc_start: 0.6957 (ptm) cc_final: 0.6501 (ptm) REVERT: A 673 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8594 (mtpp) REVERT: A 776 TYR cc_start: 0.7259 (p90) cc_final: 0.6779 (p90) REVERT: A 825 HIS cc_start: 0.6401 (m-70) cc_final: 0.6114 (m-70) REVERT: B 125 ILE cc_start: 0.8890 (mm) cc_final: 0.8417 (mt) REVERT: B 303 MET cc_start: 0.8671 (tpp) cc_final: 0.8418 (ttm) REVERT: B 305 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8445 (mtpp) REVERT: B 622 ASN cc_start: 0.7864 (t0) cc_final: 0.7468 (t0) REVERT: B 654 MET cc_start: 0.7316 (ptm) cc_final: 0.6716 (ptm) REVERT: B 713 ASP cc_start: 0.7471 (m-30) cc_final: 0.6916 (t0) REVERT: B 830 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 852 ARG cc_start: 0.8001 (tmm-80) cc_final: 0.7687 (tmm-80) REVERT: C 245 MET cc_start: 0.7800 (ttm) cc_final: 0.7582 (tpp) REVERT: C 649 LYS cc_start: 0.8308 (mttm) cc_final: 0.7746 (tptt) REVERT: C 713 ASP cc_start: 0.7711 (m-30) cc_final: 0.7229 (t0) REVERT: C 739 TYR cc_start: 0.7115 (t80) cc_final: 0.6735 (t80) REVERT: C 742 MET cc_start: 0.8429 (mtm) cc_final: 0.8096 (mpp) REVERT: C 756 GLN cc_start: 0.8851 (pt0) cc_final: 0.8256 (pp30) REVERT: C 763 ILE cc_start: 0.9245 (tp) cc_final: 0.8967 (mt) REVERT: C 866 LYS cc_start: 0.6094 (ttmm) cc_final: 0.5875 (mtmm) REVERT: D 213 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7408 (mtt180) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1358 time to fit residues: 120.9959 Evaluate side-chains 473 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 67 optimal weight: 0.0270 chunk 154 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 270 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 297 optimal weight: 0.0070 chunk 269 optimal weight: 1.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 751 ASN A 777 HIS B 298 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN D 192 ASN ** D 738 GLN ** 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 = 0.4184 r_free = 0.4184 target = 0.191859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.163445 restraints weight = 36345.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.166890 restraints weight = 21805.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.169093 restraints weight = 15146.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170689 restraints weight = 11923.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171365 restraints weight = 10032.583| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22601 Z= 0.145 Angle : 0.800 12.982 30696 Z= 0.421 Chirality : 0.044 0.258 3531 Planarity : 0.004 0.049 3910 Dihedral : 6.329 35.775 3211 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.25 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.84 % Twisted Proline : 4.63 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.17), residues: 2496 helix: -0.09 (0.14), residues: 1532 sheet: None (None), residues: 0 loop : -3.32 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 629 TYR 0.016 0.001 TYR A 336 PHE 0.036 0.002 PHE B 234 TRP 0.013 0.001 TRP C 401 HIS 0.005 0.001 HIS D 825 Details of bonding type rmsd covalent geometry : bond 0.00298 (22601) covalent geometry : angle 0.80030 (30696) hydrogen bonds : bond 0.03396 ( 974) hydrogen bonds : angle 3.74651 ( 2808) *********************** 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 564 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 0.627 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: A 213 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7463 (mtt180) REVERT: A 522 MET cc_start: 0.8223 (mtt) cc_final: 0.7841 (mtt) REVERT: A 532 MET cc_start: 0.7661 (tpp) cc_final: 0.7040 (tpp) REVERT: A 654 MET cc_start: 0.6847 (ptm) cc_final: 0.6641 (ptm) REVERT: A 673 LYS cc_start: 0.8979 (mtpp) cc_final: 0.8579 (mtpp) REVERT: A 859 GLU cc_start: 0.8182 (tp30) cc_final: 0.7368 (tm-30) REVERT: B 125 ILE cc_start: 0.8865 (mm) cc_final: 0.8488 (mt) REVERT: B 303 MET cc_start: 0.8558 (tpp) cc_final: 0.8357 (ttm) REVERT: B 305 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8424 (mtpp) REVERT: B 394 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8601 (mm-40) REVERT: B 526 PHE cc_start: 0.7744 (t80) cc_final: 0.7512 (t80) REVERT: B 654 MET cc_start: 0.7202 (ptm) cc_final: 0.6613 (ptm) REVERT: B 673 LYS cc_start: 0.9320 (mtpp) cc_final: 0.9071 (mmtt) REVERT: B 713 ASP cc_start: 0.7496 (m-30) cc_final: 0.6907 (t0) REVERT: B 744 ASN cc_start: 0.7422 (m-40) cc_final: 0.6867 (t0) REVERT: B 774 MET cc_start: 0.7348 (mmm) cc_final: 0.6716 (mtt) REVERT: B 830 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 207 SER cc_start: 0.8439 (p) cc_final: 0.7977 (t) REVERT: C 316 MET cc_start: 0.8507 (mtp) cc_final: 0.8289 (ttm) REVERT: C 402 MET cc_start: 0.8502 (tpp) cc_final: 0.8301 (tpt) REVERT: C 649 LYS cc_start: 0.8200 (mttm) cc_final: 0.7723 (tptt) REVERT: C 693 HIS cc_start: 0.8189 (t-90) cc_final: 0.7880 (t-170) REVERT: C 713 ASP cc_start: 0.7811 (m-30) cc_final: 0.7205 (t0) REVERT: C 739 TYR cc_start: 0.7068 (t80) cc_final: 0.6649 (t80) REVERT: C 742 MET cc_start: 0.8446 (mtm) cc_final: 0.8218 (mpp) REVERT: C 756 GLN cc_start: 0.8851 (pt0) cc_final: 0.8186 (pp30) REVERT: C 866 LYS cc_start: 0.6042 (ttmm) cc_final: 0.5815 (mtmm) REVERT: D 213 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7508 (mtt180) REVERT: D 297 GLN cc_start: 0.8164 (tp40) cc_final: 0.7190 (tp40) REVERT: D 558 VAL cc_start: 0.6792 (m) cc_final: 0.6556 (m) REVERT: D 620 CYS cc_start: 0.8705 (t) cc_final: 0.8361 (t) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.1415 time to fit residues: 127.3381 Evaluate side-chains 483 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 278 optimal weight: 0.0370 chunk 263 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 211 optimal weight: 0.0270 chunk 249 optimal weight: 0.3980 chunk 302 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 756 GLN ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN D 211 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164750 restraints weight = 36255.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.168184 restraints weight = 21819.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170482 restraints weight = 15190.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171768 restraints weight = 11859.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.172980 restraints weight = 10169.837| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.6276 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= 0.143 Angle : 0.792 13.307 30696 Z= 0.416 Chirality : 0.043 0.237 3531 Planarity : 0.004 0.050 3910 Dihedral : 6.125 32.543 3211 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.46 % Favored : 90.22 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.84 % Twisted Proline : 0.93 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.17), residues: 2496 helix: 0.01 (0.14), residues: 1532 sheet: None (None), residues: 0 loop : -3.18 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 629 TYR 0.031 0.001 TYR A 336 PHE 0.035 0.002 PHE C 234 TRP 0.011 0.001 TRP D 370 HIS 0.013 0.001 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00291 (22601) covalent geometry : angle 0.79182 (30696) hydrogen bonds : bond 0.03385 ( 974) hydrogen bonds : angle 3.69904 ( 2808) *********************** 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 545 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.510 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: 0.8236 (mtt) cc_final: 0.7825 (mtt) REVERT: A 532 MET cc_start: 0.7578 (tpp) cc_final: 0.7072 (tpp) REVERT: A 620 CYS cc_start: 0.9093 (t) cc_final: 0.8756 (t) REVERT: A 654 MET cc_start: 0.6929 (ptm) cc_final: 0.6682 (ptm) REVERT: A 673 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8570 (mtpp) REVERT: A 857 ARG cc_start: 0.8216 (tpp80) cc_final: 0.7922 (ttm-80) REVERT: B 125 ILE cc_start: 0.8893 (mm) cc_final: 0.8569 (mt) REVERT: B 526 PHE cc_start: 0.7814 (t80) cc_final: 0.7577 (t80) REVERT: B 654 MET cc_start: 0.7185 (ptm) cc_final: 0.6756 (ptm) REVERT: B 673 LYS cc_start: 0.9310 (mtpp) cc_final: 0.9064 (mmtt) REVERT: B 713 ASP cc_start: 0.7446 (m-30) cc_final: 0.6945 (t0) REVERT: B 739 TYR cc_start: 0.7128 (t80) cc_final: 0.6440 (t80) REVERT: B 744 ASN cc_start: 0.7347 (m-40) cc_final: 0.6733 (t0) REVERT: B 774 MET cc_start: 0.7272 (mmm) cc_final: 0.6914 (mtt) REVERT: C 313 TYR cc_start: 0.8671 (m-10) cc_final: 0.8302 (m-10) REVERT: C 402 MET cc_start: 0.8585 (tpp) cc_final: 0.8363 (tpt) REVERT: C 573 TRP cc_start: 0.7180 (t60) cc_final: 0.6927 (t60) REVERT: C 649 LYS cc_start: 0.7931 (mttm) cc_final: 0.7522 (tptt) REVERT: C 673 LYS cc_start: 0.9310 (mtpp) cc_final: 0.8986 (mtpp) REVERT: C 693 HIS cc_start: 0.8148 (t-90) cc_final: 0.7791 (t-170) REVERT: C 713 ASP cc_start: 0.7590 (m-30) cc_final: 0.7020 (t0) REVERT: C 739 TYR cc_start: 0.7160 (t80) cc_final: 0.6829 (t80) REVERT: C 829 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 866 LYS cc_start: 0.5973 (ttmm) cc_final: 0.5767 (mtmm) REVERT: D 297 GLN cc_start: 0.8172 (tp40) cc_final: 0.7255 (tp40) REVERT: D 633 PHE cc_start: 0.7283 (m-10) cc_final: 0.7034 (m-80) REVERT: D 706 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7606 (mm-30) REVERT: D 774 MET cc_start: 0.7269 (mmm) cc_final: 0.6818 (mmp) REVERT: D 776 TYR cc_start: 0.6605 (p90) cc_final: 0.6318 (p90) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.1352 time to fit residues: 118.3933 Evaluate side-chains 470 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 274 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 286 optimal weight: 5.9990 chunk 186 optimal weight: 0.4980 chunk 148 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 276 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN A 751 ASN A 756 GLN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN C 406 ASN C 731 GLN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN D 539 GLN ** D 731 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.189519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.160438 restraints weight = 36509.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163774 restraints weight = 22324.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165938 restraints weight = 15690.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.167324 restraints weight = 12350.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.168412 restraints weight = 10567.382| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22601 Z= 0.151 Angle : 0.796 13.295 30696 Z= 0.418 Chirality : 0.044 0.221 3531 Planarity : 0.004 0.047 3910 Dihedral : 6.106 32.603 3211 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.33 % Favored : 90.34 % Rotamer: Outliers : 0.11 % Allowed : 1.29 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.88 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.17), residues: 2496 helix: 0.09 (0.14), residues: 1540 sheet: None (None), residues: 0 loop : -3.36 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.014 0.001 TYR C 132 PHE 0.034 0.002 PHE C 234 TRP 0.015 0.001 TRP A 401 HIS 0.009 0.001 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00317 (22601) covalent geometry : angle 0.79648 (30696) hydrogen bonds : bond 0.03400 ( 974) hydrogen bonds : angle 3.67421 ( 2808) *********************** 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 534 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 532 time to evaluate : 0.688 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 245 MET cc_start: 0.7765 (tpp) cc_final: 0.7530 (tpp) REVERT: A 522 MET cc_start: 0.8150 (mtt) cc_final: 0.7758 (mtt) REVERT: A 530 VAL cc_start: 0.8665 (t) cc_final: 0.8434 (t) REVERT: A 532 MET cc_start: 0.7727 (tpp) cc_final: 0.7088 (tpp) REVERT: A 620 CYS cc_start: 0.9121 (t) cc_final: 0.8819 (t) REVERT: A 622 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7697 (t160) REVERT: A 654 MET cc_start: 0.6838 (ptm) cc_final: 0.6447 (ptm) REVERT: A 689 ASP cc_start: 0.8054 (t0) cc_final: 0.7447 (t0) REVERT: A 713 ASP cc_start: 0.6788 (t70) cc_final: 0.6575 (t70) REVERT: A 857 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8110 (ttm-80) REVERT: B 125 ILE cc_start: 0.8944 (mm) cc_final: 0.8624 (mt) REVERT: B 394 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8642 (mm-40) REVERT: B 526 PHE cc_start: 0.7937 (t80) cc_final: 0.7667 (t80) REVERT: B 540 GLU cc_start: 0.6583 (tt0) cc_final: 0.5861 (tt0) REVERT: B 571 LYS cc_start: 0.7716 (mttp) cc_final: 0.7313 (tppt) REVERT: B 654 MET cc_start: 0.7382 (ptm) cc_final: 0.6942 (ptm) REVERT: B 673 LYS cc_start: 0.9293 (mtpp) cc_final: 0.9088 (mmtt) REVERT: B 713 ASP cc_start: 0.7496 (m-30) cc_final: 0.6914 (t0) REVERT: B 739 TYR cc_start: 0.7404 (t80) cc_final: 0.6616 (t80) REVERT: B 774 MET cc_start: 0.7415 (mmm) cc_final: 0.7008 (mtt) REVERT: B 830 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8270 (tm-30) REVERT: C 573 TRP cc_start: 0.7273 (t60) cc_final: 0.6990 (t60) REVERT: C 649 LYS cc_start: 0.7842 (mttm) cc_final: 0.7505 (tptt) REVERT: C 693 HIS cc_start: 0.8089 (t-90) cc_final: 0.7833 (t-170) REVERT: C 713 ASP cc_start: 0.7726 (m-30) cc_final: 0.7046 (t0) REVERT: C 739 TYR cc_start: 0.7074 (t80) cc_final: 0.6790 (t80) REVERT: C 829 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7663 (mt-10) REVERT: C 866 LYS cc_start: 0.6034 (ttmm) cc_final: 0.5801 (mtmm) REVERT: D 297 GLN cc_start: 0.8237 (tp40) cc_final: 0.7468 (tp40) REVERT: D 713 ASP cc_start: 0.6882 (t70) cc_final: 0.6673 (t70) REVERT: D 774 MET cc_start: 0.7306 (mmm) cc_final: 0.6976 (mmp) REVERT: D 776 TYR cc_start: 0.6671 (p90) cc_final: 0.6428 (p90) outliers start: 2 outliers final: 0 residues processed: 533 average time/residue: 0.1367 time to fit residues: 117.7496 Evaluate side-chains 457 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 163 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 215 optimal weight: 0.1980 chunk 236 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 278 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN A 751 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 ASN C 197 ASN C 354 GLN ** C 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 756 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.186776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.158362 restraints weight = 36737.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161525 restraints weight = 22812.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163689 restraints weight = 16315.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.164860 restraints weight = 12901.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165878 restraints weight = 11187.016| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22601 Z= 0.164 Angle : 0.819 13.183 30696 Z= 0.429 Chirality : 0.045 0.271 3531 Planarity : 0.004 0.048 3910 Dihedral : 6.183 35.183 3211 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.33 % Favored : 90.34 % Rotamer: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.80 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.17), residues: 2496 helix: 0.16 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -3.31 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 857 TYR 0.028 0.001 TYR C 336 PHE 0.033 0.002 PHE D 750 TRP 0.014 0.001 TRP D 401 HIS 0.007 0.001 HIS A 825 Details of bonding type rmsd covalent geometry : bond 0.00354 (22601) covalent geometry : angle 0.81949 (30696) hydrogen bonds : bond 0.03530 ( 974) hydrogen bonds : angle 3.74595 ( 2808) *********************** 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 540 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 539 time to evaluate : 0.785 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: A 286 MET cc_start: 0.7918 (tpt) cc_final: 0.7662 (mmm) REVERT: A 522 MET cc_start: 0.8203 (mtt) cc_final: 0.7700 (mtt) REVERT: A 530 VAL cc_start: 0.8822 (t) cc_final: 0.8621 (t) REVERT: A 532 MET cc_start: 0.7810 (tpp) cc_final: 0.7306 (tpp) REVERT: A 620 CYS cc_start: 0.9233 (t) cc_final: 0.8952 (t) REVERT: A 654 MET cc_start: 0.7198 (ptm) cc_final: 0.6506 (ptm) REVERT: A 673 LYS cc_start: 0.9212 (mtpp) cc_final: 0.8735 (mttp) REVERT: A 825 HIS cc_start: 0.6516 (m-70) cc_final: 0.6292 (m-70) REVERT: A 857 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8146 (ttm-80) REVERT: A 859 GLU cc_start: 0.8341 (tp30) cc_final: 0.7625 (tm-30) REVERT: B 125 ILE cc_start: 0.8898 (mm) cc_final: 0.8554 (mt) REVERT: B 291 MET cc_start: 0.8336 (tmm) cc_final: 0.7977 (tmm) REVERT: B 295 LEU cc_start: 0.9016 (mp) cc_final: 0.8701 (mt) REVERT: B 394 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8660 (mm-40) REVERT: B 571 LYS cc_start: 0.7802 (mttp) cc_final: 0.7402 (tppt) REVERT: B 654 MET cc_start: 0.7530 (ptm) cc_final: 0.7152 (ptm) REVERT: B 693 HIS cc_start: 0.7606 (t-90) cc_final: 0.7101 (t-170) REVERT: B 713 ASP cc_start: 0.7564 (m-30) cc_final: 0.6973 (t0) REVERT: B 739 TYR cc_start: 0.7402 (t80) cc_final: 0.6772 (t80) REVERT: B 756 GLN cc_start: 0.8705 (pt0) cc_final: 0.8370 (pp30) REVERT: B 830 GLN cc_start: 0.8897 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 316 MET cc_start: 0.8599 (mtp) cc_final: 0.8357 (ttm) REVERT: C 573 TRP cc_start: 0.7370 (t60) cc_final: 0.7145 (t60) REVERT: C 649 LYS cc_start: 0.7909 (mttm) cc_final: 0.7554 (tptt) REVERT: C 713 ASP cc_start: 0.7769 (m-30) cc_final: 0.7045 (t0) REVERT: C 739 TYR cc_start: 0.7208 (t80) cc_final: 0.6847 (t80) REVERT: C 756 GLN cc_start: 0.8852 (pt0) cc_final: 0.8213 (pp30) REVERT: C 830 GLN cc_start: 0.8481 (pp30) cc_final: 0.8249 (pp30) REVERT: D 297 GLN cc_start: 0.8250 (tp40) cc_final: 0.7467 (tp40) REVERT: D 349 GLU cc_start: 0.7723 (pt0) cc_final: 0.7467 (pt0) REVERT: D 681 GLU cc_start: 0.8354 (mp0) cc_final: 0.7921 (mm-30) REVERT: D 774 MET cc_start: 0.7448 (mmm) cc_final: 0.7179 (mmp) REVERT: D 776 TYR cc_start: 0.6919 (p90) cc_final: 0.6450 (p90) outliers start: 1 outliers final: 0 residues processed: 540 average time/residue: 0.1376 time to fit residues: 120.2021 Evaluate side-chains 465 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 85 optimal weight: 9.9990 chunk 296 optimal weight: 4.9990 chunk 171 optimal weight: 0.0870 chunk 276 optimal weight: 0.6980 chunk 238 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 HIS ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** D 731 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.186880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157403 restraints weight = 36877.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160672 restraints weight = 22993.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162904 restraints weight = 16264.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164130 restraints weight = 12875.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.165252 restraints weight = 11136.671| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22601 Z= 0.159 Angle : 0.815 13.304 30696 Z= 0.428 Chirality : 0.045 0.257 3531 Planarity : 0.004 0.052 3910 Dihedral : 6.140 34.166 3211 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.02 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.84 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.17), residues: 2496 helix: 0.24 (0.14), residues: 1552 sheet: None (None), residues: 0 loop : -3.30 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 857 TYR 0.033 0.001 TYR A 336 PHE 0.033 0.002 PHE B 234 TRP 0.019 0.001 TRP A 401 HIS 0.014 0.001 HIS D 825 Details of bonding type rmsd covalent geometry : bond 0.00344 (22601) covalent geometry : angle 0.81541 (30696) hydrogen bonds : bond 0.03560 ( 974) hydrogen bonds : angle 3.72737 ( 2808) ********************** 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 528 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 0.816 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: A 286 MET cc_start: 0.8110 (tpt) cc_final: 0.7798 (mmm) REVERT: A 532 MET cc_start: 0.7781 (tpp) cc_final: 0.7327 (tpp) REVERT: A 622 ASN cc_start: 0.8044 (t0) cc_final: 0.7640 (t0) REVERT: A 654 MET cc_start: 0.7217 (ptm) cc_final: 0.6512 (ptm) REVERT: A 673 LYS cc_start: 0.9176 (mtpp) cc_final: 0.8757 (mttp) REVERT: A 693 HIS cc_start: 0.7466 (t-90) cc_final: 0.6933 (t-170) REVERT: A 825 HIS cc_start: 0.6562 (m-70) cc_final: 0.6337 (m-70) REVERT: A 857 ARG cc_start: 0.8452 (tpp80) cc_final: 0.8126 (ttm-80) REVERT: A 859 GLU cc_start: 0.8349 (tp30) cc_final: 0.7705 (tm-30) REVERT: B 125 ILE cc_start: 0.8888 (mm) cc_final: 0.8567 (mt) REVERT: B 394 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8649 (mm-40) REVERT: B 654 MET cc_start: 0.7485 (ptm) cc_final: 0.7067 (ptm) REVERT: B 673 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8548 (mmtp) REVERT: B 693 HIS cc_start: 0.7671 (t-90) cc_final: 0.7133 (t-170) REVERT: B 713 ASP cc_start: 0.7634 (m-30) cc_final: 0.7002 (t0) REVERT: B 739 TYR cc_start: 0.7323 (t80) cc_final: 0.6801 (t80) REVERT: B 756 GLN cc_start: 0.8740 (pt0) cc_final: 0.8390 (pp30) REVERT: B 830 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 649 LYS cc_start: 0.8088 (mttm) cc_final: 0.7723 (tptt) REVERT: C 673 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8804 (mmtp) REVERT: C 713 ASP cc_start: 0.7781 (m-30) cc_final: 0.6990 (t0) REVERT: C 739 TYR cc_start: 0.7153 (t80) cc_final: 0.6747 (t80) REVERT: C 756 GLN cc_start: 0.8870 (pt0) cc_final: 0.8228 (pp30) REVERT: D 349 GLU cc_start: 0.7675 (pt0) cc_final: 0.7407 (pt0) REVERT: D 526 PHE cc_start: 0.7813 (t80) cc_final: 0.7553 (t80) REVERT: D 681 GLU cc_start: 0.8340 (mp0) cc_final: 0.7979 (mm-30) REVERT: D 756 GLN cc_start: 0.8792 (pt0) cc_final: 0.8363 (pp30) REVERT: D 774 MET cc_start: 0.7549 (mmm) cc_final: 0.7341 (mmp) REVERT: D 776 TYR cc_start: 0.6956 (p90) cc_final: 0.6491 (p90) REVERT: D 860 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7678 (tm-30) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.1374 time to fit residues: 117.7308 Evaluate side-chains 457 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 204 optimal weight: 0.0970 chunk 273 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 252 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 286 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 712 ASN A 751 ASN B 298 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN C 731 GLN ** C 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN D 298 HIS ** D 731 GLN ** 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 = 0.4133 r_free = 0.4133 target = 0.188089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158740 restraints weight = 36715.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162002 restraints weight = 22857.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164240 restraints weight = 16290.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.165738 restraints weight = 12850.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166526 restraints weight = 10992.691| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.7158 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= 0.152 Angle : 0.801 14.479 30696 Z= 0.421 Chirality : 0.045 0.277 3531 Planarity : 0.004 0.081 3910 Dihedral : 6.076 34.885 3211 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.70 % Favored : 89.98 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.84 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.17), residues: 2496 helix: 0.32 (0.14), residues: 1556 sheet: None (None), residues: 0 loop : -3.15 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 629 TYR 0.027 0.001 TYR C 336 PHE 0.032 0.002 PHE B 827 TRP 0.015 0.001 TRP A 401 HIS 0.015 0.001 HIS D 825 Details of bonding type rmsd covalent geometry : bond 0.00322 (22601) covalent geometry : angle 0.80135 (30696) hydrogen bonds : bond 0.03464 ( 974) hydrogen bonds : angle 3.67273 ( 2808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4048.30 seconds wall clock time: 70 minutes 24.96 seconds (4224.96 seconds total)