Starting phenix.real_space_refine on Fri Feb 6 16:51:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ldl_63004/02_2026/9ldl_63004.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ldl_63004/02_2026/9ldl_63004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ldl_63004/02_2026/9ldl_63004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ldl_63004/02_2026/9ldl_63004.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ldl_63004/02_2026/9ldl_63004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ldl_63004/02_2026/9ldl_63004.map" } resolution = 2.55 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= 0.018 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 144 5.16 5 C 16676 2.51 5 N 4668 2.21 5 O 5032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26520 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 6630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 6630 Classifications: {'peptide': 886} Link IDs: {'PTRANS': 42, 'TRANS': 843} Restraints were copied for chains: A, B, D Time building chain proxies: 6.79, per 1000 atoms: 0.26 Number of scatterers: 26520 At special positions: 0 Unit cell: (143.17, 139.05, 85.49, 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 144 16.00 O 5032 8.00 N 4668 7.00 C 16676 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6440 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 26 sheets defined 51.5% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'C' and resid 39 through 56 Processing helix chain 'C' and resid 63 through 80 removed outlier: 3.669A pdb=" N ALA C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 96 through 101 Processing helix chain 'C' and resid 102 through 121 Processing helix chain 'C' and resid 158 through 173 removed outlier: 4.030A pdb=" N MET C 173 " --> pdb=" O HIS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.704A pdb=" N LEU C 190 " --> pdb=" O PRO C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 Processing helix chain 'C' and resid 234 through 247 removed outlier: 3.515A pdb=" N LYS C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.714A pdb=" N ASP C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 350 Processing helix chain 'C' and resid 403 through 413 Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 468 through 474 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 524 through 534 removed outlier: 4.286A pdb=" N LYS C 528 " --> pdb=" O PRO C 524 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 removed outlier: 3.678A pdb=" N THR C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 560 Processing helix chain 'C' and resid 575 through 589 Processing helix chain 'C' and resid 599 through 616 Processing helix chain 'C' and resid 618 through 623 removed outlier: 3.782A pdb=" N MET C 623 " --> pdb=" O ASN C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 671 removed outlier: 3.576A pdb=" N VAL C 671 " --> pdb=" O PRO C 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 668 through 671' Processing helix chain 'C' and resid 679 through 684 removed outlier: 4.566A pdb=" N GLY C 684 " --> pdb=" O ARG C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 705 Processing helix chain 'C' and resid 711 through 735 Proline residue: C 730 - end of helix Processing helix chain 'C' and resid 738 through 760 removed outlier: 3.875A pdb=" N VAL C 758 " --> pdb=" O TRP C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 776 removed outlier: 3.577A pdb=" N ALA C 766 " --> pdb=" O GLY C 762 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 794 Proline residue: C 788 - end of helix Processing helix chain 'C' and resid 800 through 810 Processing helix chain 'C' and resid 817 through 836 Processing helix chain 'C' and resid 841 through 846 removed outlier: 3.615A pdb=" N ASP C 844 " --> pdb=" O TYR C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 860 removed outlier: 3.540A pdb=" N MET C 860 " --> pdb=" O ALA C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 886 removed outlier: 3.782A pdb=" N VAL C 878 " --> pdb=" O GLY C 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 56 Processing helix chain 'A' and resid 63 through 80 removed outlier: 3.669A pdb=" N ALA A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 102 through 121 Processing helix chain 'A' and resid 158 through 173 removed outlier: 4.030A pdb=" N MET A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.704A pdb=" N LEU A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 234 through 247 removed outlier: 3.515A pdb=" N LYS A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.714A pdb=" N ASP A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 468 through 474 Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 524 through 534 removed outlier: 4.286A pdb=" N LYS A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 removed outlier: 3.678A pdb=" N THR A 549 " --> pdb=" O GLY A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 599 through 616 Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.782A pdb=" N MET A 623 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 671 removed outlier: 3.576A pdb=" N VAL A 671 " --> pdb=" O PRO A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 679 through 684 removed outlier: 4.566A pdb=" N GLY A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 705 Processing helix chain 'A' and resid 711 through 735 Proline residue: A 730 - end of helix Processing helix chain 'A' and resid 738 through 760 removed outlier: 3.875A pdb=" N VAL A 758 " --> pdb=" O TRP A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 776 removed outlier: 3.577A pdb=" N ALA A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 794 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 817 through 836 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.615A pdb=" N ASP A 844 " --> pdb=" O TYR A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.540A pdb=" N MET A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 886 removed outlier: 3.782A pdb=" N VAL A 878 " --> pdb=" O GLY A 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 56 Processing helix chain 'B' and resid 63 through 80 removed outlier: 3.669A pdb=" N ALA B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 102 through 121 Processing helix chain 'B' and resid 158 through 173 removed outlier: 4.030A pdb=" N MET B 173 " --> pdb=" O HIS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.704A pdb=" N LEU B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 234 through 247 removed outlier: 3.515A pdb=" N LYS B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 283 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 301 through 315 removed outlier: 3.714A pdb=" N ASP B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 524 through 534 removed outlier: 4.286A pdb=" N LYS B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 549 removed outlier: 3.678A pdb=" N THR B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 575 through 589 Processing helix chain 'B' and resid 599 through 616 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.782A pdb=" N MET B 623 " --> pdb=" O ASN B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 671 removed outlier: 3.576A pdb=" N VAL B 671 " --> pdb=" O PRO B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 671' Processing helix chain 'B' and resid 679 through 684 removed outlier: 4.566A pdb=" N GLY B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 711 through 735 Proline residue: B 730 - end of helix Processing helix chain 'B' and resid 738 through 760 removed outlier: 3.875A pdb=" N VAL B 758 " --> pdb=" O TRP B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 776 removed outlier: 3.577A pdb=" N ALA B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 794 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 817 through 836 Processing helix chain 'B' and resid 841 through 846 removed outlier: 3.615A pdb=" N ASP B 844 " --> pdb=" O TYR B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.540A pdb=" N MET B 860 " --> pdb=" O ALA B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 886 removed outlier: 3.782A pdb=" N VAL B 878 " --> pdb=" O GLY B 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 56 Processing helix chain 'D' and resid 63 through 80 removed outlier: 3.669A pdb=" N ALA D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 102 through 121 Processing helix chain 'D' and resid 158 through 173 removed outlier: 4.030A pdb=" N MET D 173 " --> pdb=" O HIS D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 3.704A pdb=" N LEU D 190 " --> pdb=" O PRO D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 234 through 247 removed outlier: 3.515A pdb=" N LYS D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 301 through 315 removed outlier: 3.714A pdb=" N ASP D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 350 Processing helix chain 'D' and resid 403 through 413 Processing helix chain 'D' and resid 426 through 435 Processing helix chain 'D' and resid 468 through 474 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 524 through 534 removed outlier: 4.286A pdb=" N LYS D 528 " --> pdb=" O PRO D 524 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 549 removed outlier: 3.678A pdb=" N THR D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 575 through 589 Processing helix chain 'D' and resid 599 through 616 Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.782A pdb=" N MET D 623 " --> pdb=" O ASN D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 671 removed outlier: 3.576A pdb=" N VAL D 671 " --> pdb=" O PRO D 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 668 through 671' Processing helix chain 'D' and resid 679 through 684 removed outlier: 4.566A pdb=" N GLY D 684 " --> pdb=" O ARG D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 705 Processing helix chain 'D' and resid 711 through 735 Proline residue: D 730 - end of helix Processing helix chain 'D' and resid 738 through 760 removed outlier: 3.875A pdb=" N VAL D 758 " --> pdb=" O TRP D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 776 removed outlier: 3.577A pdb=" N ALA D 766 " --> pdb=" O GLY D 762 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 794 Proline residue: D 788 - end of helix Processing helix chain 'D' and resid 800 through 810 Processing helix chain 'D' and resid 817 through 836 Processing helix chain 'D' and resid 841 through 846 removed outlier: 3.615A pdb=" N ASP D 844 " --> pdb=" O TYR D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 860 removed outlier: 3.540A pdb=" N MET D 860 " --> pdb=" O ALA D 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 886 removed outlier: 3.782A pdb=" N VAL D 878 " --> pdb=" O GLY D 874 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 removed outlier: 4.269A pdb=" N ASP C 2 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA C 33 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AA3, first strand: chain 'C' and resid 125 through 127 removed outlier: 8.113A pdb=" N VAL D 442 " --> pdb=" O VAL C 479 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG C 481 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE D 444 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS C 483 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE D 376 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.713A pdb=" N VAL C 149 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N SER C 230 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 151 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR C 232 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 153 " --> pdb=" O THR C 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.530A pdb=" N ILE C 376 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 416 through 417 removed outlier: 3.505A pdb=" N GLY C 417 " --> pdb=" O TYR C 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 563 through 567 removed outlier: 6.851A pdb=" N ALA C 538 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR C 567 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE C 540 " --> pdb=" O TYR C 567 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 594 " --> pdb=" O ILE C 636 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE C 638 " --> pdb=" O ILE C 594 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER C 596 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N THR C 675 " --> pdb=" O PRO C 513 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN C 515 " --> pdb=" O THR C 675 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU C 677 " --> pdb=" O ASN C 515 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE C 517 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA C 512 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR B 514 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR C 514 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA B 512 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N THR B 675 " --> pdb=" O PRO B 513 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN B 515 " --> pdb=" O THR B 675 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU B 677 " --> pdb=" O ASN B 515 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 517 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 594 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 638 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER B 596 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 538 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR B 567 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 540 " --> pdb=" O TYR B 567 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 651 through 655 Processing sheet with id=AA9, first strand: chain 'A' and resid 2 through 4 removed outlier: 4.269A pdb=" N ASP A 2 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 33 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AB2, first strand: chain 'A' and resid 125 through 127 removed outlier: 8.113A pdb=" N VAL B 442 " --> pdb=" O VAL A 479 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 481 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE B 444 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS A 483 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 376 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.713A pdb=" N VAL A 149 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N SER A 230 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 151 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A 232 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 153 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 353 through 356 removed outlier: 6.530A pdb=" N ILE A 376 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 416 through 417 removed outlier: 3.505A pdb=" N GLY A 417 " --> pdb=" O TYR A 459 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 563 through 567 removed outlier: 6.851A pdb=" N ALA A 538 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR A 567 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 540 " --> pdb=" O TYR A 567 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 594 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE A 638 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER A 596 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N THR A 675 " --> pdb=" O PRO A 513 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN A 515 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU A 677 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 517 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA A 512 " --> pdb=" O THR D 514 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR D 514 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR A 514 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA D 512 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N THR D 675 " --> pdb=" O PRO D 513 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN D 515 " --> pdb=" O THR D 675 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU D 677 " --> pdb=" O ASN D 515 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE D 517 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 594 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE D 638 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER D 596 " --> pdb=" O ILE D 638 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 538 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR D 567 " --> pdb=" O ALA D 538 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 540 " --> pdb=" O TYR D 567 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 651 through 655 Processing sheet with id=AB8, first strand: chain 'B' and resid 2 through 4 removed outlier: 4.269A pdb=" N ASP B 2 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 33 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.713A pdb=" N VAL B 149 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N SER B 230 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 151 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR B 232 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE B 153 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 416 through 417 removed outlier: 3.505A pdb=" N GLY B 417 " --> pdb=" O TYR B 459 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 651 through 655 Processing sheet with id=AC4, first strand: chain 'D' and resid 2 through 4 removed outlier: 4.269A pdb=" N ASP D 2 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA D 33 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AC6, first strand: chain 'D' and resid 206 through 208 removed outlier: 6.713A pdb=" N VAL D 149 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N SER D 230 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 151 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR D 232 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 153 " --> pdb=" O THR D 232 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 416 through 417 removed outlier: 3.505A pdb=" N GLY D 417 " --> pdb=" O TYR D 459 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 651 through 655 1452 hydrogen bonds defined for protein. 4152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.61 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9040 1.34 - 1.46: 4792 1.46 - 1.57: 12980 1.57 - 1.69: 0 1.69 - 1.81: 244 Bond restraints: 27056 Sorted by residual: bond pdb=" C LEU B 523 " pdb=" N PRO B 524 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.00e+00 bond pdb=" C LEU A 523 " pdb=" N PRO A 524 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.00e+00 bond pdb=" C LEU D 523 " pdb=" N PRO D 524 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.00e+00 bond pdb=" C LEU C 523 " pdb=" N PRO C 524 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.00e+00 bond pdb=" CB ASP C 837 " pdb=" CG ASP C 837 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 ... (remaining 27051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 35688 1.31 - 2.63: 836 2.63 - 3.94: 212 3.94 - 5.26: 36 5.26 - 6.57: 20 Bond angle restraints: 36792 Sorted by residual: angle pdb=" N VAL C 836 " pdb=" CA VAL C 836 " pdb=" C VAL C 836 " ideal model delta sigma weight residual 111.91 117.82 -5.91 8.90e-01 1.26e+00 4.41e+01 angle pdb=" N VAL B 836 " pdb=" CA VAL B 836 " pdb=" C VAL B 836 " ideal model delta sigma weight residual 111.91 117.82 -5.91 8.90e-01 1.26e+00 4.41e+01 angle pdb=" N VAL D 836 " pdb=" CA VAL D 836 " pdb=" C VAL D 836 " ideal model delta sigma weight residual 111.91 117.82 -5.91 8.90e-01 1.26e+00 4.41e+01 angle pdb=" N VAL A 836 " pdb=" CA VAL A 836 " pdb=" C VAL A 836 " ideal model delta sigma weight residual 111.91 117.82 -5.91 8.90e-01 1.26e+00 4.41e+01 angle pdb=" C LYS C 460 " pdb=" CA LYS C 460 " pdb=" CB LYS C 460 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.27e+01 ... (remaining 36787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 14704 17.87 - 35.74: 1096 35.74 - 53.62: 256 53.62 - 71.49: 60 71.49 - 89.36: 32 Dihedral angle restraints: 16148 sinusoidal: 6076 harmonic: 10072 Sorted by residual: dihedral pdb=" CA SER D 642 " pdb=" C SER D 642 " pdb=" N GLY D 643 " pdb=" CA GLY D 643 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA SER A 642 " pdb=" C SER A 642 " pdb=" N GLY A 643 " pdb=" CA GLY A 643 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA SER B 642 " pdb=" C SER B 642 " pdb=" N GLY B 643 " pdb=" CA GLY B 643 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 16145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2880 0.036 - 0.072: 872 0.072 - 0.108: 344 0.108 - 0.144: 96 0.144 - 0.180: 16 Chirality restraints: 4208 Sorted by residual: chirality pdb=" CA HIS B 838 " pdb=" N HIS B 838 " pdb=" C HIS B 838 " pdb=" CB HIS B 838 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA HIS A 838 " pdb=" N HIS A 838 " pdb=" C HIS A 838 " pdb=" CB HIS A 838 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA HIS C 838 " pdb=" N HIS C 838 " pdb=" C HIS C 838 " pdb=" CB HIS C 838 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 4205 not shown) Planarity restraints: 4836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 837 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ASP C 837 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP C 837 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS C 838 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 837 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ASP A 837 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP A 837 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS A 838 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 837 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ASP B 837 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP B 837 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS B 838 " -0.016 2.00e-02 2.50e+03 ... (remaining 4833 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3908 2.76 - 3.29: 25392 3.29 - 3.83: 44614 3.83 - 4.36: 54804 4.36 - 4.90: 95944 Nonbonded interactions: 224662 Sorted by model distance: nonbonded pdb=" NE2 GLN C 431 " pdb=" OD2 ASP A 560 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP B 560 " pdb=" NE2 GLN D 431 " model vdw 2.222 3.120 nonbonded pdb=" NE2 GLN B 431 " pdb=" OD2 ASP D 560 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP C 560 " pdb=" NE2 GLN A 431 " model vdw 2.222 3.120 nonbonded pdb=" OE1 GLN A 572 " pdb=" N ASP A 573 " model vdw 2.282 3.120 ... (remaining 224657 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: 0.08 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.680 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 : 0.002 0.029 27056 Z= 0.125 Angle : 0.543 6.574 36792 Z= 0.339 Chirality : 0.043 0.180 4208 Planarity : 0.004 0.050 4836 Dihedral : 14.332 89.358 9708 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.38 (0.14), residues: 3536 helix: 1.70 (0.13), residues: 1632 sheet: 0.77 (0.24), residues: 484 loop : 0.15 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 723 TYR 0.010 0.001 TYR D 459 PHE 0.030 0.002 PHE B 793 TRP 0.008 0.001 TRP D 443 HIS 0.003 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00247 (27056) covalent geometry : angle 0.54280 (36792) hydrogen bonds : bond 0.15168 ( 1452) hydrogen bonds : angle 6.15308 ( 4152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.993 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.7903 time to fit residues: 382.7122 Evaluate side-chains 296 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 GLN A 212 GLN B 212 GLN D 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.074526 restraints weight = 34816.654| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.15 r_work: 0.2741 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 27056 Z= 0.297 Angle : 0.594 5.402 36792 Z= 0.323 Chirality : 0.049 0.172 4208 Planarity : 0.005 0.050 4836 Dihedral : 4.577 22.057 3800 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.04 % Allowed : 10.77 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.13 (0.14), residues: 3536 helix: 1.44 (0.13), residues: 1700 sheet: 0.54 (0.23), residues: 532 loop : 0.05 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 537 TYR 0.019 0.002 TYR B 459 PHE 0.016 0.002 PHE B 793 TRP 0.009 0.002 TRP B 52 HIS 0.007 0.002 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00721 (27056) covalent geometry : angle 0.59375 (36792) hydrogen bonds : bond 0.05246 ( 1452) hydrogen bonds : angle 4.90886 ( 4152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 1.022 Fit side-chains REVERT: C 290 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: C 569 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8320 (mpp-170) REVERT: C 571 GLU cc_start: 0.8770 (pm20) cc_final: 0.8548 (pm20) REVERT: C 657 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8413 (mttt) REVERT: C 756 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8258 (p90) REVERT: C 870 ARG cc_start: 0.7788 (ttt180) cc_final: 0.7440 (ttt180) REVERT: A 290 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 569 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8321 (mpp-170) REVERT: A 571 GLU cc_start: 0.8776 (pm20) cc_final: 0.8555 (pm20) REVERT: A 657 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8428 (mttt) REVERT: A 756 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8255 (p90) REVERT: A 870 ARG cc_start: 0.7789 (ttt180) cc_final: 0.7448 (ttt180) REVERT: B 290 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: B 569 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8326 (mpp-170) REVERT: B 571 GLU cc_start: 0.8765 (pm20) cc_final: 0.8545 (pm20) REVERT: B 657 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8418 (mttt) REVERT: B 756 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8262 (p90) REVERT: B 870 ARG cc_start: 0.7787 (ttt180) cc_final: 0.7441 (ttt180) REVERT: D 290 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: D 569 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8318 (mpp-170) REVERT: D 571 GLU cc_start: 0.8780 (pm20) cc_final: 0.8560 (pm20) REVERT: D 657 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8420 (mttt) REVERT: D 756 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8245 (p90) REVERT: D 870 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7441 (ttt180) outliers start: 56 outliers final: 8 residues processed: 332 average time/residue: 0.7882 time to fit residues: 297.5660 Evaluate side-chains 292 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 69 optimal weight: 10.0000 chunk 123 optimal weight: 0.0470 chunk 172 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 309 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 ASN A 37 GLN A 240 ASN B 240 ASN D 37 GLN D 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.076055 restraints weight = 34974.363| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.17 r_work: 0.2739 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27056 Z= 0.142 Angle : 0.484 5.189 36792 Z= 0.262 Chirality : 0.044 0.148 4208 Planarity : 0.004 0.045 4836 Dihedral : 4.211 21.006 3800 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.60 % Allowed : 12.23 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.45 (0.14), residues: 3536 helix: 1.78 (0.13), residues: 1672 sheet: 0.50 (0.23), residues: 532 loop : 0.22 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 661 TYR 0.011 0.001 TYR B 459 PHE 0.016 0.002 PHE C 793 TRP 0.008 0.001 TRP C 443 HIS 0.005 0.001 HIS C 775 Details of bonding type rmsd covalent geometry : bond 0.00332 (27056) covalent geometry : angle 0.48424 (36792) hydrogen bonds : bond 0.03884 ( 1452) hydrogen bonds : angle 4.61558 ( 4152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.828 Fit side-chains REVERT: C 290 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: C 345 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8449 (ttmm) REVERT: C 657 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8321 (mttt) REVERT: C 727 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 870 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7442 (ttt180) REVERT: A 290 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: A 345 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8451 (ttmm) REVERT: A 657 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8326 (mttt) REVERT: A 727 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 870 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7448 (ttt180) REVERT: B 290 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: B 345 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8461 (ttmm) REVERT: B 657 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8321 (mttt) REVERT: B 727 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7297 (tm-30) REVERT: B 870 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7451 (ttt180) REVERT: D 290 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: D 345 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8456 (ttmm) REVERT: D 657 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8325 (mttt) REVERT: D 727 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 870 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7442 (ttt180) outliers start: 44 outliers final: 16 residues processed: 304 average time/residue: 0.8211 time to fit residues: 282.9405 Evaluate side-chains 300 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 129 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 313 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 0.0270 chunk 28 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN C 572 GLN A 572 GLN B 37 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.080549 restraints weight = 34911.073| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.17 r_work: 0.2849 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 27056 Z= 0.086 Angle : 0.427 4.833 36792 Z= 0.228 Chirality : 0.042 0.142 4208 Planarity : 0.004 0.040 4836 Dihedral : 3.793 18.989 3800 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.31 % Allowed : 12.63 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.70 (0.14), residues: 3536 helix: 2.01 (0.13), residues: 1672 sheet: 0.66 (0.23), residues: 524 loop : 0.31 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 723 TYR 0.008 0.001 TYR D 141 PHE 0.010 0.001 PHE C 756 TRP 0.008 0.001 TRP C 443 HIS 0.005 0.001 HIS C 775 Details of bonding type rmsd covalent geometry : bond 0.00183 (27056) covalent geometry : angle 0.42683 (36792) hydrogen bonds : bond 0.02838 ( 1452) hydrogen bonds : angle 4.36837 ( 4152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 292 time to evaluate : 0.993 Fit side-chains REVERT: C 345 LYS cc_start: 0.8721 (ttpp) cc_final: 0.8499 (ttmm) REVERT: C 657 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8288 (mtpt) REVERT: C 727 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7229 (tm-30) REVERT: C 737 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7770 (p90) REVERT: C 816 MET cc_start: 0.8098 (ttp) cc_final: 0.7857 (ttp) REVERT: C 870 ARG cc_start: 0.7775 (ttt180) cc_final: 0.7446 (ttt180) REVERT: A 345 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8488 (ttmm) REVERT: A 657 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (mtpt) REVERT: A 727 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 737 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7778 (p90) REVERT: A 816 MET cc_start: 0.8101 (ttp) cc_final: 0.7859 (ttp) REVERT: A 870 ARG cc_start: 0.7772 (ttt180) cc_final: 0.7446 (ttt180) REVERT: B 345 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8488 (ttmm) REVERT: B 657 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (mtpt) REVERT: B 727 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 737 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7778 (p90) REVERT: B 816 MET cc_start: 0.8081 (ttp) cc_final: 0.7835 (ttp) REVERT: B 870 ARG cc_start: 0.7783 (ttt180) cc_final: 0.7449 (ttt180) REVERT: D 345 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8498 (ttmm) REVERT: D 657 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (mtpt) REVERT: D 727 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 737 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7775 (p90) REVERT: D 816 MET cc_start: 0.8113 (ttp) cc_final: 0.7870 (ttp) REVERT: D 870 ARG cc_start: 0.7775 (ttt180) cc_final: 0.7446 (ttt180) outliers start: 36 outliers final: 8 residues processed: 304 average time/residue: 0.7901 time to fit residues: 273.0560 Evaluate side-chains 280 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 264 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 737 HIS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 737 HIS Chi-restraints excluded: chain D residue 756 PHE Chi-restraints excluded: chain D residue 761 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 74 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 316 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 342 optimal weight: 0.6980 chunk 327 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 572 GLN A 572 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.078045 restraints weight = 35039.292| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.18 r_work: 0.2808 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27056 Z= 0.118 Angle : 0.452 4.862 36792 Z= 0.240 Chirality : 0.043 0.146 4208 Planarity : 0.004 0.039 4836 Dihedral : 3.859 19.540 3800 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.60 % Allowed : 12.95 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.69 (0.14), residues: 3536 helix: 2.03 (0.13), residues: 1672 sheet: 0.61 (0.23), residues: 524 loop : 0.27 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 661 TYR 0.011 0.001 TYR A 141 PHE 0.020 0.001 PHE D 793 TRP 0.006 0.001 TRP C 443 HIS 0.004 0.001 HIS D 775 Details of bonding type rmsd covalent geometry : bond 0.00278 (27056) covalent geometry : angle 0.45209 (36792) hydrogen bonds : bond 0.03357 ( 1452) hydrogen bonds : angle 4.40109 ( 4152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.989 Fit side-chains REVERT: C 345 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8472 (ttmm) REVERT: C 870 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7338 (ttt180) REVERT: A 345 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8456 (ttmm) REVERT: A 870 ARG cc_start: 0.7736 (ttt180) cc_final: 0.7342 (ttt180) REVERT: B 345 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8464 (ttmm) REVERT: B 870 ARG cc_start: 0.7734 (ttt180) cc_final: 0.7336 (ttt180) REVERT: D 345 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8473 (ttmm) REVERT: D 870 ARG cc_start: 0.7741 (ttt180) cc_final: 0.7344 (ttt180) outliers start: 44 outliers final: 8 residues processed: 300 average time/residue: 0.7940 time to fit residues: 270.8914 Evaluate side-chains 280 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 272 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 9 optimal weight: 3.9990 chunk 330 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 85 optimal weight: 50.0000 chunk 105 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 340 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 572 GLN A 572 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.074033 restraints weight = 34849.429| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.16 r_work: 0.2781 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 27056 Z= 0.273 Angle : 0.562 5.123 36792 Z= 0.299 Chirality : 0.048 0.168 4208 Planarity : 0.005 0.041 4836 Dihedral : 4.335 21.849 3800 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.60 % Allowed : 13.10 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.35 (0.14), residues: 3536 helix: 1.76 (0.13), residues: 1700 sheet: 0.42 (0.23), residues: 532 loop : 0.05 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 661 TYR 0.013 0.002 TYR B 459 PHE 0.016 0.002 PHE C 756 TRP 0.009 0.002 TRP C 52 HIS 0.005 0.002 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00666 (27056) covalent geometry : angle 0.56207 (36792) hydrogen bonds : bond 0.04786 ( 1452) hydrogen bonds : angle 4.65637 ( 4152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 288 time to evaluate : 0.941 Fit side-chains REVERT: C 345 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8556 (ttmm) REVERT: C 569 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8493 (mpp-170) REVERT: C 657 LYS cc_start: 0.8584 (mptm) cc_final: 0.8314 (mptm) REVERT: C 727 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7388 (tm-30) REVERT: C 870 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7498 (ttt180) REVERT: A 345 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8565 (ttmm) REVERT: A 569 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (mpp-170) REVERT: A 657 LYS cc_start: 0.8592 (mptm) cc_final: 0.8322 (mptm) REVERT: A 727 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 870 ARG cc_start: 0.7826 (ttt180) cc_final: 0.7503 (ttt180) REVERT: B 345 LYS cc_start: 0.8812 (ttpp) cc_final: 0.8566 (ttmm) REVERT: B 569 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8502 (mpp-170) REVERT: B 657 LYS cc_start: 0.8586 (mptm) cc_final: 0.8317 (mptm) REVERT: B 727 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7364 (tm-30) REVERT: B 870 ARG cc_start: 0.7824 (ttt180) cc_final: 0.7503 (ttt180) REVERT: D 345 LYS cc_start: 0.8819 (ttpp) cc_final: 0.8571 (ttmm) REVERT: D 569 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8491 (mpp-170) REVERT: D 657 LYS cc_start: 0.8579 (mptm) cc_final: 0.8308 (mptm) REVERT: D 727 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7383 (tm-30) REVERT: D 870 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7510 (ttt180) outliers start: 44 outliers final: 28 residues processed: 316 average time/residue: 0.8333 time to fit residues: 297.1576 Evaluate side-chains 308 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 569 ARG Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 569 ARG Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 569 ARG Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 569 ARG Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 47 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 572 GLN A 572 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.075713 restraints weight = 35015.749| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.15 r_work: 0.2757 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27056 Z= 0.172 Angle : 0.494 4.898 36792 Z= 0.263 Chirality : 0.044 0.149 4208 Planarity : 0.004 0.040 4836 Dihedral : 4.162 21.468 3800 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.46 % Allowed : 13.54 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.46 (0.14), residues: 3536 helix: 1.87 (0.13), residues: 1676 sheet: 0.44 (0.23), residues: 532 loop : 0.13 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 723 TYR 0.012 0.001 TYR C 459 PHE 0.026 0.002 PHE D 793 TRP 0.006 0.001 TRP C 156 HIS 0.004 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00412 (27056) covalent geometry : angle 0.49418 (36792) hydrogen bonds : bond 0.03955 ( 1452) hydrogen bonds : angle 4.56261 ( 4152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 1.070 Fit side-chains REVERT: C 345 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8495 (ttmm) REVERT: C 727 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 737 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7652 (p90) REVERT: C 870 ARG cc_start: 0.7794 (ttt180) cc_final: 0.7517 (ttt180) REVERT: A 345 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8493 (ttmm) REVERT: A 727 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 737 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7654 (p90) REVERT: A 870 ARG cc_start: 0.7793 (ttt180) cc_final: 0.7518 (ttt180) REVERT: B 345 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8503 (ttmm) REVERT: B 727 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 737 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7654 (p90) REVERT: B 870 ARG cc_start: 0.7796 (ttt180) cc_final: 0.7521 (ttt180) REVERT: D 345 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8505 (ttmm) REVERT: D 727 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 737 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7658 (p90) REVERT: D 870 ARG cc_start: 0.7800 (ttt180) cc_final: 0.7521 (ttt180) outliers start: 40 outliers final: 24 residues processed: 304 average time/residue: 0.7969 time to fit residues: 274.7713 Evaluate side-chains 300 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 737 HIS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 737 HIS Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 138 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 262 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 572 GLN A 572 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.076324 restraints weight = 35113.384| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.16 r_work: 0.2767 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27056 Z= 0.176 Angle : 0.500 4.850 36792 Z= 0.266 Chirality : 0.045 0.152 4208 Planarity : 0.004 0.039 4836 Dihedral : 4.173 21.636 3800 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.56 % Allowed : 14.16 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.45 (0.14), residues: 3536 helix: 1.87 (0.13), residues: 1676 sheet: 0.43 (0.23), residues: 532 loop : 0.12 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 723 TYR 0.012 0.001 TYR B 459 PHE 0.014 0.002 PHE D 756 TRP 0.006 0.001 TRP D 52 HIS 0.004 0.001 HIS C 775 Details of bonding type rmsd covalent geometry : bond 0.00424 (27056) covalent geometry : angle 0.50011 (36792) hydrogen bonds : bond 0.04026 ( 1452) hydrogen bonds : angle 4.58249 ( 4152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 1.091 Fit side-chains REVERT: C 345 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8484 (ttmm) REVERT: C 731 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7853 (mtm110) REVERT: C 737 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7710 (p90) REVERT: A 345 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8481 (ttmm) REVERT: A 731 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7855 (mtm110) REVERT: A 737 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7707 (p90) REVERT: B 345 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8485 (ttmm) REVERT: B 731 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7852 (mtm110) REVERT: B 737 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7703 (p90) REVERT: D 345 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8497 (ttmm) REVERT: D 731 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7865 (mtm110) REVERT: D 737 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7714 (p90) outliers start: 43 outliers final: 32 residues processed: 300 average time/residue: 0.7714 time to fit residues: 263.1465 Evaluate side-chains 316 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 737 HIS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 737 HIS Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 15 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 265 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 305 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 572 GLN A 572 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.074820 restraints weight = 35227.598| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.17 r_work: 0.2791 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27056 Z= 0.206 Angle : 0.535 6.291 36792 Z= 0.285 Chirality : 0.046 0.157 4208 Planarity : 0.005 0.040 4836 Dihedral : 4.256 21.934 3800 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.35 % Allowed : 14.08 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.38 (0.14), residues: 3536 helix: 1.81 (0.13), residues: 1676 sheet: 0.41 (0.23), residues: 532 loop : 0.08 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 723 TYR 0.012 0.001 TYR A 459 PHE 0.037 0.002 PHE C 793 TRP 0.007 0.001 TRP D 52 HIS 0.004 0.001 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.00500 (27056) covalent geometry : angle 0.53501 (36792) hydrogen bonds : bond 0.04299 ( 1452) hydrogen bonds : angle 4.65269 ( 4152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 0.960 Fit side-chains REVERT: C 345 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8567 (ttmm) REVERT: A 345 LYS cc_start: 0.8795 (ttpp) cc_final: 0.8562 (ttmm) REVERT: B 345 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8560 (ttmm) REVERT: D 345 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8575 (ttmm) outliers start: 37 outliers final: 32 residues processed: 297 average time/residue: 0.7867 time to fit residues: 264.9036 Evaluate side-chains 300 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 155 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 326 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 194 optimal weight: 0.0670 chunk 87 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 572 GLN A 572 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.073125 restraints weight = 33622.441| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.16 r_work: 0.2686 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27056 Z= 0.153 Angle : 0.505 7.163 36792 Z= 0.270 Chirality : 0.044 0.146 4208 Planarity : 0.004 0.040 4836 Dihedral : 4.111 21.529 3800 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.60 % Allowed : 14.59 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.49 (0.14), residues: 3536 helix: 1.99 (0.13), residues: 1652 sheet: 0.42 (0.23), residues: 532 loop : 0.06 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 723 TYR 0.012 0.001 TYR B 459 PHE 0.014 0.001 PHE C 756 TRP 0.006 0.001 TRP A 443 HIS 0.004 0.001 HIS D 775 Details of bonding type rmsd covalent geometry : bond 0.00364 (27056) covalent geometry : angle 0.50499 (36792) hydrogen bonds : bond 0.03750 ( 1452) hydrogen bonds : angle 4.57129 ( 4152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 1.068 Fit side-chains REVERT: C 345 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8335 (ttmm) REVERT: C 737 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7736 (p90) REVERT: A 345 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8318 (ttmm) REVERT: A 737 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7732 (p90) REVERT: B 345 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8328 (ttmm) REVERT: B 737 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7734 (p90) REVERT: D 345 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8333 (ttmm) REVERT: D 737 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7733 (p90) outliers start: 44 outliers final: 30 residues processed: 296 average time/residue: 0.7791 time to fit residues: 261.2753 Evaluate side-chains 302 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 737 HIS Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 737 HIS Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 737 HIS Chi-restraints excluded: chain D residue 756 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 98 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 249 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 572 GLN A 572 GLN B 572 GLN D 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.072534 restraints weight = 33587.355| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.15 r_work: 0.2676 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27056 Z= 0.173 Angle : 0.528 6.256 36792 Z= 0.280 Chirality : 0.045 0.167 4208 Planarity : 0.004 0.039 4836 Dihedral : 4.179 21.791 3800 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.24 % Allowed : 14.63 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.44 (0.14), residues: 3536 helix: 1.96 (0.13), residues: 1652 sheet: 0.39 (0.23), residues: 532 loop : 0.02 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 723 TYR 0.011 0.001 TYR D 459 PHE 0.044 0.002 PHE C 793 TRP 0.007 0.001 TRP B 156 HIS 0.004 0.001 HIS B 775 Details of bonding type rmsd covalent geometry : bond 0.00417 (27056) covalent geometry : angle 0.52805 (36792) hydrogen bonds : bond 0.04008 ( 1452) hydrogen bonds : angle 4.61470 ( 4152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9626.24 seconds wall clock time: 164 minutes 31.28 seconds (9871.28 seconds total)